Merge branch 'galaxyproject:main' into mmseqs2

galaxyproject · Nov 19, 2024 · 78ba0c6 · 78ba0c6
2 parents 3efd6ab + ff35237
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diff --git a/README.md b/README.md
@@ -13,7 +13,8 @@ These repositories are maintained and developed by the [Intergalactic Utilities
 
 Pull Requests with dependencies specified as conda-package will be automatically tested and verified using [planemo](https://github.com/galaxyproject/planemo). If the tests pass and the pull request is merged, the tool will be automatically uploaded to the [Test](http://testtoolshed.g2.bx.psu.edu/)- and [Main Tool Shed](http://toolshed.g2.bx.psu.edu/).
 
-Other repositories with Galaxy tools:
+## Other repositories with Galaxy tools
+
  * [Björn Grüning repo](https://github.com/bgruening/galaxytools)
  * [Galaxy devteam repo](https://github.com/galaxyproject/tools-devteam)
  * Peter Cock's repos:

diff --git a/data_managers/data_manager_build_kraken2_database/data_manager/kraken2_build_database.py b/data_managers/data_manager_build_kraken2_database/data_manager/kraken2_build_database.py
@@ -28,6 +28,7 @@ class KrakenDatabaseTypes(Enum):
     standard_local_build = 'standard_local_build'
     standard_prebuilt = 'standard_prebuilt'
     minikraken = 'minikraken'
+    special_prebuilt = 'special_prebuilt'
     special = 'special'
     custom = 'custom'
 
@@ -64,6 +65,7 @@ class StandardPrebuiltSizes(Enum):
     pluspfp = "pluspfp"
     pluspfp_08gb = "pluspfp_08gb"
     pluspfp_16gb = "pluspfp_16gb"
+    eupathdb48 = "eupathdb48"
 
     def __str__(self):
         return self.value
@@ -144,7 +146,8 @@ def kraken2_build_standard_prebuilt(prebuilt_db, prebuilt_date, target_directory
         'pluspf_16gb': "PlusPF-16 (PlusPF with DB capped at 16 GB)",
         'pluspfp': "PlusPFP (Standard plus protozoa, fungi and plant)",
         'pluspfp_08gb': "PlusPFP-8 (PlusPFP with DB capped at 8 GB)",
-        'pluspfp_16gb': "PlusPFP-16 (PlusPFP with DB capped at 16 GB)"
+        'pluspfp_16gb': "PlusPFP-16 (PlusPFP with DB capped at 16 GB)",
+        'eupathdb48': "EuPathDB-46",
     }
 
     database_value = "_".join([
@@ -408,7 +411,7 @@ def main():
     parser.add_argument('--threads', dest='threads', default=1, help='threads')
     parser.add_argument('--database-type', dest='database_type', type=KrakenDatabaseTypes, choices=list(KrakenDatabaseTypes), required=True, help='type of kraken database to build')
     parser.add_argument('--minikraken2-version', dest='minikraken2_version', type=Minikraken2Versions, choices=list(Minikraken2Versions), help='MiniKraken2 version (only applies to --database-type minikraken)')
-    parser.add_argument('--prebuilt-db', dest='prebuilt_db', type=StandardPrebuiltSizes, choices=list(StandardPrebuiltSizes), help='Prebuilt database to download. Only applies to --database-type standard_prebuilt.')
+    parser.add_argument('--prebuilt-db', dest='prebuilt_db', type=StandardPrebuiltSizes, choices=list(StandardPrebuiltSizes), help='Prebuilt database to download. Only applies to --database-type standard_prebuilt or special_prebuilt.')
     parser.add_argument('--prebuilt-date', dest='prebuilt_date', help='Database build date (YYYY-MM-DD). Only applies to --database-type standard_prebuilt.')
     parser.add_argument('--special-database-type', dest='special_database_type', type=SpecialDatabaseTypes, choices=list(SpecialDatabaseTypes), help='type of special database to build (only applies to --database-type special)')
     parser.add_argument('--custom-fasta', dest='custom_fasta', help='fasta file for custom database (only applies to --database-type custom)')
@@ -446,7 +449,7 @@ def main():
             kraken2_args,
             target_directory,
         )
-    elif str(args.database_type) == 'standard_prebuilt':
+    elif str(args.database_type) in ('standard_prebuilt', 'special_prebuilt'):
         data_manager_output = kraken2_build_standard_prebuilt(
             str(args.prebuilt_db),
             str(args.prebuilt_date),

diff --git a/data_managers/data_manager_build_kraken2_database/data_manager/kraken2_build_database.xml b/data_managers/data_manager_build_kraken2_database/data_manager/kraken2_build_database.xml
@@ -1,9 +1,8 @@
-<?xml version="1.0"?>
 <tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>database builder</description>
     <macros>
         <token name="@TOOL_VERSION@">2.1.3</token>
-        <token name="@VERSION_SUFFIX@">3</token>
+        <token name="@VERSION_SUFFIX@">4</token>
         <token name="@PROFILE@">22.01</token>
         <xml name="common_params">
             <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" />
@@ -70,6 +69,9 @@ python '$__tool_directory__/kraken2_build_database.py'
     --prebuilt-date '$database_type.prebuild.prebuilt_date'
 #else if $database_type.database_type == "minikraken"
     --minikraken2-version '$database_type.minikraken2_version'
+#else if $database_type.database_type == "special_prebuilt"
+    --prebuilt-db '$database_type.special_prebuild.prebuilt_db'
+    --prebuilt-date '$database_type.special_prebuild.prebuilt_date'
 #else if $database_type.database_type == "special"
     --threads \${GALAXY_SLOTS:-1}
     --special-database-type '$database_type.special_database_type'
@@ -98,6 +100,7 @@ python '$__tool_directory__/kraken2_build_database.py'
                 <option value="standard_local_build">Standard, Local Build</option>
                 <option value="standard_prebuilt">Pre-Built Refseq indexes</option>
                 <option value="minikraken">MiniKraken</option>
+                <option value="special_prebuilt">Special Pre-Built indexes</option>
                 <option value="special">Special</option>
                 <option value="custom">Custom</option>
             </param>
@@ -223,6 +226,22 @@ python '$__tool_directory__/kraken2_build_database.py'
                     </when>
                 </conditional>
             </when>
+            <when value="special_prebuilt">
+                <conditional name="special_prebuild">
+                    <param name="special_prebuilt_db" type="select" multiple="false" label="Select pre-built database to download">
+                        <option value="eupathdb48_20230407">EuPathDB-46 (April 7, 2023)</option>
+                        <option value="eupathdb48_20201113">EuPathDB-46 (November 13, 2020)</option>
+                    </param>
+                    <when value="eupathdb48_20230407">
+                        <param name="prebuilt_db" type="hidden" value="eupathdb48"/>
+                        <param name="prebuilt_date" type="hidden" value="2023-04-07"/>
+                    </when>
+                    <when value="eupathdb48_20201113">
+                        <param name="prebuilt_db" type="hidden" value="eupathdb48"/>
+                        <param name="prebuilt_date" type="hidden" value="2020-11-13"/>
+                    </when>
+                </conditional>
+            </when>
             <when value="minikraken">
                 <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download">
                     <option value="v2">Version 2</option>

diff --git a/...manager_groot_database_downloader/data_manager/data_manager_groot_database_downloader.xml b/...manager_groot_database_downloader/data_manager/data_manager_groot_database_downloader.xml
@@ -2,7 +2,7 @@
     <description> Download pre-clustered ARG database that are ready to be indexed</description>
     <macros>
         <token name="@TOOL_VERSION@">1.1.2</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
         <token name="@PROFILE@">22.05</token>
     </macros>
     <requirements>
@@ -12,7 +12,9 @@
     </requirements>
     <command><![CDATA[
         if [ -f '/usr/local/ssl/cacert.pem' ] ; then export SSL_CERT_FILE='/usr/local/ssl/cacert.pem' ; fi &&
+        mkdir -p '$out_file.extra_files_path' &&
         groot get -d '$database' --identity '$identity' &&
+        mv ${database}.${identity} '$out_file.extra_files_path' &&
         cp '$dmjson' '$out_file'
     ]]></command>
     <configfiles>
@@ -24,7 +26,7 @@
       {
         "value": "$database.$identity-@TOOL_VERSION@-#echo date.today().strftime('%d%m%Y')#",
         "name": "$database ($identity percent identity)",
-        "path": "/$database.$identity",
+        "path": "$database.$identity",
         "version": "@TOOL_VERSION@"
       }
     ]
@@ -57,7 +59,7 @@
                     <has_text text='"version": "1.1.2"'/>
                     <has_text_matching expression='"value": "arg-annot.90-1.1.2-[0-9]{8}"'/>
                     <has_text text='"name": "arg-annot (90 percent identity)"'/>
-                    <has_text text='"path": "/arg-annot.90"'/>
+                    <has_text text='"path": "arg-annot.90"'/>
                 </assert_contents>
             </output>
         </test>

diff --git a/data_managers/data_manager_groot_database_downloader/data_manager_conf.xml b/data_managers/data_manager_groot_database_downloader/data_manager_conf.xml
@@ -8,9 +8,9 @@
                 <column name="path" output_ref="out_file">
                     <move type="directory">
                         <source>${path}</source>
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">groot_database/data/${value}</target>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">groot_database/${path}</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/groot_database/data/${value}</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/groot_database/${path}</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
                 <column name="version"/> <!-- columns that are going to be specified by the Data Manager Tool -->

diff --git a/data_managers/data_manager_groot_database_downloader/test-data/groot_database.loc b/data_managers/data_manager_groot_database_downloader/test-data/groot_database.loc
@@ -1,2 +1 @@
-arg-annot.90-16102024	arg-annot (90 percent identity)	/tmp/tmpjmmj2x3o/galaxy-dev/tool-data/groot_database/data/arg-annot.90-16102024	1.1.2
-arg-annot.90-1.1.2-16102024	arg-annot (90 percent identity)	/tmp/tmpqdkgcsoq/galaxy-dev/tool-data/groot_database/data/arg-annot.90-1.1.2-16102024	1.1.2
+arg-annot.90-1.1.2-18112024	arg-annot (90 percent identity)	/tmp/tmprimr087u/galaxy-dev/tool-data/groot_database/arg-annot.90	1.1.2
diff --git a/tool_collections/snpeff/snpEff.xml b/tool_collections/snpeff/snpEff.xml
@@ -1,4 +1,4 @@
-<tool id="snpEff" name="SnpEff eff:" version="@SNPEFF_VERSION@+galaxy@WRAPPER_VERSION@" profile="23.0">
+<tool id="snpEff" name="SnpEff eff:" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description> annotate variants</description>
     <macros>
         <import>snpEff_macros.xml</import>

diff --git a/tool_collections/snpeff/snpEff_create_db.xml b/tool_collections/snpeff/snpEff_create_db.xml
@@ -1,4 +1,4 @@
-<tool id="snpEff_build_gb" name="SnpEff build:" version="@SNPEFF_VERSION@+galaxy@WRAPPER_VERSION@" profile="23.0">
+<tool id="snpEff_build_gb" name="SnpEff build:" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description> database from Genbank or GFF record</description>
     <macros>
         <import>snpEff_macros.xml</import>

diff --git a/tool_collections/snpeff/snpEff_databases.xml b/tool_collections/snpeff/snpEff_databases.xml
@@ -1,4 +1,4 @@
-<tool id="snpEff_databases" name="SnpEff databases:" version="@SNPEFF_VERSION@+galaxy@WRAPPER_VERSION@" profile="23.0">
+<tool id="snpEff_databases" name="SnpEff databases:" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description> list available databases</description>
     <macros>
         <import>snpEff_macros.xml</import>
@@ -48,7 +48,7 @@
         </param>
     </inputs>
     <outputs>
-        <data name="snpeff_dbs" format="tabular" label="${tool.name} @SNPEFF_VERSION@ available databases" />
+        <data name="snpeff_dbs" format="tabular" label="@SNPEFF_VERSION@ available databases" />
     </outputs>
     <tests>
         <test>

diff --git a/tool_collections/snpeff/snpEff_download.xml b/tool_collections/snpeff/snpEff_download.xml
@@ -1,4 +1,4 @@
-<tool id="snpEff_download" name="SnpEff download:" version="@SNPEFF_VERSION@+galaxy@WRAPPER_VERSION@" profile="23.0">
+<tool id="snpEff_download" name="SnpEff download:" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description> download a pre-built database</description>
     <macros>
         <import>snpEff_macros.xml</import>
@@ -19,7 +19,7 @@ mv temp/'$genome_version' '$snpeff_db.files_path'
         </param>
     </inputs>
     <outputs>
-        <data name="snpeff_db" format="snpeffdb" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}"/>
+        <data name="snpeff_db" format="snpeffdb" label="@SNPEFF_VERSION@ ${genome_version} database"/>
     </outputs>
     <tests>
         <test>

diff --git a/tool_collections/snpeff/snpEff_macros.xml b/tool_collections/snpeff/snpEff_macros.xml
@@ -1,8 +1,11 @@
 <macros>
-    <xml name="requirement">
-        <requirement type="package" version="5.2">snpeff</requirement>
-        <yield/>
-    </xml>
+  <token name="@TOOL_VERSION@">5.2</token>
+  <token name="@VERSION_SUFFIX@">0</token>
+  <token name="@SNPEFF_VERSION@">SnpEff5.2</token>
+  <xml name="requirement">
+      <requirement type="package" version="@TOOL_VERSION@">snpeff</requirement>
+      <yield/>
+  </xml>
   <xml name="stdio">
     <stdio>
         <exit_code range=":-1"  level="fatal" description="Error: Cannot open file" />
@@ -14,8 +17,6 @@
 snpEff -version
     ]]></version_command>
   </xml>
-  <token name="@WRAPPER_VERSION@">0</token>
-  <token name="@SNPEFF_VERSION@">5.2</token>
   <token name="@JAVA_OPTIONS@">-Xmx\${GALAXY_MEMORY_MB:-8192}m</token>
   <xml name="ref_select">
     <conditional name="reference_source">

diff --git a/tool_collections/snpeff/snpeff_get_chr_names.xml b/tool_collections/snpeff/snpeff_get_chr_names.xml
@@ -1,4 +1,4 @@
-<tool id="snpEff_get_chr_names" name="SnpEff chromosome-info:" version="@SNPEFF_VERSION@+galaxy@WRAPPER_VERSION@" profile="23.0">
+<tool id="snpEff_get_chr_names" name="SnpEff chromosome-info:" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description>list chromosome names/lengths</description>
     <macros>
         <import>snpEff_macros.xml</import>

diff --git a/tools/abyss/abyss-pe.xml b/tools/abyss/abyss-pe.xml
@@ -1,7 +1,7 @@
-<tool id="abyss-pe" name="ABySS" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="abyss-pe" name="ABySS" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.02" license="GPL-3.0">
     <description>de novo sequence assembler</description>
     <macros>
-        <token name="@TOOL_VERSION@">2.3.9</token>
+        <token name="@TOOL_VERSION@">2.3.10</token>
         <token name="@VERSION_SUFFIX@">0</token>
         <xml name="reads_conditional">
             <conditional name="reads">
@@ -281,12 +281,9 @@ This tool performs the complete ABySS pipeline using abyss-pe, described in http
 
 **License and citation**
 
-This Galaxy tool is Copyright © 2015-2021 `Earlham Institute`_ and is released under the `MIT license`_.
+This Galaxy tool is Copyright © 2015-2021 `Earlham Institute`_
 
 .. _Earlham Institute: http://www.earlham.ac.uk/
-.. _MIT license: https://opensource.org/licenses/MIT
-
-You can use this tool only if you agree to the license terms of: `ABySS`_.
 
 .. _ABySS: https://github.com/bcgsc/abyss
     ]]></help>

diff --git a/tools/ampvis2/heatmap.xml b/tools/ampvis2/heatmap.xml
@@ -1,4 +1,4 @@
-<tool id="ampvis2_heatmap" name="ampvis2 heatmap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
+<tool id="ampvis2_heatmap" name="ampvis2 heatmap" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@" license="MIT">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -63,7 +63,7 @@
                 #if $scale_by
                     scale_by = "$scale_by",
                 #end if
-                ## color_vector = NULL
+                 color_vector = c("$color_palette_start", "$color_palette_end"),
                 ## round = 1,
                 #if $output_options.out_format == "tabular"
                     textmap = TRUE,
@@ -150,6 +150,8 @@
                 </param>
             </when>
         </conditional>
+        <param argument="color_palette_start" type="color" label="Start color for the heatmap" help="Choose the start color for the heatmap."/>
+        <param argument="color_palette_end" type="color" label="End color for the heatmap" help="Choose the end color for the heatmap."/>
         <!-- https://github.com/KasperSkytte/ampvis2/issues/168 
             if this is possible again reuse: metadata_sample_or_variable_select ? -->
         <expand macro="metadata_sample_select" argument="normalise_by" label="Normalize counts by a variable or a specific sample"/>
@@ -294,6 +296,19 @@
             </conditional>
             <output name="plot" value="AalborgWWTPs-heatmap-plot_foo_file.pdf" ftype="pdf" compare="sim_size"/>
         </test>
+        <!-- test with different color palettes -->
+        <test expect_num_outputs="1">
+            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
+            <param name="color_palette_start" value="red"/>
+            <param name="color_palette_end" value="yellow"/>
+            <output name="plot" value="AalborgWWTPs-heatmap-red-yellow.pdf" ftype="pdf" compare="sim_size"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
+            <param name="color_palette_start" value="blue"/>
+            <param name="color_palette_end" value="green"/>
+            <output name="plot" value="AalborgWWTPs-heatmap-blue-green.pdf" ftype="pdf" compare="sim_size"/>
+        </test>
 
     </tests>
     <help><![CDATA[
@@ -330,4 +345,4 @@ Heatmap in the chosen output format.
 If table output is chosen the data presented in the heatmap is written into a tabular dataset.
     ]]></help>
     <expand macro="citations"/>
-</tool>
+</tool>
diff --git a/tools/ampvis2/test-data/AalborgWWTPs-heatmap-blue-green.pdf b/tools/ampvis2/test-data/AalborgWWTPs-heatmap-blue-green.pdf
diff --git a/tools/ampvis2/test-data/AalborgWWTPs-heatmap-red-yellow.pdf b/tools/ampvis2/test-data/AalborgWWTPs-heatmap-red-yellow.pdf
diff --git a/tools/anndata/export.xml b/tools/anndata/export.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[

diff --git a/tools/anndata/import.xml b/tools/anndata/import.xml
@@ -12,6 +12,7 @@
             <param name="gex_only" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Keep only 'Gene Expression' data and ignore other feature types?"/>
         </xml>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements">
         <requirement type="package" version="1.10.2">scanpy</requirement>
     </expand>
@@ -279,10 +280,10 @@ print(adata)
 
 This tool creates an AnnData from several input types:
 
-- Loom (`read_loom method <https://anndata.readthedocs.io/en/latest/generated/anndata.read_loom.html>`__)
-- Tabular (`read_csv method <https://anndata.readthedocs.io/en/latest/generated/anndata.read_csv.html>`__)
-- Matrix Market (mtx), from Cell ranger or not (`read_mtx method <https://anndata.readthedocs.io/en/latest/generated/anndata.read_mtx.html>`__)
-- UMI tools (`read_umi_tools method <https://anndata.readthedocs.io/en/latest/generated/anndata.read_umi_tools.html>`__)
+- Loom (`read_loom method <https://anndata.readthedocs.io/en/latest/generated/anndata.io.read_loom.html>`__)
+- Tabular (`read_csv method <https://anndata.readthedocs.io/en/latest/generated/anndata.io.read_csv.html>`__)
+- Matrix Market (mtx), from Cell ranger or not (`read_mtx method <https://anndata.readthedocs.io/en/latest/generated/anndata.io.read_mtx.html>`__)
+- UMI tools (`read_umi_tools method <https://anndata.readthedocs.io/en/latest/generated/anndata.io.read_umi_tools.html>`__)
 
 @HELP@
     ]]></help>

diff --git a/tools/anndata/inspect.xml b/tools/anndata/inspect.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[

diff --git a/tools/anndata/macros.xml b/tools/anndata/macros.xml
@@ -78,4 +78,9 @@ and cells, such as Name, Chromosome, Position (for genes), and Strain, Sex, Age
             </valid>
        </sanitizer>
     </xml>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">anndata</xref>
+        </xrefs>
+    </xml>
 </macros>
diff --git a/tools/anndata/manipulate.xml b/tools/anndata/manipulate.xml
@@ -11,6 +11,7 @@
             </param>
         </xml>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[

diff --git a/tools/anndata/modify_loom.xml b/tools/anndata/modify_loom.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements">
         <requirement type="package" version="1.26.4">numpy</requirement><!-- loompy seems to adapt to numpy 2.x. Remove this in the next update -->
     </expand>

diff --git a/tools/bigwig_outlier_bed/bigwig_outlier_bed.xml b/tools/bigwig_outlier_bed/bigwig_outlier_bed.xml
@@ -1,9 +1,9 @@
 <tool name="Bigwig outliers to bed features" id="bigwig_outlier_bed" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
   <description>Writes high and low bigwig runs as features in a bed file</description>
   <macros>
-  <token name="@TOOL_VERSION@">0.2.0</token>
+  <token name="@TOOL_VERSION@">0.2.2</token>
   <token name="@PYTHON_VERSION@">3.12.3</token>
-  <token name="@VERSION_SUFFIX@">2</token>
+  <token name="@VERSION_SUFFIX@">0</token>
   </macros>
   <edam_topics>
       <edam_topic>topic_0157</edam_topic>
@@ -17,7 +17,7 @@
   </xrefs>
   <requirements>
     <requirement type="package" version="@PYTHON_VERSION@">python</requirement>
-    <requirement type="package" version="2.0.0">numpy</requirement>
+    <requirement type="package" version="2.1.3">numpy</requirement>
     <requirement type="package" version="@TOOL_VERSION@">pybigtools</requirement>
   </requirements>
   <required_files>