Revert "update other converters using ucsc* and bedtools"

This reverts commit 8912293.
galaxyproject · Sep 9, 2023 · b2a3208 · b2a3208
1 parent 8912293
commit b2a3208
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Showing 8 changed files with 19 additions and 25 deletions.
diff --git a/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
@@ -1,9 +1,9 @@
-<tool id="CONVERTER_bam_to_bigwig_0" name="Convert BAM to BigWig" version="1.0.3" hidden="true">
+<tool id="CONVERTER_bam_to_bigwig_0" name="Convert BAM to BigWig" version="1.0.2" hidden="true">
     <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="445">ucsc-bedgraphtobigwig</requirement>
-        <requirement type="package" version="2.31.0">bedtools</requirement>
-        <requirement type="package" version="9.4">coreutils</requirement>
+        <requirement type="package" version="377">ucsc-bedgraphtobigwig</requirement>
+        <requirement type="package" version="2.29.2">bedtools</requirement>
+        <requirement type="package" version="8.25">coreutils</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
 bedtools genomecov -bg -split -ibam '$input'

diff --git a/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
@@ -1,8 +1,8 @@
-<tool id="CONVERTER_bed_gff_or_vcf_to_bigwig_0" name="Convert BED, GFF, or VCF to BigWig" version="1.0.2" hidden="true">
+<tool id="CONVERTER_bed_gff_or_vcf_to_bigwig_0" name="Convert BED, GFF, or VCF to BigWig" version="1.0.1" hidden="true">
     <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="445">ucsc-bedgraphtobigwig</requirement>
-        <requirement type="package" version="2.31.0">bedtools</requirement>
+        <requirement type="package" version="357">ucsc-bedgraphtobigwig</requirement>
+        <requirement type="package" version="2.27.1">bedtools</requirement>
     </requirements>
     <command>
 <![CDATA[

diff --git a/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
@@ -1,7 +1,7 @@
-<tool id="CONVERTER_bedgraph_to_bigwig" name="Convert BedGraph to BigWig" version="1.0.2" hidden="true">
+<tool id="CONVERTER_bedgraph_to_bigwig" name="Convert BedGraph to BigWig" version="1.0.1" hidden="true">
     <!-- Used internally to generate track indexes -->
     <requirements>
-        <requirement type="package" version="445">ucsc-wigtobigwig</requirement>
+        <requirement type="package" version="357">ucsc-wigtobigwig</requirement>
     </requirements>
     <command>grep -v "^track" '$input' | wigToBigWig -clip stdin '$chromInfo' '$output'</command>
     <inputs>

diff --git a/lib/galaxy/datatypes/converters/bigwig_to_wig_converter.xml b/lib/galaxy/datatypes/converters/bigwig_to_wig_converter.xml
@@ -1,7 +1,7 @@
 <tool id="bigwigtowig" name="Convert BigWig to Wiggle" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="20.01">
     <description>Convert bigWig to wig</description>
     <macros>
-        <token name="@TOOL_VERSION@">445</token>
+        <token name="@TOOL_VERSION@">377</token>
         <token name="@SUFFIX_VERSION@">0</token>
     </macros>
     <requirements>

diff --git a/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
@@ -1,4 +1,4 @@
-<tool id="CONVERTER_interval_to_bgzip_0" name="Convert Interval to BGZIP" version="1.0.4" hidden="true" profile="16.04">
+<tool id="CONVERTER_interval_to_bgzip_0" name="Convert Interval to BGZIP" version="1.0.3" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <macros>
         <xml name="assert_size" tokens="value" token_delta="10">
@@ -9,8 +9,8 @@
         </xml>
     </macros>
     <requirements>
-        <requirement type="package" version="9.4">coreutils</requirement>
-        <requirement type="package" version="1.17">htslib</requirement>
+        <requirement type="package" version="9.1">coreutils</requirement>
+        <requirement type="package" version="1.16">htslib</requirement>
     </requirements>
     <command><![CDATA[
         ## Skip any lines starting with '#' and 'track'

diff --git a/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
@@ -1,9 +1,9 @@
-<tool id="CONVERTER_interval_to_bigwig_0" name="Convert Genomic Intervals To Coverage" version="1.0.2">
+<tool id="CONVERTER_interval_to_bigwig_0" name="Convert Genomic Intervals To Coverage" version="1.0.1">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="445">ucsc-bedgraphtobigwig</requirement>
-        <requirement type="package" version="2.31.0">bedtools</requirement>
-        <requirement type="package" version="9.4">coreutils</requirement>
+        <requirement type="package" version="377">ucsc-bedgraphtobigwig</requirement>
+        <requirement type="package" version="2.29.2">bedtools</requirement>
+        <requirement type="package" version="8.25">coreutils</requirement>
     </requirements>
     <command>
 <![CDATA[

diff --git a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
@@ -1,4 +1,4 @@
-<tool id="CONVERTER_wig_to_bigwig" name="Convert Wiggle to BigWig" version="1.0.2" hidden="true">
+<tool id="CONVERTER_wig_to_bigwig" name="Convert Wiggle to BigWig" version="1.0.1" hidden="true">
     <!-- Used internally to generate track indexes -->
     <requirements>
         <requirement type="package" version="357">ucsc-wigtobigwig</requirement>

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
@@ -297,19 +297,13 @@ class safe_update(NamedTuple):
     "Show beginning1": safe_update(parse_version("1.0.0"), parse_version("1.0.2")),
     "Show tail1": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
     "sort1": safe_update(parse_version("1.1.0"), parse_version("1.2.0")),
-    "bigwigtowig": safe_update(parse_version("377+galaxy0"), parse_version("445+galaxy0")),
-    "CONVERTER_interval_to_bgzip_0": safe_update(parse_version("1.0.1"), parse_version("1.0.4")),
+    "CONVERTER_interval_to_bgzip_0": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
     "CONVERTER_Bam_Bai_0": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
-    "CONVERTER_bed_gff_or_vcf_to_bigwig_0": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
-    "CONVERTER_bedgraph_to_bigwig": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
     "CONVERTER_cram_to_bam_0": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
     "CONVERTER_fasta_to_fai": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
-    "CONVERTER_interval_to_bigwig_0": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
     "CONVERTER_sam_to_bigwig_0": safe_update(parse_version("1.0.2"), parse_version("1.0.3")),
-    "CONVERTER_bam_to_bigwig_0": safe_update(parse_version("1.0.2"), parse_version("1.0.3")),
     "CONVERTER_bam_to_coodinate_sorted_bam": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
     "CONVERTER_bam_to_qname_sorted_bam": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
-    "CONVERTER_wig_to_bigwig": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
 }