Add biotools to CAT (galaxyproject#5763)

* Add biotools to CAT * Fix some linting error * Try to fix tests
pavanvidem · Feb 16, 2024 · 47be73f · 47be73f
1 parent 06828a4
commit 47be73f
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Showing 6 changed files with 16 additions and 6 deletions.
diff --git a/tools/cat/cat_add_names.xml b/tools/cat/cat_add_names.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/cat/cat_bins.xml b/tools/cat/cat_bins.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[
@@ -51,7 +52,7 @@
         <expand macro="outputs" />
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="mags" ftype="fasta" value="genome2.fna"/>
             <expand macro="test_catdb"/>
             <param name="select_outputs" value="bin2classification"/>
@@ -61,7 +62,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="mags" ftype="fasta" value="genome3.fna"/>
             <expand macro="test_catdb"/>
             <param name="select_outputs" value="bin2classification"/>
@@ -71,7 +72,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/>
             <expand macro="test_catdb"/>
             <param name="select_outputs" value="bin2classification"/>
@@ -82,7 +83,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="4">
             <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/>
             <expand macro="test_catdb"/>
             <param name="select_outputs" value="bin2classification"/>

diff --git a/tools/cat/cat_contigs.xml b/tools/cat/cat_contigs.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[
@@ -30,7 +31,7 @@
         <expand macro="outputs" />
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/>
             <expand macro="test_catdb"/>
             <param name="select_outputs" value="contig2classification"/>
@@ -40,7 +41,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="4">
             <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/>
             <expand macro="test_catdb"/>
             <param name="select_outputs" value="predicted_proteins_faa"/>

diff --git a/tools/cat/cat_prepare.xml b/tools/cat/cat_prepare.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/cat/cat_summarise.xml b/tools/cat/cat_summarise.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/cat/macros.xml b/tools/cat/macros.xml
@@ -1,6 +1,11 @@
 <macros>
     <token name="@TOOL_VERSION@">5.2.3</token>
     <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">cat_bins</xref>
+        </xrefs>
+    </xml>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">cat</requirement>