Add perl dependency for tools using perl

Fixes galaxyproject#12603. Also need to add new tool versions to safe udpates
mvdbeek · Sep 30, 2021 · 2e4d263 · 2e4d263
1 parent 5d59042
commit 2e4d263
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Showing 12 changed files with 47 additions and 16 deletions.
diff --git a/tools/evolution/codingSnps.xml b/tools/evolution/codingSnps.xml
@@ -1,7 +1,8 @@
-<tool id="hgv_codingSnps" name="aaChanges" version="1.0.1">
+<tool id="hgv_codingSnps" name="aaChanges" version="1.0.2">
   <description>amino-acid changes caused by a set of SNPs</description>
 
   <requirements>
+    <requirement type="package" version="5.32.1">perl</requirement>
     <requirement type="package" version="8.25">coreutils</requirement>
     <requirement type="package" version="357">ucsc-twobittofa</requirement>
     <requirement type="package" version="357">ucsc-nibfrag</requirement>

diff --git a/tools/filters/CreateInterval.xml b/tools/filters/CreateInterval.xml
@@ -1,5 +1,8 @@
-<tool id="createInterval" name="Create single interval" version="1.0.0">
+<tool id="createInterval" name="Create single interval" version="1.0.1">
   <description>as a new dataset</description>
+  <requirements>
+    <requirement type="package" version="5.32.1">perl</requirement>
+  </requirements>
   <command>
 perl '$__tool_directory__/CreateInterval.pl' '$chrom' $start $end '$name' $strand '$out_file1'
   </command>

diff --git a/tools/filters/changeCase.xml b/tools/filters/changeCase.xml
@@ -1,5 +1,8 @@
-<tool id="ChangeCase" name="Change Case" version="1.0.0">
+<tool id="ChangeCase" name="Change Case" version="1.0.1">
   <description> of selected columns</description>
+  <requirements>
+    <requirement type="package" version="5.32.1">perl</requirement>
+  </requirements>
   <stdio>
     <exit_code range="1:" err_level="fatal" />
   </stdio>

diff --git a/tools/filters/commWrapper.xml b/tools/filters/commWrapper.xml
@@ -1,5 +1,8 @@
-<tool id="Comm1" name="Find Similarities and Differences" version="1.0.0">
+<tool id="Comm1" name="Find Similarities and Differences" version="1.0.1">
   <description>between two datasets</description>
+  <requirements>
+    <requirement type="package" version="5.32.1">perl</requirement>
+  </requirements>
   <edam_operations>
     <edam_operation>operation_3695</edam_operation>
   </edam_operations>

diff --git a/tools/filters/condense_characters.xml b/tools/filters/condense_characters.xml
@@ -1,5 +1,8 @@
-<tool id="Condense characters1" name="Condense" version="1.0.0">
+<tool id="Condense characters1" name="Condense" version="1.0.1">
   <description>consecutive characters</description>
+  <requirements>
+    <requirement type="package" version="5.32.1">perl</requirement>
+  </requirements>
   <command><![CDATA[
 perl '$__tool_directory__/condense_characters.pl'
 '$input'

diff --git a/tools/filters/cutWrapper.xml b/tools/filters/cutWrapper.xml
@@ -1,5 +1,8 @@
-<tool id="Cut1" name="Cut" version="1.0.2">
+<tool id="Cut1" name="Cut" version="1.0.3">
   <description>columns from a table</description>
+  <requirements>
+    <requirement type="package" version="5.32.1">perl</requirement>
+  </requirements>
   <edam_operations>
     <edam_operation>operation_3695</edam_operation>
   </edam_operations>

diff --git a/tools/filters/fixedValueColumn.xml b/tools/filters/fixedValueColumn.xml
@@ -1,5 +1,8 @@
-<tool id="addValue" name="Add column" version="1.0.0">
+<tool id="addValue" name="Add column" version="1.0.1">
   <description>to an existing dataset</description>
+  <requirements>
+    <requirement type="package" version="5.32.1">perl</requirement>
+  </requirements>
   <edam_operations>
     <edam_operation>operation_3096</edam_operation>
   </edam_operations>

diff --git a/tools/filters/pasteWrapper.xml b/tools/filters/pasteWrapper.xml
@@ -1,5 +1,8 @@
-<tool id="Paste1" name="Paste" version="1.0.0">
+<tool id="Paste1" name="Paste" version="1.0.1">
   <description>two files side by side</description>
+  <requirements>
+    <requirement type="package" version="5.32.1">perl</requirement>
+  </requirements>
   <command>perl '$__tool_directory__/pasteWrapper.pl' '$input1' '$input2' $delimiter '$out_file1'</command>
   <inputs>
 <!--    <display>paste $input1 and $input2 using $delimiter as delimiter</display> -->

diff --git a/tools/filters/remove_beginning.xml b/tools/filters/remove_beginning.xml
@@ -1,14 +1,17 @@
-<tool id="Remove beginning1" name="Remove beginning" version="1.0.0">
+<tool id="Remove beginning1" name="Remove beginning" version="1.0.1">
   <description>of a file</description>
+  <requirements>
+    <requirement type="package" version="5.32.1">perl</requirement>
+  </requirements>
   <command>
 perl '$__tool_directory__/remove_beginning.pl' '$input' $num_lines '$out_file1'
   </command>
   <inputs>
-    <param name="num_lines" type="integer" value="1" label="Remove first" help="lines" />
-    <param name="input" type="data" format="txt" label="from" />
+    <param name="num_lines" type="integer" value="1" label="Remove first" help="lines"/>
+    <param name="input" type="data" format="txt" label="from"/>
   </inputs>
   <outputs>
-    <data name="out_file1" format="input" metadata_source="input" />
+    <data name="out_file1" format="input" metadata_source="input"/>
   </outputs>
   <tests>
     <test>

diff --git a/tools/phenotype_association/linkToGProfile.xml b/tools/phenotype_association/linkToGProfile.xml
@@ -1,6 +1,8 @@
-<tool id="hgv_linkToGProfile" name="g:Profiler" version="1.0.0">
+<tool id="hgv_linkToGProfile" name="g:Profiler" version="1.0.1">
   <description>tools for functional profiling of gene lists</description>
-
+  <requirements>
+    <requirement type="package" version="5.32.1">perl</requirement>
+  </requirements>
   <command detect_errors="exit_code">
 perl '$__tool_directory__/linkToGProfile.pl' '$input' $type '$out_file1' -region='$region' -gene=$genes -chr=${input.metadata.chromCol} -start=${input.metadata.startCol} -end=${input.metadata.endCol}
   </command>

diff --git a/tools/phenotype_association/master2gd_snp.xml b/tools/phenotype_association/master2gd_snp.xml
@@ -1,5 +1,6 @@
-<tool id="master2gd_snp" name="MasterVar to gd_snp" version="1.0.0">
+<tool id="master2gd_snp" name="MasterVar to gd_snp" version="1.0.1">
     <description>Convert from MasterVar to gd_snp table</description>
+    <requirement type="package" version="5.32.1">perl</requirement>
     <command>
 perl '$__tool_directory__/master2gd_snp.pl' '$input1' -name='$indName' -build=${input1.metadata.dbkey}
 #if $snptab.tab2 == "yes"

diff --git a/tools/phenotype_association/master2pg.xml b/tools/phenotype_association/master2pg.xml
@@ -1,5 +1,8 @@
-<tool id="master2pgSnp" name="MasterVar to pgSnp" version="1.0.0">
+<tool id="master2pgSnp" name="MasterVar to pgSnp" version="1.0.1">
     <description>Convert from MasterVar to pgSnp format</description>
+    <requirements>
+        <requirement type="package" version="5.32.1">perl</requirement>
+    </requirements>
     <command>
 perl '$__tool_directory__/master2pg.pl' $indel '$input1' > '$out_file1'
     </command>