Mercurial > repos > iuc > vsnp_add_zero_coverage

diff vsnp_add_zero_coverage.xml @ 7:6dc6dd4666e3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
author iuc
date Tue, 16 Nov 2021 20:10:48 +0000
parents 9ddeef840a07
children 40b97055bb99
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line diff
--- a/vsnp_add_zero_coverage.xml	Tue Nov 16 08:26:14 2021 +0000
+++ b/vsnp_add_zero_coverage.xml	Tue Nov 16 20:10:48 2021 +0000
@@ -1,12 +1,12 @@
-<tool id="vsnp_add_zero_coverage" name="vSNP: add zero coverage" version="@WRAPPER_VERSION@.2+galaxy0" profile="@PROFILE@">
+<tool id="vsnp_add_zero_coverage" name="vSNP: add zero coverage" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description></description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="3.0.7">openpyxl</requirement>
-        <requirement type="package" version="1.79">biopython</requirement>
-        <requirement type="package" version="1.3.0">pandas</requirement>
+        <expand macro="biopython_requirement"/>
+        <expand macro="openpyxl_requirement"/>
+        <expand macro="pandas_requirement"/>
         <requirement type="package" version="0.16.0.1">pysam</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
@@ -58,15 +58,31 @@
             <param name="vcf_input" value="vcf_input.vcf" ftype="vcf" dbkey="89"/>
             <param name="reference_source" value="history"/>
             <param name="reference" value="NC_002945v4.fasta" ftype="fasta"/>
-            <output name="output_vcf" value="output_vcf.vcf" ftype="vcf" compare="contains"/>
-            <output name="output_metrics" file="output_metrics.tabular" ftype="tabular"/>
+            <output name="output_vcf" ftype="vcf">
+                <assert_contents>
+                    <has_size value="259726"/>
+                </assert_contents>
+            </output>
+            <output name="output_metrics" ftype="tabular">
+                <assert_contents>
+                    <has_size value="109"/>
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="2">
             <param name="bam_input" value="bam_input.bam" ftype="bam" dbkey="89"/>
             <param name="vcf_input" value="vcf_input.vcf" ftype="vcf" dbkey="89"/>
             <param name="reference_source" value="cached"/>
-            <output name="output_vcf" value="output_vcf.vcf" ftype="vcf" compare="contains"/>
-            <output name="output_metrics" file="output_metrics.tabular" ftype="tabular" compare="contains"/>
+            <output name="output_vcf" ftype="vcf">
+                <assert_contents>
+                    <has_size value="259726"/>
+                </assert_contents>
+            </output>
+            <output name="output_metrics" ftype="tabular">
+                <assert_contents>
+                    <has_size value="109"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help>
@@ -83,6 +99,6 @@
 
  * **Choose the source for the reference genome** - select "locally cached" if the reference associated with the BAM and VCF files is available within the Galaxy environment or "from history" to select the reference from the current history.
     </help>
-    <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>