Mercurial > repos > iuc > vsnp_add_zero_coverage

diff vsnp_add_zero_coverage.xml @ 9:40b97055bb99 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
author iuc
date Fri, 10 Jun 2022 06:08:02 +0000
parents 6dc6dd4666e3
children
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line diff
--- a/vsnp_add_zero_coverage.xml	Mon Dec 06 18:30:02 2021 +0000
+++ b/vsnp_add_zero_coverage.xml	Fri Jun 10 06:08:02 2022 +0000
@@ -7,7 +7,7 @@
         <expand macro="biopython_requirement"/>
         <expand macro="openpyxl_requirement"/>
         <expand macro="pandas_requirement"/>
-        <requirement type="package" version="0.16.0.1">pysam</requirement>
+        <requirement type="package" version="0.19.1">pysam</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 #import re
@@ -20,6 +20,7 @@
 ln -s '${vcf_input}' '${vcf_identifier}' &&
 
 python '$__tool_directory__/vsnp_add_zero_coverage.py'
+--dbkey '$bam_input.metadata.dbkey'
 --bam_input '$bam_identifier'
 --vcf_input '$vcf_identifier'
 #if str($reference_cond.reference_source) == 'cached'
@@ -61,11 +62,13 @@
             <output name="output_vcf" ftype="vcf">
                 <assert_contents>
                     <has_size value="259726"/>
+                    <has_text text="##fileformat=VCFv4.2"/>
                 </assert_contents>
             </output>
             <output name="output_metrics" ftype="tabular">
                 <assert_contents>
-                    <has_size value="109"/>
+                    <has_size value="190"/>
+                    <has_text text="# BAM File"/>
                 </assert_contents>
             </output>
         </test>
@@ -76,11 +79,13 @@
             <output name="output_vcf" ftype="vcf">
                 <assert_contents>
                     <has_size value="259726"/>
+                    <has_text text="##fileformat=VCFv4.2"/>
                 </assert_contents>
             </output>
             <output name="output_metrics" ftype="tabular">
                 <assert_contents>
-                    <has_size value="109"/>
+                    <has_size value="190"/>
+                    <has_text text="# BAM File"/>
                 </assert_contents>
             </output>
         </test>
@@ -92,8 +97,8 @@
 combination whose positions with no coverage are represented as "N".  These outputs are restricted to SNPs and those regions
 along the reference with no coverage.
 
-A metrics file is produced for each combination which provides the number of good SNPs, the average coverage and the genome
-coverage percentage.
+A metrics file is produced for each combination which provides the reference length, genome coverage, average coverage, 
+total zero coverage, zero coverage percent and quality SNPs.
 
 **Required Options**