Mercurial > repos > iuc > ivar_variants

diff ivar_variants.xml @ 12:ed28dd32141c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 02d1d482bda9804c69d2d03c890151bc491e5c73
author iuc
date Mon, 13 Feb 2023 17:29:40 +0000
parents 38b91a3190cd
children 045d6d00f606
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--- a/ivar_variants.xml	Wed Jan 11 09:53:09 2023 +0000
+++ b/ivar_variants.xml	Mon Feb 13 17:29:40 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="ivar_variants" name="ivar variants" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@">
+<tool id="ivar_variants" name="ivar variants" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>Call variants from aligned BAM file</description>
     <macros>
         <import>macros.xml</import>
@@ -27,7 +27,7 @@
     <inputs>
         <param name="input_bam" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>
         <param name="ref" type="data" format="fasta" label="Reference"/>
-        <param name="min_qual" argument="-q" type="integer" min="1" value="20" label="Minimum quality score threshold to count base"/>
+        <param name="min_qual" argument="-q" type="integer" min="0" max="255" value="20" label="Minimum quality score threshold to count base"/>
         <param name="min_freq" argument="-t" type="float" min="0" max="1" value="0.03" label="Minimum frequency threshold"/>
         <conditional name="output_format">
             <param name="choice" type="select" label="Output format">
@@ -51,7 +51,7 @@
         <data name="output_variants_tabular" from_work_dir="./variants.tsv" format="tabular" label="${tool.name} tabular output on ${on_string}">
             <filter>output_format['choice'] == 'tabular' or output_format['choice'] == 'tabular_and_vcf'</filter>
             <actions>
-                <action name="column_names" type="metadata" default="REGION,POS,REF,ALT,REF_DP,REF_RV,REF_QUAL,ALT_DP,ALT_RV,ALT_QUAL,ALT_FREQ,TOTAL_DP,PVAL,PASS,GFF_FEATURE,REF_CODON,REF_AA,ALT_CODON,ALT_AA"/>
+                <action name="column_names" type="metadata" default="REGION,POS,REF,ALT,REF_DP,REF_RV,REF_QUAL,ALT_DP,ALT_RV,ALT_QUAL,ALT_FREQ,TOTAL_DP,PVAL,PASS,GFF_FEATURE,REF_CODON,REF_AA,ALT_CODON,ALT_AA,POS_AA"/>
             </actions>
         </data>
         <data name="output_variants_vcf" from_work_dir="./variants.vcf" format="vcf" label="${tool.name} VCF on ${on_string}">