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comparison 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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11:38b91a3190cd 12:ed28dd32141c
1 <tool id="ivar_variants" name="ivar variants" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@"> 1 <tool id="ivar_variants" name="ivar variants" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <description>Call variants from aligned BAM file</description> 2 <description>Call variants from aligned BAM file</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
25 #end if 25 #end if
26 ]]></command> 26 ]]></command>
27 <inputs> 27 <inputs>
28 <param name="input_bam" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/> 28 <param name="input_bam" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>
29 <param name="ref" type="data" format="fasta" label="Reference"/> 29 <param name="ref" type="data" format="fasta" label="Reference"/>
30 <param name="min_qual" argument="-q" type="integer" min="1" value="20" label="Minimum quality score threshold to count base"/> 30 <param name="min_qual" argument="-q" type="integer" min="0" max="255" value="20" label="Minimum quality score threshold to count base"/>
31 <param name="min_freq" argument="-t" type="float" min="0" max="1" value="0.03" label="Minimum frequency threshold"/> 31 <param name="min_freq" argument="-t" type="float" min="0" max="1" value="0.03" label="Minimum frequency threshold"/>
32 <conditional name="output_format"> 32 <conditional name="output_format">
33 <param name="choice" type="select" label="Output format"> 33 <param name="choice" type="select" label="Output format">
34 <option value="tabular">Tabular (native tool output)</option> 34 <option value="tabular">Tabular (native tool output)</option>
35 <option value="vcf">VCF</option> 35 <option value="vcf">VCF</option>
49 </inputs> 49 </inputs>
50 <outputs> 50 <outputs>
51 <data name="output_variants_tabular" from_work_dir="./variants.tsv" format="tabular" label="${tool.name} tabular output on ${on_string}"> 51 <data name="output_variants_tabular" from_work_dir="./variants.tsv" format="tabular" label="${tool.name} tabular output on ${on_string}">
52 <filter>output_format['choice'] == 'tabular' or output_format['choice'] == 'tabular_and_vcf'</filter> 52 <filter>output_format['choice'] == 'tabular' or output_format['choice'] == 'tabular_and_vcf'</filter>
53 <actions> 53 <actions>
54 <action name="column_names" type="metadata" default="REGION,POS,REF,ALT,REF_DP,REF_RV,REF_QUAL,ALT_DP,ALT_RV,ALT_QUAL,ALT_FREQ,TOTAL_DP,PVAL,PASS,GFF_FEATURE,REF_CODON,REF_AA,ALT_CODON,ALT_AA"/> 54 <action name="column_names" type="metadata" default="REGION,POS,REF,ALT,REF_DP,REF_RV,REF_QUAL,ALT_DP,ALT_RV,ALT_QUAL,ALT_FREQ,TOTAL_DP,PVAL,PASS,GFF_FEATURE,REF_CODON,REF_AA,ALT_CODON,ALT_AA,POS_AA"/>
55 </actions> 55 </actions>
56 </data> 56 </data>
57 <data name="output_variants_vcf" from_work_dir="./variants.vcf" format="vcf" label="${tool.name} VCF on ${on_string}"> 57 <data name="output_variants_vcf" from_work_dir="./variants.vcf" format="vcf" label="${tool.name} VCF on ${on_string}">
58 <filter>output_format['choice'] == 'vcf' or output_format['choice'] == 'tabular_and_vcf'</filter> 58 <filter>output_format['choice'] == 'vcf' or output_format['choice'] == 'tabular_and_vcf'</filter>
59 </data> 59 </data>