comparison ivar_variants.xml @ 12:ed28dd32141c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 02d1d482bda9804c69d2d03c890151bc491e5c73

11:38b91a3190cd

<tool id="ivar_variants" name="ivar variants" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@">
    <description>Call variants from aligned BAM file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

        #end if
    ]]></command>
    <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_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">
                <option value="tabular">Tabular (native tool output)</option>
                <option value="vcf">VCF</option>

    </inputs>
    <outputs>
        <data name="output_variants_tabular" from_work_dir="./variants.tsv" format="tabular" label="${tool.name} tabular output on ${on_string}">
            <filter>output_format['choice'] == 'tabular' or output_format['choice'] == 'tabular_and_vcf'</filter>
            <actions>
                <action name="column_names" type="metadata" default="REGION,POS,REF,ALT,REF_DP,REF_RV,REF_QUAL,ALT_DP,ALT_RV,ALT_QUAL,ALT_FREQ,TOTAL_DP,PVAL,PASS,GFF_FEATURE,REF_CODON,REF_AA,ALT_CODON,ALT_AA"/>
            </actions>
        </data>
        <data name="output_variants_vcf" from_work_dir="./variants.vcf" format="vcf" label="${tool.name} VCF on ${on_string}">
            <filter>output_format['choice'] == 'vcf' or output_format['choice'] == 'tabular_and_vcf'</filter>
        </data>

12:ed28dd32141c

<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>
    </macros>
    <expand macro="requirements"/>

        #end if
    ]]></command>
    <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="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">
                <option value="tabular">Tabular (native tool output)</option>
                <option value="vcf">VCF</option>

    </inputs>
    <outputs>
        <data name="output_variants_tabular" from_work_dir="./variants.tsv" format="tabular" label="${tool.name} tabular output on ${on_string}">
            <filter>output_format['choice'] == 'tabular' or output_format['choice'] == 'tabular_and_vcf'</filter>
            <actions>
                <action name="column_names" type="metadata" default="REGION,POS,REF,ALT,REF_DP,REF_RV,REF_QUAL,ALT_DP,ALT_RV,ALT_QUAL,ALT_FREQ,TOTAL_DP,PVAL,PASS,GFF_FEATURE,REF_CODON,REF_AA,ALT_CODON,ALT_AA,POS_AA"/>
            </actions>
        </data>
        <data name="output_variants_vcf" from_work_dir="./variants.vcf" format="vcf" label="${tool.name} VCF on ${on_string}">
            <filter>output_format['choice'] == 'vcf' or output_format['choice'] == 'tabular_and_vcf'</filter>
        </data>