comparison irissv.xml @ 3:3242dbeea69c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 00d6705a08a9d9cc9093846b730c4dec247cf5e7

2:b4b6b660293a

<tool id="irissv" name="Iris" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
    <description>Refine insertion sequences</description>
    <macros>
        <import>macros.xml</import>
    </macros>

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

    <command detect_errors="aggressive"><![CDATA[
    @REF_FASTA@

    ln -s '$in_bam' reads.bam &&
    ln -s '$in_bam.metadata.bam_index' 'reads.bam.bai' &&

        <!--log_out param doesn't seem to produce output for some reason, commenting out.-->
        <!-- <param name="output_log" type="boolean" label="Output log file?" checked="true"/> -->
        <!--
            Optional arguments
        -->
        <param argument="padding_before" type="integer" value="1" min="1" label="The number of bases to output before the variant in REF/ALT fields" />
        <param argument="padding_after" type="integer" value="0" min="0" label="The number of bases to output after the variant in REF/ALT fields" />
        <param argument="genome_buffer" type="integer" value="100000" min="1" label="The genome region on each side of the SV to align assembled reads to" />
        <param argument="min_ins_length" type="integer" value="30" min="1" label="The min length allowed for a refined insertion sequence" />
        <param argument="max_ins_dist" type="integer" value="100" min="0" label="The max distance a refined insertion call can be from its old position" />
        <param argument="max_out_length" type="integer" value="100000" min="0" label="The max length of variant which will be output" />
        <param argument="max_len_change" type="float" value="0.25" min="0.0" label="The max proportion by which a variant's length can change" />
        
        <param name="aligner" type="select">
            <option value="" selected="true">Use minimap2 for mapping</option>
            <option value="--pacbio" selected="true">Use minimap2 for mapping in PacBio mode</option>
            <option value="--hifi">Use minimap2 in hifi mode</option>
        </param>
        <param argument="--rerunracon" type="boolean" truevalue="--rerunracon" falsevalue="" checked="false" label="Use racon twice for consensus finding" />
        <!--
            Flags
        -->
        <param argument="--also_deletions" type="boolean" truevalue="also_deletions" falsevalue="" checked="false" label="also try to refine deletion positions/lengths"/>
        <param argument="--keep_long_variants" type="boolean" truevalue="--keep_long_variants" falsevalue="" checked="false" label="output original VCF line for very long variants instead of ignoring them"/>

    <tests>
        <!-- #1 default -->
        <test expect_num_outputs="1">
            <conditional name="reference_source">
                <param name="reference_source_selector" value="history"/>
                <param name="ref_file" ftype="fasta.gz" value="genome.fa.gz"/>
            </conditional>
            <param name="in_vcf" value="sniffles.vcf"/>
            <param name="in_bam" value="iris.bam"/>
            <output name="out_vcf" file="test_out.vcf"/>
        </test>

3:3242dbeea69c

<tool id="irissv" name="Iris" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>Refine insertion sequences</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="aggressive"><![CDATA[
    @REF_FASTA@

    ln -s '$in_bam' reads.bam &&
    ln -s '$in_bam.metadata.bam_index' 'reads.bam.bai' &&

        <!--log_out param doesn't seem to produce output for some reason, commenting out.-->
        <!-- <param name="output_log" type="boolean" label="Output log file?" checked="true"/> -->
        <!--
            Optional arguments
        -->
        <param argument="padding_before" type="integer" min="1" value="1" label="The number of bases to output before the variant in REF/ALT fields"/>
        <param argument="padding_after" type="integer" min="0" value="0" label="The number of bases to output after the variant in REF/ALT fields"/>
        <param argument="genome_buffer" type="integer" min="1" value="100000" label="The genome region on each side of the SV to align assembled reads to"/>
        <param argument="min_ins_length" type="integer" min="1" value="30" label="The min length allowed for a refined insertion sequence"/>
        <param argument="max_ins_dist" type="integer" min="0" value="100" label="The max distance a refined insertion call can be from its old position"/>
        <param argument="max_out_length" type="integer" min="0" value="100000" label="The max length of variant which will be output"/>
        <param argument="max_len_change" type="float" min="0.0" value="0.25" label="The max proportion by which a variant's length can change"/>
        <param name="aligner" type="select">
            <option value="" selected="true">Use minimap2 for mapping</option>
            <option value="--pacbio" selected="true">Use minimap2 for mapping in PacBio mode</option>
            <option value="--hifi">Use minimap2 in hifi mode</option>
        </param>
        <param argument="--rerunracon" type="boolean" truevalue="--rerunracon" falsevalue="" checked="false" label="Use racon twice for consensus finding"/>
        <!--
            Flags
        -->
        <param argument="--also_deletions" type="boolean" truevalue="also_deletions" falsevalue="" checked="false" label="also try to refine deletion positions/lengths"/>
        <param argument="--keep_long_variants" type="boolean" truevalue="--keep_long_variants" falsevalue="" checked="false" label="output original VCF line for very long variants instead of ignoring them"/>

    <tests>
        <!-- #1 default -->
        <test expect_num_outputs="1">
            <conditional name="reference_source">
                <param name="reference_source_selector" value="history"/>
                <param name="ref_file" value="genome.fa.gz" ftype="fasta.gz"/>
            </conditional>
            <param name="in_vcf" value="sniffles.vcf"/>
            <param name="in_bam" value="iris.bam"/>
            <output name="out_vcf" file="test_out.vcf"/>
        </test>