comparison basil.xml @ 1:77fc7640abc7 draft default tip

planemo upload commit 49a2861a9b3480ea25f1e5526d2edf9dc8cb5334

0:e6ef29001647

<tool id="basil" name="basil" version="1.2.0">
    <description>Breakpoint detection, including large insertions</description>
    <requirements>
        <requirement type="package" version="1.2.0">anise_basil</requirement>
    </requirements>
    <version_command>basil --version 2>&amp;1 | grep 'basil version' | cut -f 3 -d ' '</version_command>
    <command detect_errors="aggressive"><![CDATA[
        ln -s '$ref' 'ref.fa' &&
        ln -s '$bam' 'in.bam' &&
        ln -s '$vcf' 'out.vcf' &&
        basil
        --input-reference 'ref.fa'
        --input-mapping 'in.bam'
        --out-vcf 'out.vcf'
        --oea-min-support-each-side '$min_oea_each_side'
    ]]></command>
    <inputs>
        <param name="ref" argument="--input-reference" type="data" format="Fasta" label="Reference Sequence File" help="FASTA file with the reference."/>
        <param name="bam" argument="--input-mapping" type="data" format="sam,bam" label="Alignment File" help="SAM/BAM file to use as the input."/>
        <param name="min_oea_each_side" argument="--oea-min-support-each-side" type="integer" value="2" label="Minimum supporting reads, each side" help="Smallest number of OEA (one-end-anchor) reads on each side to support an insertion.  In range [1..inf].  This is the minimum number of supporting reads (without mapped partners) on each side of an insertion breakpoint required to not be filtered." />
    </inputs>
    <outputs>
        <data name="vcf" format="vcf" />
    </outputs>
    <tests>
        <test>
            <param name="ref" value="ref.fa"/>
            <param name="bam" value="simulated.bam"/>
            <param name="min_oea_each_side"  value="2"/>
            <output name="vcf" file="basil.vcf"/>
        </test>
    </tests>
    <help><![CDATA[
        BASIL is a method to detect breakpoints for structural variants (including insertion breakpoints) from aligned paired HTS reads in BAM format.  Use BASIL to analyze BAM files for tentative insertion sites.

1:77fc7640abc7

<tool id="basil" name="basil" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
    <description>Breakpoint detection, including large insertions</description>
    <macros>
        <token name="@TOOL_VERSION@">1.2.0</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">anise_basil</requirement>
    </requirements>
    <version_command>basil --version 2&gt;&amp;1 | grep 'basil version' | cut -f 3 -d ' '</version_command>
    <command detect_errors="aggressive"><![CDATA[
        #if $reference_source.reference_source_selector == 'history':
            ln -f -s '$reference_source.ref' ref.fa &&
        #else:
            ln -f -s '$reference_source.ref.fields.path' ref.fa &&
        #end if
        ln -s '$bam' 'in.bam' &&
        ln -s '$vcf' 'out.vcf' &&
        basil
        --input-reference 'ref.fa'
        --input-mapping 'in.bam'
        --out-vcf 'out.vcf'
        --oea-min-support-each-side '$min_oea_each_side'
    ]]></command>
    <inputs>
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below. If you would like to perform self-mapping select `history` here, then choose your input file as reference.">
                <option value="cached">Use a built-in genome index</option>
                <option value="history">Use a genome from history and build index</option>
            </param>
            <when value="cached">
                <param name="ref" type="select" label="Using reference genome" help="Select genome from the list">
                    <options from_data_table="all_fasta">
                        <filter type="sort_by" column="2"/>
                        <validator type="no_options" message="No reference genomes are available"/>
                    </options>
                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                </param>
            </when>
            <when value="history">
                <param name="ref" argument="--input-reference" type="data" format="Fasta" label="Reference Sequence File" help="FASTA file with the reference."/>
            </when>
        </conditional>
        <param name="bam" argument="--input-mapping" type="data" format="sam,bam" label="Alignment File" help="SAM/BAM file to use as the input."/>
        <param name="min_oea_each_side" argument="--oea-min-support-each-side" type="integer" value="2" label="Minimum supporting reads, each side" help="Smallest number of OEA (one-end-anchor) reads on each side to support an insertion.  In range [1..inf].  This is the minimum number of supporting reads (without mapped partners) on each side of an insertion breakpoint required to not be filtered."/>
    </inputs>
    <outputs>
        <data name="vcf" format="vcf"/>
    </outputs>
    <tests>
        <test>
            <conditional name="reference_source">
                <param name="reference_source_selector" value="history" />
                <param name="ref" ftype="fasta" value="ref.fa"/>
            </conditional>
            <param name="ref" value="ref.fa"/>
            <param name="bam" value="simulated.bam"/>
            <param name="min_oea_each_side" value="2"/>
            <output name="vcf" file="basil.vcf"/>
        </test>
        <test>
            <conditional name="reference_source">
                <param name="reference_source_selector" value="cached" />
                <param name="ref" value="genome"/>
            </conditional>
            <param name="bam" value="simulated.bam"/>
            <param name="min_oea_each_side" value="2"/>
            <output name="vcf" file="basil.vcf"/>
        </test>
    </tests>
    <help><![CDATA[
        BASIL is a method to detect breakpoints for structural variants (including insertion breakpoints) from aligned paired HTS reads in BAM format.  Use BASIL to analyze BAM files for tentative insertion sites.