comparison sambamba.xml @ 2:7ad3484aa5db draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"

1:6195f15d4541

<tool id="sambamba_sample_or_filter" name="Sample or Filter BAM" version="0.6">
    <description>
        on flags, fields, and tags using Sambamba
    </description>
    <requirements>
        <requirement type="package" version="0.7.1">sambamba</requirement>

    </stdio>
    <!-- <version_command>sambamba 2>&amp;1 | grep "sambamba v" | sed 's/^sambamba v\(.*\)/\1/'</version_command> -->
    <command detect_errors="exit_code"><![CDATA[
        ln -s $input input.bam &&
        ln -s $input.metadata.bam_index input.bai &&
        #if $sambamba_options.selector == 'filter'
            sambamba view -h -t \${GALAXY_SLOTS:-4}
            #if $sambamba_options.query != '':
                --filter='$sambamba_options.query'
            #end if
                -f '$format' -o $outfile input.bam $sambamba_options.region
         #else
             sambamba view -h -t \${GALAXY_SLOTS:-4} -f '$format'
             --subsampling-seed='$sambamba_options.seed'
             -s '$sambamba_options.fraction' -o '$outfile' input.bam
         #end if
    ]]></command>
    <inputs>
        <param name="input" type="data" format="bam" label="BAM or SAM file to filter"/>
        <param name="format" type="select" label="format of the tool output">
            <option value="bam">BAM</option>
            <option value="sam">SAM</option>
        </param>
        <conditional name="sambamba_options">
            <param name="selector" type="select" label="Filter or Down-sample alignments">
                <option value="sample">Down-sample bam or sam alignments</option>
                <option value="filter" selected="true">Filter bam or sam alignements</option>
            </param>
            <when value="filter">
                <param name="query" type="text" size="80">
                    <sanitizer invalid_char="X">
                        <valid initial="string.ascii_letters,string.digits, string.punctuation">
                            <add value=" " />
                        </valid>

                    (region between 1,000,000 and 2,000,000bp including the end points).
                    The coordinates are 1-based.
                    </help>
                </param>
            </when>
            <when value="sample">
                <param name="seed" type="integer" value="123" size="10">
                    <label>Seed value for randomisation</label>
                    <help>
                    Be careful at selecting different seed values if you
                    re-subsample a subsample output of this tool

                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="outfile" format="bam">
            <change_format>
                <when input="format" value="sam" format="sam" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="ex1_header.sam" ftype="sam" />
            <param name="selector" value="filter" />
            <param name="query" value="[H0] == 1 and read_name =~ /^EAS51_62/" />
            <param name="format" value="bam" />
            <param name="region" value="" />
            <output name="outfile" file="ex1_header_filtered.bam" ftype="bam" />
        </test>
        <test>
            <param name="input" value="c1215_fixmate.bam" ftype="bam" />
            <param name="selector" value="filter" />
            <param name="query" value="[MD] =~ /^\d+T\d+A\d+/ and first_of_pair" />

            <param name="selector" value="filter" />
            <param name="query" value='' />
            <param name="format" value="sam" />
            <param name="region" value="AL096846:1000-5000" />
            <output name="outfile" file="c1215_fixmate_region-filtered.sam" ftype="sam" lines_diff="2"/>
        </test>
         <test>
            <param name="input" value="ex1_header.sam" ftype="sam" />
            <param name="selector" value="sample" />
            <param name="seed" value="123" />
            <param name="fraction" value="0.1" />
            <param name="format" value="bam" />
            <output name="outfile" file="ex1_header_sampled.bam" ftype="bam" />
        </test>
        <test>
            <param name="input" value="c1215_fixmate.bam" ftype="bam" />
            <param name="selector" value="sample" />
            <param name="seed" value="123" />

2:7ad3484aa5db

<tool id="sambamba_sample_or_filter" name="Sample or Filter BAM" version="0.7.1+galaxy0">
    <description>
        on flags, fields, and tags using Sambamba
    </description>
    <requirements>
        <requirement type="package" version="0.7.1">sambamba</requirement>

    </stdio>
    <!-- <version_command>sambamba 2>&amp;1 | grep "sambamba v" | sed 's/^sambamba v\(.*\)/\1/'</version_command> -->
    <command detect_errors="exit_code"><![CDATA[
        ln -s $input input.bam &&
        ln -s $input.metadata.bam_index input.bai &&

        #if $sambamba_options.selector == 'filter'
            sambamba view -h -t \${GALAXY_SLOTS:-4}
            #if $sambamba_options.query != '':
                --filter='$sambamba_options.query'
            #end if
                -f '$sambamba_options.format'
                -o $outfile input.bam $sambamba_options.region

        #else if $sambamba_options.selector == 'sample'
            sambamba view -h -t \${GALAXY_SLOTS:-4} -f '$sambamba_options.format'
                 --subsampling-seed='$sambamba_options.seed'
                 -s '$sambamba_options.fraction'
                 -o '$outfile' input.bam

        #else
            sambamba slice -o '$outfile' input.bam $sambamba_options.region
        #end if
    ]]></command>
    <inputs>
        <param name="input" type="data" format="bam" label="BAM or SAM input file(s)"/>
        <conditional name="sambamba_options">
            <param name="selector" type="select" label="Filter, Down-sample or slice alignments">
                <option value="sample">Down-sample bam or sam alignments</option>
                <option value="filter" selected="true">Filter bam or sam alignements</option>
                <option value="slice">Slice bam or sam alignements by chromosome or chromosome region</option>
            </param>
            <when value="filter">
                <param name="format" type="select" label="format of the tool output">
                    <option value="bam">BAM</option>
                    <option value="sam">SAM</option>
                </param>
                <param name="query" type="text" size="80">
                    <sanitizer invalid_char="X">
                        <valid initial="string.ascii_letters,string.digits, string.punctuation">
                            <add value=" " />
                        </valid>

                    (region between 1,000,000 and 2,000,000bp including the end points).
                    The coordinates are 1-based.
                    </help>
                </param>
            </when>

            <when value="slice">
                <param name="region" type="text" size="40" label="Region in format chr:beg-end">
                    <help>
                    Regions can be specified as 'chr2' (the whole chr2), 'chr2:1000000'
                    (region starting from 1,000,000bp) or 'chr2:1,000,000-2,000,000'
                    (region between 1,000,000 and 2,000,000bp including the end points).
                    The coordinates are 1-based. NOTE that sambamba slice only outputs
                    BAM-format datasets.
                    </help>
                </param>
            </when>

            <when value="sample">
                <param name="format" type="select" label="format of the tool output">
                    <option value="bam">BAM</option>
                    <option value="sam">SAM</option>
                </param>
                <param name="seed" type="integer" value="123" size="10">
                    <label>Seed value for randomisation</label>
                    <help>
                    Be careful at selecting different seed values if you
                    re-subsample a subsample output of this tool

                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="outfile" format="bam" label="Filter, slice or sample on ${on_string}">
            <change_format>
                <when input="sambamba_options['format']" value="sam" format="sam" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="ex1_header.sam" ftype="sam" />
            <param name="selector" value="filter" />
            <param name="query" value="[H0] == 1 and read_name =~ /^EAS51_62/" />
            <param name="format" value="bam" />
            <param name="region" value="" />
            <output name="outfile" file="ex1_header_filtered.bam" ftype="bam" lines_diff="2"/>
        </test>
        <test>
            <param name="input" value="c1215_fixmate.bam" ftype="bam" />
            <param name="selector" value="filter" />
            <param name="query" value="[MD] =~ /^\d+T\d+A\d+/ and first_of_pair" />

            <param name="selector" value="filter" />
            <param name="query" value='' />
            <param name="format" value="sam" />
            <param name="region" value="AL096846:1000-5000" />
            <output name="outfile" file="c1215_fixmate_region-filtered.sam" ftype="sam" lines_diff="2"/>
        </test>
        <test>
            <param name="input" value="c1215_fixmate.bam" ftype="bam" />
            <param name="selector" value="slice" />
            <param name="query" value='' />
            <param name="region" value="AL096846:1000-2000 AL096846:4000-5000" />
            <output name="outfile" file="c1215_fixmate_region-sliced.bam" ftype="bam"/>
        </test>
         <test>
            <param name="input" value="ex1_header.sam" ftype="sam" />
            <param name="selector" value="sample" />
            <param name="seed" value="123" />
            <param name="fraction" value="0.1" />
            <param name="format" value="bam" />
            <output name="outfile" file="ex1_header_sampled.bam" ftype="bam" lines_diff="2"/>
        </test>
        <test>
            <param name="input" value="c1215_fixmate.bam" ftype="bam" />
            <param name="selector" value="sample" />
            <param name="seed" value="123" />