comparison macros.xml @ 9:fa7ad9b89f4a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2

8:583abf29fc8e

<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="1.3.1">samtools</requirement>
            <yield/>
        </requirements>
    </xml>
    <token name="@TOOL_VERSION@">1.3.1</token>
    <xml name="citations">
        <citations>
            <citation type="bibtex">
                @misc{SAM_def,
                title={Definition of SAM/BAM format},

9:fa7ad9b89f4a

<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>
            <yield/>
        </requirements>
    </xml>
    <token name="@TOOL_VERSION@">1.9</token>
    <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token>
    <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[
        ##prepare input and indices 
        #for $i, $bam in enumerate( $input_bams ):
            ln -s '$bam' '${i}' &&
            #if $bam.is_of_type('bam'):
                #if str( $bam.metadata.bam_index ) != "None":
                    ln -s '${bam.metadata.bam_index}' '${i}.bai' &&
                #else:
                    samtools index '${i}' '${i}.bai' &&
                #end if
            #elif $bam.is_of_type('cram'):
                #if str( $bam.metadata.cram_index ) != "None":
                    ln -s '${bam.metadata.cram_index}' '${i}.crai' &&
                #else:
                    samtools index '${i}' '${i}.crai' &&
                #end if
            #end if
        #end for
    ]]></token>
    <xml name="flag_options">
        <option value="1">read is paired</option>
        <option value="2">read is mapped in a proper pair</option>
        <option value="4">read is unmapped</option>
        <option value="8">mate is unmapped</option>
        <option value="16">read reverse strand</option>
        <option value="32">mate reverse strand</option>
        <option value="64">read is the first in a pair</option>
        <option value="128">read is the second in a pair</option>
        <option value="256">alignment or read is not primary</option>
        <option value="512">read fails platform/vendor quality checks</option>
        <option value="1024">read is a PCR or optical duplicate</option>
        <option value="2048">supplementary alignment</option>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">
                @misc{SAM_def,
                title={Definition of SAM/BAM format},