comparison macros.xml @ 4:0ff4b0e5a3bc draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit bc3831e3648809bd3d46611b2a74bd26a17985e5

3:bb3f59096c8e

<macros>
    <token name="@TOOL_VERSION@">0.6.1</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <token name="@PROFILE@">22.01</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">coverm</requirement>
        </requirements>

            <option value="paired">Paired end</option>
            <option value="paired_collection" selected="true">Paired collection</option>
            <option value="interleaved">Interleaved</option>
        </param>
    </xml>
    <xml name="paired_reads">
        <param name="paired_reads" type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" label="Collection of paired-end FASTA/Q files(s) for mapping" help="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order." />
    </xml>
    <xml name="individual_assembly_reads">
        <conditional name="read_type">
            <expand macro="read_type"/>
            <when value="single">
                <param argument="--single" type="data" format="@INPUT_FORMATS@" label="Single Read" />

            <when value="paired">
                <param argument="-1" name="read1" type="data" format="@INPUT_FORMATS@" label="Forward FASTA/Q file for mapping" />
                <param argument="-2" name="read2" type="data" format="@INPUT_FORMATS@" label="Reverse FASTA/Q file for mapping" />
            </when>
            <when value="paired_collection">
                <expand macro="paired_reads"/>
            </when>
            <when value="interleaved">
                <param argument="--interleaved" type="data" format="@INPUT_FORMATS@" label="Interleaved FASTA/Q files for mapping" />
            </when>
        </conditional>

            #set $fn = "fw/" + $id
            #silent $fw_fp.append( $fn )
ln -s '$reads.paired_reads.forward' '$fn' &&
            #set $fn = "rv/" + $id
            #silent $rv_fp.append( $fn )
ln -s '$mreads.paired_reads.reverse' '${fn}' &&
        #else if $reads.type == 'interleaved'
            #set $fn = "interl/" + re.sub('[^\s\w\-\\.]', '_', str($reads.interleaved.element_identifier))
            #silent $interl_fp.append( $fn )
ln -s '$reads.interleaved' '$fn' &&
        #end if

            <when value="paired">
                <param argument="-1" name="read1" type="data" format="@INPUT_FORMATS@" multiple="true" label="Forward FASTA/Q file(s) for mapping" />
                <param argument="-2" name="read2" type="data" format="@INPUT_FORMATS@" multiple="true" label="Reverse FASTA/Q file(s) for mapping" />
            </when>
            <when value="paired_collection">
                <expand macro="paired_reads"/>
            </when>
            <when value="interleaved">
                <param argument="--interleaved" type="data" format="@INPUT_FORMATS@" multiple="true" label="Interleaved FASTA/Q files(s) for mapping" />
            </when>
        </conditional>

4:0ff4b0e5a3bc

<macros>
    <token name="@TOOL_VERSION@">0.6.1</token>
    <token name="@VERSION_SUFFIX@">2</token>
    <token name="@PROFILE@">22.01</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">coverm</requirement>
        </requirements>

            <option value="paired">Paired end</option>
            <option value="paired_collection" selected="true">Paired collection</option>
            <option value="interleaved">Interleaved</option>
        </param>
    </xml>
    <xml name="individual_assembly_reads">
        <conditional name="read_type">
            <expand macro="read_type"/>
            <when value="single">
                <param argument="--single" type="data" format="@INPUT_FORMATS@" label="Single Read" />

            <when value="paired">
                <param argument="-1" name="read1" type="data" format="@INPUT_FORMATS@" label="Forward FASTA/Q file for mapping" />
                <param argument="-2" name="read2" type="data" format="@INPUT_FORMATS@" label="Reverse FASTA/Q file for mapping" />
            </when>
            <when value="paired_collection">
                <param name="paired_reads" type="data_collection" collection_type="paired" format="@INPUT_FORMATS@" label="Collection of paired-end FASTA/Q files(s) for mapping" help="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order." />
            </when>
            <when value="interleaved">
                <param argument="--interleaved" type="data" format="@INPUT_FORMATS@" label="Interleaved FASTA/Q files for mapping" />
            </when>
        </conditional>

            #set $fn = "fw/" + $id
            #silent $fw_fp.append( $fn )
ln -s '$reads.paired_reads.forward' '$fn' &&
            #set $fn = "rv/" + $id
            #silent $rv_fp.append( $fn )
ln -s '$reads.paired_reads.reverse' '$fn' &&
        #else if $reads.type == 'interleaved'
            #set $fn = "interl/" + re.sub('[^\s\w\-\\.]', '_', str($reads.interleaved.element_identifier))
            #silent $interl_fp.append( $fn )
ln -s '$reads.interleaved' '$fn' &&
        #end if

            <when value="paired">
                <param argument="-1" name="read1" type="data" format="@INPUT_FORMATS@" multiple="true" label="Forward FASTA/Q file(s) for mapping" />
                <param argument="-2" name="read2" type="data" format="@INPUT_FORMATS@" multiple="true" label="Reverse FASTA/Q file(s) for mapping" />
            </when>
            <when value="paired_collection">
                <param name="paired_reads" type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" label="Collection of paired-end FASTA/Q files(s) for mapping" help="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order." />
            </when>
            <when value="interleaved">
                <param argument="--interleaved" type="data" format="@INPUT_FORMATS@" multiple="true" label="Interleaved FASTA/Q files(s) for mapping" />
            </when>
        </conditional>