comparison macros.xml @ 2:223e7778451a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty

1:a46f1e803437

<?xml version="1.0"?>
<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@WRAPPER_VERSION@">stacks</requirement>
            <yield/>
        </requirements>
    </xml>

    <token name="@WRAPPER_VERSION@">2.2</token>

    <xml name="stdio">
        <stdio>
            <exit_code range="1:" level="fatal" description="Error in Stacks execution" />
        </stdio>

    ln -s '$sample' '${data_path}' &&
    ]]></token>

    <!-- macro and token for BAM input-->
    <xml name="bam_input_macro">
        <conditional name="input_type">
            <param name="input_type_selector" type="select" label="BAM files">
                <option value="list">data set list</option>
                <option value="manual">data sets</option>
            </param>
            <when value="manual">
                <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="BAM files" />
            </when>
            <when value="list">
                <param name="input_bam" format="bam" type="data_collection" collection_type="list" label="BAM files" />
            </when>
        </conditional>
    </xml>
    <token name="@BAM_INPUT@"><![CDATA[
    #set $bamlist = ""
    #for $bam in $input_type.input_bam:
        #set $filename = $clean_ext($bam.element_identifier)+".bam"
        #if re.search('.*\.bam$', $filename)
            ln -s '$bam' bam_inputs/$filename &&
            #set bamlist += " -B 'bam_inputs/"+$filename+"'"
        #end if

2:223e7778451a

<?xml version="1.0"?>
<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@STACKS_VERSION@">stacks</requirement>
            <yield/>
        </requirements>
    </xml>

    <token name="@STACKS_VERSION@">2.2</token>
    <token name="@WRAPPER_VERSION@">1</token>

    <xml name="stdio">
        <stdio>
            <exit_code range="1:" level="fatal" description="Error in Stacks execution" />
        </stdio>

    ln -s '$sample' '${data_path}' &&
    ]]></token>

    <!-- macro and token for BAM input-->
    <xml name="bam_input_macro">
        <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="BAM files" />
    </xml>
    <token name="@BAM_INPUT@"><![CDATA[
    #set $bamlist = ""
    #for $bam in $input_bam:
        #set $filename = $clean_ext($bam.element_identifier)+".bam"
        #if re.search('.*\.bam$', $filename)
            ln -s '$bam' bam_inputs/$filename &&
            #set bamlist += " -B 'bam_inputs/"+$filename+"'"
        #end if