comparison macros.xml @ 1:2b62154e39c8 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit 600a9e3c1d884e5cf106e4477c7b8223ef105cdb"

0:630e2929a131

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">1.0.11</token>
    <token name="@VERSION_SUFFIX@">0</token>    
    <token name="@PROFILE@">20.01</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">jasminesv</requirement>
        </requirements>

    <!--
        Command
    -->
    <token name="@REF_FASTA@"><![CDATA[
        #if $dup_to_ins.reference_source.reference_source_selector == 'history':
            ln -f -s '$dup_to_ins.reference_source.ref_file' reference.fa &&
        #else:
            ln -f -s '$dup_to_ins.reference_source.ref_file.fields.path' reference.fa &&
        #end if
    ]]></token>

    <xml name="reference">
        <conditional name="reference_source">

                    </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_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference"/>
            </when>
        </conditional>
    </xml>
    <!--
        Help

]]></token>
    <token name="@REFERENCES@"><![CDATA[
More information is available in the `github <https://github.com/mkirsche/Jasmine>`_.
    ]]></token>
</macros>

1:2b62154e39c8

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">1.0.11</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <token name="@PROFILE@">20.01</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">jasminesv</requirement>
        </requirements>

    <!--
        Command
    -->
    <token name="@REF_FASTA@"><![CDATA[
        #if $dup_to_ins.reference_source.reference_source_selector == 'history':
            #set reference = $dup_to_ins.reference_source.ref_file
            #set ext = $reference.ext
        #else:
            #set reference = $dup_to_ins.reference_source.ref_file.fields.path
            #set ext = $dup_to_ins.reference_source.ref_file.fields.path
        #end if
        #if $ext.endswith(".gz"):
            gunzip -c '$reference' > reference &&
        #else:
            ln -sf '$reference' reference &&
        #end if
    ]]></token>

    <xml name="reference">
        <conditional name="reference_source">

                    </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_file" type="data" format="fasta,fasta.gz,fastq,fastq.gz" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference"/>
            </when>
        </conditional>
    </xml>
    <!--
        Help

]]></token>
    <token name="@REFERENCES@"><![CDATA[
More information is available in the `github <https://github.com/mkirsche/Jasmine>`_.
    ]]></token>
</macros>