comparison data_manager/macros.xml @ 6:64deddb6a8ec draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"

5:f5eb9afa8f8a

<macros>
    <!-- REMEMBER to bump the version of rna_star_index_builder_data_manager
    whenever you make changes to the following two version tokens!
    The data manager uses a symlink to this macro file to keep the versions in
    sync. -->
    <!-- STAR version to be used -->
    <token name="@VERSION@">2.7.2a</token>
    <!-- STAR index version compatible with this version of STAR
    This is the STAR version that introduced the index structure expected
    by the current version.
    It can be found for any specific version of STAR with:
    STAR -h | grep versionGenome

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">star</requirement>
            <requirement type="package" version="1.9">samtools</requirement>
        </requirements>
    </xml>

    <xml name="index_selection" token_with_gene_model="1">
        <param argument="--genomeDir" name="genomeDir" type="select"
        label="Select reference genome"
        help="If your genome of interest is not listed, contact the Galaxy team">
            <options from_data_table="rnastar_index2_versioned">
                <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" />

            #end if
            --runThreadN \${GALAXY_SLOTS:-4}
        &&
    #end if
    ]]></token>
    <token name="@REFGENOMEHANDLING" ><![CDATA[
    --runThreadN \${GALAXY_SLOTS:-4}
    --genomeLoad NoSharedMemory
    --genomeDir
    #if str($refGenomeSource.geneSource) == 'history':
        tempstargenomedir
    #else:
        '${refGenomeSource.GTFconditional.genomeDir.fields.path}'
        ## Handle difference between indices with/without annotations
        #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
            #if $refGenomeSource.GTFconditional.sjdbGTFfile:
                --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
                --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
                #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
                    --sjdbGTFtagExonParentTranscript Parent

        <stdio>
            <regex match="FATAL error" source="both" level="fatal"/>
            <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
            <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
            <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
        </stdio>
    </xml>
    <xml name="refgenomehandling" >
        <conditional name="refGenomeSource">
            <param name="geneSource" type="select" label="Custom or built-in reference genome" help="Built-ins were indexed using default options">

            <when value="indexed">
                <conditional name="GTFconditional">
                    <param name="GTFselect" type="select"
                           label="Reference genome with or without an annotation"
                           help="Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions.">
                        <option value="without-gtf">use genome reference with builtin gene-model</option>
                        <option value="with-gtf">use genome reference without builtin gene-model</option>
                    </param>
                    <when value="with-gtf">
                        <expand macro="index_selection" with_gene_model="0" />
                        <expand macro="@SJDBOPTIONS@" />
                    </when>
                    <when value="without-gtf">
                        <expand macro="index_selection" with_gene_model="1" />
                    </when>
                </conditional>
            </when>
            <when value="history">
                <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />

6:64deddb6a8ec

<macros>
    <!-- REMEMBER to bump the version of rna_star_index_builder_data_manager
    whenever you make changes to the following two version tokens!
    The data manager uses a symlink to this macro file to keep the STAR and
    the index versions in sync, but you should manually adjust the +galaxy
    version number. -->
    <!-- STAR version to be used -->
    <token name="@VERSION@">2.7.2b</token>
    <!-- STAR index version compatible with this version of STAR
    This is the STAR version that introduced the index structure expected
    by the current version.
    It can be found for any specific version of STAR with:
    STAR -h | grep versionGenome

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">star</requirement>
            <requirement type="package" version="1.9">samtools</requirement>
            <yield />
        </requirements>
    </xml>

    <xml name="index_selection" token_with_gene_model="0">
        <param argument="--genomeDir" name="genomeDir" type="select"
        label="Select reference genome"
        help="If your genome of interest is not listed, contact the Galaxy team">
            <options from_data_table="rnastar_index2_versioned">
                <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" />

            #end if
            --runThreadN \${GALAXY_SLOTS:-4}
        &&
    #end if
    ]]></token>
    <token name="@REFGENOMEHANDLING@" ><![CDATA[
    --runThreadN \${GALAXY_SLOTS:-4}
    --genomeLoad NoSharedMemory
    --genomeDir
    #if str($refGenomeSource.geneSource) == 'history':
        tempstargenomedir
    #else:
        '${refGenomeSource.GTFconditional.genomeDir.fields.path}'
        ## Handle difference between indices with/without annotations
        #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf':
            #if $refGenomeSource.GTFconditional.sjdbGTFfile:
                --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
                --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
                #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
                    --sjdbGTFtagExonParentTranscript Parent

        <stdio>
            <regex match="FATAL error" source="both" level="fatal"/>
            <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
            <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
            <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
            <yield />
        </stdio>
    </xml>
    <xml name="refgenomehandling" >
        <conditional name="refGenomeSource">
            <param name="geneSource" type="select" label="Custom or built-in reference genome" help="Built-ins were indexed using default options">

            <when value="indexed">
                <conditional name="GTFconditional">
                    <param name="GTFselect" type="select"
                           label="Reference genome with or without an annotation"
                           help="Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions.">
                        <option value="without-gtf" selected='true'>use genome reference without builtin gene-model</option>
                        <option value="with-gtf">use genome reference with builtin gene-model</option>
                    </param>
                    <when value="with-gtf">
                        <expand macro="index_selection" with_gene_model="1" />
                    </when>
                    <when value="without-gtf">
                        <expand macro="index_selection" with_gene_model="0" />
                        <expand macro="@SJDBOPTIONS@" />
                    </when>
                </conditional>
            </when>
            <when value="history">
                <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />