comparison macros.xml @ 17:7ed2edc1337f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"

16:e132e7d02a3e

    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@">2.7.6a</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

        </edam_topics>
        <edam_operations>
            <edam_operation>operation_0292</edam_operation>
        </edam_operations>
    </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="@IDX_DATA_TABLE@">

                #end if
            #end if
        #end if
        #end if
        ]]></token>
    <xml name="ref_selection">
        <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />
        <!-- Currently, this parameter is not exposed in the wrapper,
             but used only in the tests to avoid excessive index sizes for
             the tiny test genomes. -->

            <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>
</macros>

17:7ed2edc1337f

    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@">2.7.7a</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

        </edam_topics>
        <edam_operations>
            <edam_operation>operation_0292</edam_operation>
        </edam_operations>
    </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="@IDX_DATA_TABLE@">

                #end if
            #end if
        #end if
        #end if
        ]]></token>
    <token name="@READSHANDLING@" ><![CDATA[
    ## Check that the input pairs are of the same type
    ## otherwise STARsolo will run for a long time and then error out.
    ## We consume either repeats of two inputs R1 + R2
    ## or a collection of paired reads.
    #if str($sc.input_types.use) == "repeat":
        #set $reads1 = []
        #set $reads2 = []
        #for $r1, $r2 in zip($sc.input_types.input1, $sc.input_types.input2):
            #assert $r1.datatype == $r2.datatype
            #silent $reads1.append(str($r1))
            #silent $reads2.append(str($r2))
        #end for
        #set $reads1 = ','.join($reads1)
        #set $reads2 = ','.join($reads2)
    #elif str($sc.input_types.use) == "list_paired":
        #set $r1 = $sc.input_types.input_collection.forward
        #set $r2 = $sc.input_types.input_collection.reverse
        #set $reads1 = $r1
        #set $reads2 = $r2
    #end if
    ## cDNA sequence(s) [R2] always go first, then barcode(s) [R1]
    ## see: Section 3.2 of STAR manual for multiple inputs, and Section 13 for STARsolo inputs
    --readFilesIn $reads2 $reads1
    --soloCBmatchWLtype $sc.soloCBmatchWLtype
    #if $r1.is_of_type('fastq.gz', 'fastqsanger.gz'):
        @FASTQ_GZ_OPTION@
    #end if
    ]]></token>
    <xml name="ref_selection">
        <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />
        <!-- Currently, this parameter is not exposed in the wrapper,
             but used only in the tests to avoid excessive index sizes for
             the tiny test genomes. -->

            <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="input_selection">
        <conditional name="input_types" >
            <param name="use" type="select" label="Input Type" >
                <option value="repeat" >Separate barcode and cDNA reads</option>
                <option value="list_paired" >Paired collection of barcode and cDNA reads</option>
            </param>
            <when value="repeat">
                <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data"  multiple="true"
                label="RNA-Seq FASTQ/FASTA file, Barcode reads" />
                <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data"  multiple="true"
                label="RNA-Seq FASTQ/FASTA file, cDNA reads"/>
            </when>
            <when value="list_paired">
                <param name="input_collection" collection_type="paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="Collection of Pairs" />
            </when>
        </conditional>
    </xml>
    <xml name="input_selection_smart_seq">
        <conditional name="input_types_smart_seq" >
            <param name="use" type="select" label="Input Type" >
                <option value="list_single_end" >Single-end FASTQ collection</option>
                <option value="list_paired_end" >Paired FASTQ collection</option>
            </param>
            <when value="list_single_end">
                <param name="single_end_collection" collection_type="list" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of single-end FASTQ files" />
            </when>
            <when value="list_paired_end">
                <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of paired-end FASTQ files" />
            </when>
        </conditional>
    </xml>
    <xml name="umidedup_options">
        <option value="1MM_All" selected="true">All</option>
        <option value="1MM_Directional" >Directional</option>
    </xml>
    <xml name="anchor_types">
        <option value="0">Read start</option>
        <option value="1">Read end</option>
        <option value="2">Adapter start</option>
        <option value="3">Adapter end</option>
    </xml>
    <xml name="cb_match_wl_common">
        <option value="Exact" >Exact</option>
        <option value="1MM" >Single match</option>
    </xml>
    <xml name="cb_match_wl_cellranger">
        <option value="1MM_multi" selected="true" >Multiple matches (CellRanger 2)</option>
        <option value="1MM_multi_pseudocounts" >Multiple matches (CellRanger 3)</option>
    </xml>
</macros>