comparison macros.xml @ 13:9ee34ba73ebf draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266

12:79b885ce78d7

<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@">2.7.8a</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
    or by looking for the versionGenome parameter in source/parametersDefault
    of STAR's source code -->
    <token name="@IDX_VERSION@">2.7.4a</token>
    <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token>

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

    <xml name="edam">

            <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@">
                <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" />
                <filter type="static_value" column="5" value="@IDX_VERSION@" />

    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/bioinformatics/bts635</citation>
        </citations>
    </xml>
    <xml name="@SJDBOPTIONS@" token_optional="true">
         <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="@OPTIONAL@" help="Exon junction information for mapping splices"/>
         <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/>
    </xml>
    <xml name="dbKeyActions">
        <actions>
            <conditional name="refGenomeSource.geneSource">

        </actions>
    </xml>
    <token name="@TEMPINDEX@"><![CDATA[
    ## Create temporary index for custom reference
    #if str($refGenomeSource.geneSource) == 'history':
        mkdir -p tempstargenomedir &&
        STAR
            --runMode genomeGenerate
            --genomeDir 'tempstargenomedir'
            --genomeFastaFiles '${refGenomeSource.genomeFastaFiles}'
            ## Handle difference between indices with/without annotations
            #if 'GTFconditional' in $refGenomeSource:
                ## GTFconditional exists only in STAR, but not STARsolo
                #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
                    --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}'

            #end if
            #if str($refGenomeSource.genomeSAindexNbases):
                --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases}
            #end if
            --runThreadN \${GALAXY_SLOTS:-4}
        &&
    #end if
    ]]></token>
    <token name="@REFGENOMEHANDLING@" ><![CDATA[
    --runThreadN \${GALAXY_SLOTS:-4}

    #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
                #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.

    --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" />
          <param argument="--genomeSAindexNbases" type="integer" min="2" max="16" value="14" label="Length of the SA pre-indexing string" help="Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, the parameter --genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1)"/>
    </xml>
    <xml name="stdio" >
        <stdio>
            <regex match="FATAL error" source="both" level="fatal"/>

            <option value="Hamming" selected="true" >Adapter clipping based on Hamming distance</option>
            <option value="CellRanger4" >5p and 3p adapter clipping similar to CellRanger4</option>
            <option value="None" >No adapter clipping</option>
        </param>
    </xml>
</macros>

13:9ee34ba73ebf

<macros>
    <!-- REMEMBER to bump the version of @IDX_VERSION_SUFFIX@
    whenever you make changes to the @TOOL_VERSION@ token!
    The data manager uses a symlink to this macro file to keep the STAR and
    the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ -->
    <!-- STAR version to be used -->
    <token name="@TOOL_VERSION@">2.7.10b</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">21.01</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
    or by looking for the versionGenome parameter in source/parametersDefault
    of STAR's source code -->
    <token name="@IDX_VERSION@">2.7.4a</token>
    <token name="@IDX_VERSION_SUFFIX@">1</token>
    <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token>

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">star</requirement>
            <requirement type="package" version="1.16.1">samtools</requirement>
            <requirement type="package" version="1.12">gzip</requirement>
            <yield />
        </requirements>
    </xml>

    <xml name="edam">

            <edam_operation>operation_0292</edam_operation>
        </edam_operations>
    </xml>

    <xml name="index_selection" token_with_gene_model="0">
        <param argument="--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@">
                <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" />
                <filter type="static_value" column="5" value="@IDX_VERSION@" />

    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/bioinformatics/bts635</citation>
        </citations>
    </xml>
    <xml name="SJDBOPTIONS">
         <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="false" help="Exon junction information for mapping splices"/>
         <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/>
    </xml>
    <xml name="dbKeyActions">
        <actions>
            <conditional name="refGenomeSource.geneSource">

        </actions>
    </xml>
    <token name="@TEMPINDEX@"><![CDATA[
    ## Create temporary index for custom reference
    #if str($refGenomeSource.geneSource) == 'history':
        #if $refGenomeSource.genomeFastaFiles.ext == "fasta"
            ln -s '$refGenomeSource.genomeFastaFiles' refgenome.fa &&
        #else
            gunzip -c '$refGenomeSource.genomeFastaFiles' > refgenome.fa &&
        #end if
        mkdir -p tempstargenomedir &&
        STAR
            --runMode genomeGenerate
            --genomeDir 'tempstargenomedir'
            --genomeFastaFiles refgenome.fa
            ## Handle difference between indices with/without annotations
            #if 'GTFconditional' in $refGenomeSource:
                ## GTFconditional exists only in STAR, but not STARsolo
                #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
                    --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}'

            #end if
            #if str($refGenomeSource.genomeSAindexNbases):
                --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases}
            #end if
            --runThreadN \${GALAXY_SLOTS:-4}
            ## in bytes
            --limitGenomeGenerateRAM \$((\${GALAXY_MEMORY_MB:-31000} * 1000000))
        &&
    #end if
    ]]></token>
    <token name="@REFGENOMEHANDLING@" ><![CDATA[
    --runThreadN \${GALAXY_SLOTS:-4}

    #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-with-gtf':
            --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
            --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
            #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
                --sjdbGTFtagExonParentTranscript Parent
            #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.

    --soloCBmatchWLtype $sc.soloCBmatchWLtype
    #if $r1.is_of_type('fastq.gz', 'fastqsanger.gz'):
        @FASTQ_GZ_OPTION@
    #end if
    ]]></token>
    <token name="@LIMITS@" ><![CDATA[
        --limitOutSJoneRead $getVar('algo.params.junction_limits.limitOutSJoneRead', $getVar('solo.junction_limits.limitOutSJoneRead', 1000))
        --limitOutSJcollapsed $getVar('algo.params.junction_limits.limitOutSJcollapsed', $getVar('solo.junction_limits.limitOutSJcollapsed', 1000000))
        --limitSjdbInsertNsj $getVar('algo.params.junction_limits.limitSjdbInsertNsj', $getVar('solo.junction_limits.limitSjdbInsertNsj', 1000000))
    ]]></token>
    <xml name="ref_selection">
        <param argument="--genomeFastaFiles" type="data" format="fasta,fasta.gz" label="Select a reference genome" />
          <param argument="--genomeSAindexNbases" type="integer" min="2" max="16" value="14" label="Length of the SA pre-indexing string" help="Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, the parameter --genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1)"/>
    </xml>
    <xml name="stdio" >
        <stdio>
            <regex match="FATAL error" source="both" level="fatal"/>

            <option value="Hamming" selected="true" >Adapter clipping based on Hamming distance</option>
            <option value="CellRanger4" >5p and 3p adapter clipping similar to CellRanger4</option>
            <option value="None" >No adapter clipping</option>
        </param>
    </xml>
    <xml name="common_SAM_attributes">
        <option value="NH" selected="true">NH (number of reported alignments/hits for the read)</option>
        <option value="HI" selected="true">HI (query hit index)</option>
        <option value="AS" selected="true">AS (local alignment score)</option>
        <option value="nM" selected="true">nM (number of mismatches per (paired) alignment)</option>
        <option value="NM">NM (edit distance of the aligned read to the reference)</option>
        <option value="MD">MD (string for mismatching positions)</option>
        <option value="jM">jM (intron motifs for all junctions)</option>
        <option value="jI">jI (1-based start and end of introns for all junctions)</option>
    </xml>
    <xml name="limits">
        <section name="junction_limits" title="Junction Limits" expanded="false">
            <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)" />
            <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions" />
            <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly." />
        </section>
    </xml>
    <xml name="outCountActions">
        <actions>
            <action name="column_names" type="metadata" default="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" />
        </actions>
    </xml>
    <xml name="outWig">
        <conditional name="outWig">
            <param name="outWigType" type="select" label="Compute coverage">
                <option value="None">No coverage</option>
                <option value="bedGraph">Yes in bedgraph format</option>
                <option value="wiggle">Yes in wiggle format</option>
            </param>
            <when value="None">
                <!-- This is necessary for the filtering of output -->
                <param name="outWigStrand" type="hidden" value="false" />
            </when>
            <when value="bedGraph">
                <expand macro="outWigParams"/>
            </when>
            <when value="wiggle">
                <expand macro="outWigParams"/>
            </when>
        </conditional>
    </xml>
    <xml name="outWigParams">
        <param name="outWigTypeSecondWord" type="select" label="Input for coverage">
            <option value="">Default (everything that mapped)</option>
            <option value="read_5p">signal from only 5’ of the 1st read</option>
            <option value="read2">signal from only 2nd read</option>
        </param>
        <param argument="--outWigStrand" type="boolean" truevalue="Stranded" falsevalue="Unstranded" checked="true" label="collapse strands (unstranded coverage)" help="By default, the strands are separated."/>
        <param argument="--outWigReferencesPrefix" type="text" value="-" label="prefix matching reference name" help="For example, set 'chr' if you mapped on an ensembl genome but you want to display on UCSC"/>
        <param argument="--outWigNorm" type="boolean" truevalue="RPM" falsevalue="None" checked="true" label="Normalize coverage to million of mapped reads (RPM)"/>
    </xml>
    <token name="@OUTWIG@"><![CDATA[
        #if str($outWig.outWigType) != 'None':
            --outWigType '$outWig.outWigType' '$outWig.outWigTypeSecondWord'
            --outWigStrand '$outWig.outWigStrand'
            --outWigReferencesPrefix '$outWig.outWigReferencesPrefix'
            --outWigNorm '$outWig.outWigNorm'
        #end if
    ]]></token>
    <token name="@OUTWIGOUTPUTS@"><![CDATA[
        #if str($outWig.outWigType) == "bedGraph":
            && mv Signal.Unique.str1.out.bg Signal.Unique.str1.out
            && mv Signal.UniqueMultiple.str1.out.bg Signal.UniqueMultiple.str1.out
            #if str($outWig.outWigStrand) == "Stranded":
                && mv Signal.Unique.str2.out.bg Signal.Unique.str2.out
                && mv Signal.UniqueMultiple.str2.out.bg Signal.UniqueMultiple.str2.out
            #end if
        #elif str($outWig.outWigType) == "wiggle":
            && mv Signal.Unique.str1.out.wig Signal.Unique.str1.out
            && mv Signal.UniqueMultiple.str1.out.wig Signal.UniqueMultiple.str1.out
            #if str($outWig.outWigStrand) == "Stranded":
                && mv Signal.Unique.str2.out.wig Signal.Unique.str2.out
                && mv Signal.UniqueMultiple.str2.out.wig Signal.UniqueMultiple.str2.out
            #end if
        #end if
    ]]></token>
    <xml name="outWigOutputs">
        <data format="bedgraph" name="signal_unique_str1" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 1" from_work_dir="Signal.Unique.str1.out">
            <filter>outWig['outWigType'] != "None"</filter>
            <expand macro="dbKeyActions" />
            <change_format>
                <when input="outWig.outWigType" value="wiggle" format="wig" />
            </change_format>
        </data>
        <data format="bedgraph" name="signal_uniquemultiple_str1" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 1" from_work_dir="Signal.UniqueMultiple.str1.out">
            <filter>outWig['outWigType'] != "None"</filter>
            <expand macro="dbKeyActions" />
            <change_format>
                <when input="outWig.outWigType" value="wiggle" format="wig" />
            </change_format>
        </data>
        <data format="bedgraph" name="signal_unique_str2" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 2" from_work_dir="Signal.Unique.str2.out">
            <filter>outWig['outWigType'] != "None" and outWig['outWigStrand']</filter>
            <expand macro="dbKeyActions" />
            <change_format>
                <when input="outWig.outWigType" value="wiggle" format="wig" />
            </change_format>
        </data>
        <data format="bedgraph" name="signal_uniquemultiple_str2" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 2" from_work_dir="Signal.UniqueMultiple.str2.out">
            <filter>outWig['outWigType'] != "None" and outWig['outWigStrand']</filter>
            <expand macro="dbKeyActions" />
            <change_format>
                <when input="outWig.outWigType" value="wiggle" format="wig" />
            </change_format>
        </data>
    </xml>
    <xml name="quantMode">
        <conditional name="quantmode_output">
            <param argument="--quantMode" type="select"
            label="Per gene/transcript output"
            help="STAR can provide analysis results not only with respect to the reference genome, but also with respect to genes and transcripts described by a gene model. Note: This functionality requires either the selection above of a cached index with a gene model, or a gene model provided alongside the index/reference genome in GTF or GFF3 format!">
                <option value="-">No per gene or transcript output</option>
                <option value="GeneCounts">Per gene read counts (GeneCounts)</option>
                <option value="TranscriptomeSAM">Transcript-based BAM output (TranscriptomeSAM)</option>
                <option value="TranscriptomeSAM GeneCounts">Both per gene read counts and transcript-based BAM output (TranscriptomeSAM GeneCounts)</option>
            </param>
            <when value="-" />
            <when value="GeneCounts" />
            <when value="TranscriptomeSAM">
                <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend"
                label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?"
                help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled." />
            </when>
            <when value="TranscriptomeSAM GeneCounts">
                <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend"
                label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?"
                help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled." />
            </when>
        </conditional>
    </xml>
    <xml name="quantModeNoGTF">
        <conditional name="quantmode_output">
            <param argument="--quantMode" type="select"
            label="Per gene/transcript output">
                <option value="-">No per gene or transcript output as no GTF was provided</option>
            </param>
            <when value="-" />
        </conditional>
    </xml>
</macros>