comparison macros.xml @ 11:e661a3269313 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042

10:e4c01dcece8b

<macros>
    <token name="@VERSION@">1.5.1</token>
    <token name="@GALAXY_VERSION@">galaxy0</token>
    <token name="@IDX_VERSION@">q7</token>
    <token name="@PROFILE_VERSION@">20.01</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">salmon</requirement>
            <requirement type="package" version="1.3">seqtk</requirement>
            <requirement type="package" version="1.12">samtools</requirement>
            <requirement type="package" version="0.2.0">vpolo</requirement>
            <requirement type="package" version="1.3.0">pandas</requirement>
            <requirement type="package" version="1.7.0">scipy</requirement>
        </requirements>
    </xml>
    <xml name="orient">
        <param name="orientation" type="select" label="Relative orientation of reads within a pair">
            <option value="M">Mates are oriented in the same direction (M = matching)</option>

                    </options>
                </param>
            </when>  <!-- build-in -->
            <when value="history">
                <section name="s_index" title="Salmon index" expanded="true">
                    <param name="fasta" type="data" format="fasta" label="Transcripts fasta file"/>
                    <param name="kmer" type="integer" value="31" label="Kmer length"/>
                    <param name="phash" type="boolean" label="Perfect Hash" truevalue="--perfectHash" falsevalue="" checked="false"
                        help="Build the index using a perfect hash rather than a dense hash.  This will require less memory (especially during quantification), but will take longer to construct"/>
                </section>
            </when>
        </conditional>
    </xml>
    <xml name="reads">

        label="Consensus Slack"
        help="The amount of slack allowed in the quasi-mapping consensus mechanism.  Normally, a transcript must cover all hits to be considered for mapping. If this is set to a value, X, greater than 0, then a transcript can fail to cover up to X hits before it is discounted as a mapping candidate.  The default value of this option is 1 if --validateMappings is given and 0 otherwise."/>
        <param name="dovetail" label="Allow Dovetail" type="boolean" truevalue="--allowDovetail" falsevalue="" checked="False" help="Allow dovetail mappings"/>
        <param name="recoverOrphans" label="Recover Orphans" type="boolean" truevalue="--recoverOrphans" falsevalue="" checked="False"
        help="Attempt to recover the mates of orphaned reads. This uses edlib for orphan recovery, and so introduces some computational overhead, but it can improve sensitivity."/>
        <param name="writeMappings" type="boolean" truevalue="--writeMappings=./output/samout.sam" falsevalue="" checked="False"
        label="Write Mappings to Bam File"
        help="If this option is provided, then the quasi-mapping results will be written out in SAM-compatible format.  By default, output will be directed to stdout, but an alternative file name can be provided instead"/>
        <param name="consistentHits" type="boolean" truevalue="--consistentHits" falsevalue="" checked="False"
        label="Consistent Hits"
        help="Force hits gathered during quasi-mapping to be 'consistent' (i.e. co-linear and approximately the right distance apart)."/>
        <param name="quasiCoverage" type="integer" optional="True" label="Quasi Coverage"
        help="[Experimental]: The fraction of the read that must be covered by MMPs (of length >= 31) if this read is to be considered as 'mapped'. This may help to avoid 'spurious' mappings. A value of 0 (the default) denotes no coverage threshold (a single 31-mer can yield a mapping). Since coverage by exact matching, large, MMPs is a rather strict condition, this value should likely be set to something low, if used."/>

    <token name="@bam_sort@"><![CDATA[samtools sort -@ \${GALAXY_SLOTS} --output-fmt=BAM -o ./output/bamout.bam]]></token>
    <token name="@indexing@"><![CDATA[
        mkdir ./index &&
        mkdir ./output &&
        #if $quant_type.refTranscriptSource.TranscriptSource != "indexed":
            salmon index -i ./index
                --kmerLen '${quant_type.refTranscriptSource.s_index.kmer}'
                --gencode
                --transcripts '${quant_type.refTranscriptSource.s_index.fasta}'
            &&
            #set $index_path = './index'
        #else
            #set $index_path = $quant_type.refTranscriptSource.index.fields.path
        #end if

            #if $quant_type.consensusSlack:
                --consensusSlack '${quant_type.consensusSlack}'
            #end if
            ${quant_type.dovetail}
            ${quant_type.recoverOrphans}
            ${quant_type.writeMappings}
            ${quant_type.consistentHits}
            #if $quant_type.quasiCoverage:
                --quasiCoverage '${quant_type.quasiCoverage}'
            #end if
        ]]>

11:e661a3269313

<macros>
    <token name="@TOOL_VERSION@">1.9.0</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <token name="@IDX_VERSION@">q7</token>
    <token name="@PROFILE_VERSION@">20.01</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">salmon</requirement>
            <requirement type="package" version="1.3">seqtk</requirement>
            <requirement type="package" version="1.16.1">samtools</requirement>
            <requirement type="package" version="0.2.0">vpolo</requirement>
            <requirement type="package" version="1.5.2">pandas</requirement>
            <requirement type="package" version="3.0.0">graphviz</requirement>
            <requirement type="package" version="1.9.3">scipy</requirement>
        </requirements>
    </xml>
    <xml name="orient">
        <param name="orientation" type="select" label="Relative orientation of reads within a pair">
            <option value="M">Mates are oriented in the same direction (M = matching)</option>

                    </options>
                </param>
            </when>  <!-- build-in -->
            <when value="history">
                <section name="s_index" title="Salmon index" expanded="true">
                    <param name="fasta" type="data" format="fasta" label="Transcripts FASTA file"/>
                    <param name="genome" type="data" format="fasta" optional="true" label="Reference genome" 
                        help="The reference genome is required for generating a decoy-away index. The decoy sequences are regions of the target genome 
                            that are sequence similar to annotated transcripts. These are the regions of the genome most likely to cause mismapping." />
                    <param name="kmer" type="integer" value="31" label="Kmer length"/>
                    <param name="phash" type="boolean" label="Perfect Hash" truevalue="--perfectHash" falsevalue="" checked="false"
                        help="Build the index using a perfect hash rather than a dense hash.  This will require less memory (especially during quantification), 
                            but will take longer to construct"/>
                </section>
            </when>
        </conditional>
    </xml>
    <xml name="reads">

        label="Consensus Slack"
        help="The amount of slack allowed in the quasi-mapping consensus mechanism.  Normally, a transcript must cover all hits to be considered for mapping. If this is set to a value, X, greater than 0, then a transcript can fail to cover up to X hits before it is discounted as a mapping candidate.  The default value of this option is 1 if --validateMappings is given and 0 otherwise."/>
        <param name="dovetail" label="Allow Dovetail" type="boolean" truevalue="--allowDovetail" falsevalue="" checked="False" help="Allow dovetail mappings"/>
        <param name="recoverOrphans" label="Recover Orphans" type="boolean" truevalue="--recoverOrphans" falsevalue="" checked="False"
        help="Attempt to recover the mates of orphaned reads. This uses edlib for orphan recovery, and so introduces some computational overhead, but it can improve sensitivity."/>
        <conditional name="bam_options">
            <param argument="--writeMappings" type="select" label="Write Mappings to BAM File" help="If this option is provided, then the quasi-mapping results will be written out in SAM-compatible format.  By default, output will be directed to stdout, but an alternative file name can be provided instead">
                <option value="--writeMappings=./output/samout.sam">Enabled</option>
                <option value="" selected="true">Disabled</option>
            </param>
            <when value="--writeMappings=./output/samout.sam">
                <param argument="--writeQualities" type="boolean" truevalue="--writeQualities" falsevalue="" checked="false" label="Write qualities" help="If this flag is 
                provided, then the output SAM file will contain quality strings as well as read sequences." />
            </when>
            <when value=""/>
        </conditional>
        <param name="writeMappings" type="boolean" truevalue="" falsevalue="" checked="False"
            label="Write Mappings to Bam File"
            help="If this option is provided, then the quasi-mapping results will be written out in SAM-compatible format.  By default, output will be directed to stdout, but an alternative file name can be provided instead"/>
        <param name="consistentHits" type="boolean" truevalue="--consistentHits" falsevalue="" checked="False"
        label="Consistent Hits"
        help="Force hits gathered during quasi-mapping to be 'consistent' (i.e. co-linear and approximately the right distance apart)."/>
        <param name="quasiCoverage" type="integer" optional="True" label="Quasi Coverage"
        help="[Experimental]: The fraction of the read that must be covered by MMPs (of length >= 31) if this read is to be considered as 'mapped'. This may help to avoid 'spurious' mappings. A value of 0 (the default) denotes no coverage threshold (a single 31-mer can yield a mapping). Since coverage by exact matching, large, MMPs is a rather strict condition, this value should likely be set to something low, if used."/>

    <token name="@bam_sort@"><![CDATA[samtools sort -@ \${GALAXY_SLOTS} --output-fmt=BAM -o ./output/bamout.bam]]></token>
    <token name="@indexing@"><![CDATA[
        mkdir ./index &&
        mkdir ./output &&
        #if $quant_type.refTranscriptSource.TranscriptSource != "indexed":
            #if $quant_type.refTranscriptSource.s_index.genome
                cat '${quant_type.refTranscriptSource.s_index.genome}' | grep "^>" | cut -d " " -f 1 > 'decoys.txt' &&
                sed -i.bak -e 's/>//g' 'decoys.txt' &&
                cat '${quant_type.refTranscriptSource.s_index.fasta}' '${quant_type.refTranscriptSource.s_index.genome}' > 'input_index.fasta' &&
            #else
                ln -s '${quant_type.refTranscriptSource.s_index.fasta}' 'input_index.fasta' &&
            #end if
            salmon index -i ./index
                --kmerLen '${quant_type.refTranscriptSource.s_index.kmer}'
                --gencode
                --threads "\${GALAXY_SLOTS:-4}"
                --transcripts 'input_index.fasta'
                #if $quant_type.refTranscriptSource.s_index.genome
                    --decoy 'decoys.txt'
                #end if
            &&
            #set $index_path = './index'
        #else
            #set $index_path = $quant_type.refTranscriptSource.index.fields.path
        #end if

            #if $quant_type.consensusSlack:
                --consensusSlack '${quant_type.consensusSlack}'
            #end if
            ${quant_type.dovetail}
            ${quant_type.recoverOrphans}
            ${quant_type.bam_options.writeMappings}
            #if $quant_type.bam_options.writeMappings:
                ${quant_type.bam_options.writeQualities}
            #end if
            ${quant_type.consistentHits}
            #if $quant_type.quasiCoverage:
                --quasiCoverage '${quant_type.quasiCoverage}'
            #end if
        ]]>