comparison rg_rnaStar.xml @ 5:99b17b74a8cd draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 528ca3b14c2ca9b7ac18a0f9d80a5f4a235707bf

4:d681e989ac95

<tool id="rna_star" name="RNA STAR" version="2.5.2b-0" profile="17.01">
    <description>Gapped-read mapper for RNA-seq data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

                --chimScoreDropMax "$params.chim.chimScoreDropMax"
                --chimScoreSeparation "$params.chim.chimScoreSeparation"
                --chimScoreJunctionNonGTAG "$params.chim.chimScoreJunctionNonGTAG"
                --chimJunctionOverhangMin "$params.chim.chimJunctionOverhangMin"
            #end if
        #end if

    ## Convert chimeric reads.
    #if str($params.settingsType) == "star_fusion" or ( str($params.settingsType) == "full" and str($params.chim.chim_select) == "yes" and int($params.chim.chimSegmentMin) > 0 ):
        &&

          <when value="no"/>
        </conditional>

        <!-- Other parameter settings. -->
        <conditional name="params">
            <param name="settingsType" type="select" label="Other parameters (seed, alignment, and chimeric alignment)">
                <option value="default" selected="true">Use Defaults</option>
                <option value="star_fusion">Use parameters suggested for STAR-Fusion</option>
                <option value="full">Extended parameter list</option>
            </param>
            <when value="default"/>

                    <param argument="--alignWindowsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of windows per read"/>
                    <param argument="--alignTranscriptsPerWindowNmax" type="integer" min="1" value="100" label="Maximum number of transcripts per window"/>
                    <param argument="--alignTranscriptsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of different alignments per read to consider"/>
                    <param argument="--alignEndsType" type="boolean" truevalue="EndToEnd" falsevalue="Local" checked="false" label="Use end-to-end read alignments, with no soft-clipping?"/>
                </section>
    
                <conditional name="chim">
                    <param name="chim_select" type="select" label="Would you like to set chimeric alignment parameters?">
                        <option value="no" selected="true">No</option>
                        <option value="yes">Yes</option>

5:99b17b74a8cd

<tool id="rna_star" name="RNA STAR" version="2.5.2b-1" profile="17.01">
    <description>Gapped-read mapper for RNA-seq data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

                --chimScoreDropMax "$params.chim.chimScoreDropMax"
                --chimScoreSeparation "$params.chim.chimScoreSeparation"
                --chimScoreJunctionNonGTAG "$params.chim.chimScoreJunctionNonGTAG"
                --chimJunctionOverhangMin "$params.chim.chimJunctionOverhangMin"
            #end if

            ## Limits
            --limitBAMsortRAM "$params.limits.limitBAMsortRAM"
            --limitOutSJoneRead "$params.limits.limitOutSJoneRead"
            --limitOutSJcollapsed "$params.limits.limitOutSJcollapsed"
            --limitSjdbInsertNsj "$params.limits.limitSjdbInsertNsj"

        #end if

    ## Convert chimeric reads.
    #if str($params.settingsType) == "star_fusion" or ( str($params.settingsType) == "full" and str($params.chim.chim_select) == "yes" and int($params.chim.chimSegmentMin) > 0 ):
        &&

          <when value="no"/>
        </conditional>

        <!-- Other parameter settings. -->
        <conditional name="params">
            <param name="settingsType" type="select" label="Other parameters (seed, alignment, limits and chimeric alignment)">
                <option value="default" selected="true">Use Defaults</option>
                <option value="star_fusion">Use parameters suggested for STAR-Fusion</option>
                <option value="full">Extended parameter list</option>
            </param>
            <when value="default"/>

                    <param argument="--alignWindowsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of windows per read"/>
                    <param argument="--alignTranscriptsPerWindowNmax" type="integer" min="1" value="100" label="Maximum number of transcripts per window"/>
                    <param argument="--alignTranscriptsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of different alignments per read to consider"/>
                    <param argument="--alignEndsType" type="boolean" truevalue="EndToEnd" falsevalue="Local" checked="false" label="Use end-to-end read alignments, with no soft-clipping?"/>
                </section>

                <section name="limits" title="Limits" expanded="False">
                    <param argument="--limitBAMsortRAM" type="integer" min="0" value="0" label="Maximum available RAM (in bytes) for sorting" help="If 0, this will be set to the genome index size. This is typically only changed in cases where an error is produced." />
	            <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>
    
                <conditional name="chim">
                    <param name="chim_select" type="select" label="Would you like to set chimeric alignment parameters?">
                        <option value="no" selected="true">No</option>
                        <option value="yes">Yes</option>