comparison rg_rnaStar.xml @ 6:2055c2667eb3 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 427913231c5894bde2b2ed428da2b8aee30bc311

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"/>

            --chimSegmentMin 12
            --chimJunctionOverhangMin 12
            --alignSJDBoverhangMin 10
            --alignMatesGapMax 200000
            --alignIntronMax 200000

            ## --twopass1readsN 100000000  
            ## --chimSegmentReadGapMax 3              ## not an option in STAR 2.4.0
            ## --alignSJstitchMismatchNmax 5 -1 5 5   ## not an option in STAR 2.4.0

        #elif str( $params.settingsType ) == "full":
            ## Extended parameter options

            --alignSplicedMateMapLminOverLmate "$params.align.alignSplicedMateMapLminOverLmate"
            --alignWindowsPerReadNmax "$params.align.alignWindowsPerReadNmax"
            --alignTranscriptsPerWindowNmax "$params.align.alignTranscriptsPerWindowNmax"
            --alignTranscriptsPerReadNmax "$params.align.alignTranscriptsPerReadNmax"
            --alignEndsType $params.align.alignEndsType

            ## Chimeric alignment parameter options
            #if str( $params.chim.chim_select ) == "yes":
                --chimSegmentMin "$params.chim.chimSegmentMin"
                --chimScoreMin "$params.chim.chimScoreMin"

                    <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>

**STAR-Fusion**

STAR-Fusion_ is used to identify candidate fusion transcripts. The recommended_ parameters for running
STAR prior to STAR-Fusion can be pre-selected, with the following exceptions::

  --twopassMode Basic                   # not an option in STAR 2.4.0
  --chimSegmentReadGapMax 3             # not an option in STAR 2.4.0
  --alignSJstitchMismatchNmax 5 -1 5 5  # not an option in STAR 2.4.0

**Attributions**

6:2055c2667eb3

<tool id="rna_star" name="RNA STAR" version="2.5.2b-2" profile="17.01">
    <description>Gapped-read mapper for RNA-seq data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

            --chimSegmentMin 12
            --chimJunctionOverhangMin 12
            --alignSJDBoverhangMin 10
            --alignMatesGapMax 200000
            --alignIntronMax 200000
            --twopassMode Basic
            --twopass1readsN -1

            ## --chimSegmentReadGapMax 3              ## not an option in STAR 2.4.0
            ## --alignSJstitchMismatchNmax 5 -1 5 5   ## not an option in STAR 2.4.0

        #elif str( $params.settingsType ) == "full":
            ## Extended parameter options

            --alignSplicedMateMapLminOverLmate "$params.align.alignSplicedMateMapLminOverLmate"
            --alignWindowsPerReadNmax "$params.align.alignWindowsPerReadNmax"
            --alignTranscriptsPerWindowNmax "$params.align.alignTranscriptsPerWindowNmax"
            --alignTranscriptsPerReadNmax "$params.align.alignTranscriptsPerReadNmax"
            --alignEndsType $params.align.alignEndsType

            ## Two pass mode
            --twopassMode "$params.twopass.twopassMode"
            #if str( $params.twopass.twopassMode ) == "Basic":
                --twopass1readsN "$params.twopass.twopass1readsN"
            #end if

            ## Chimeric alignment parameter options
            #if str( $params.chim.chim_select ) == "yes":
                --chimSegmentMin "$params.chim.chimSegmentMin"
                --chimScoreMin "$params.chim.chimScoreMin"

                    <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="twopass" title="Two pass mode" expanded="False">
                    <param argument="--twopassMode" type="boolean" truevalue="Basic" falsevalue="None" checked="false" label="Use two pass mode to better map reads to unknown splice junctions"/>
                    <param argument="--twopass1readsN" type="integer" min="-1" value="-1" label="Number of reads to map in the first pass (-1: all)"/>
                </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>

**STAR-Fusion**

STAR-Fusion_ is used to identify candidate fusion transcripts. The recommended_ parameters for running
STAR prior to STAR-Fusion can be pre-selected, with the following exceptions::

  --chimSegmentReadGapMax 3             # not an option in STAR 2.4.0
  --alignSJstitchMismatchNmax 5 -1 5 5  # not an option in STAR 2.4.0

**Attributions**