comparison rg_rnaStar.xml @ 35:e2dd4a5fad65 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar_240d commit 344140b8df53b8b7024618bb04594607a045c03a

34:99ea1fc51f4b

    <description>Gapped-read mapper for RNA-seq data</description>
    <requirements>
        <requirement type="package" version="2.4.0d">rnastar</requirement>
        <requirement type="package" version="0.1.19">samtools</requirement>
    </requirements>
    <command>
    ##
    ## Run STAR.
    ##
    #if str($refGenomeSource.genomeSource) == 'history':

    ## Can adjust this as appropriate for the system.
    --genomeLoad NoSharedMemory
    #if str($refGenomeSource.genomeSource) == 'history':
        --genomeDir "tempstargenomedir"
    #else
        --genomeDir "$refGenomeSource.index.fields.path" 
    #end if
    --readFilesIn $singlePaired.input1 
    #if str($singlePaired.sPaired) == "paired"
            $singlePaired.input2
    #end if
        --runThreadN 4
    #if str($params.settingsType) == "full":

    ##
    ## BAM conversion.
    ##

    ## Convert aligned reads.
    samtools view -Shb Aligned.out.sam | samtools sort - AlignedSorted 2>/dev/null 

    ## Convert chimeric reads.
    #if str($params.settingsType) == "full" and $params.chim_segment_min > 0:
        ; samtools view -Shb Chimeric.out.sam | samtools sort - ChimericSorted 2>/dev/null 
    #end if
    </command>

    <stdio>
        <regex match=".*" source="both" level="warning" description="Some stderr/stdout text"/>
    </stdio>

    <inputs>
        <param name="jobName" type="text" size="120" value="rna-star run" label="Job narrative (added to output names)" 
          help="Only letters, numbers and underscores (_) will be retained in this field">
           <sanitizer invalid_char="">
              <valid initial="string.letters,string.digits"><add value="_" /> </valid>
           </sanitizer>
        </param>

            </param>
            <when value="single">
                <param format="fastqsanger,fastq,fasta" name="input1" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33"/>
            </when>
            <when value="paired">
                <param format="fastqsanger,fastq,fasta" name="input1" type="data" label="RNA-Seq FASTQ file, forward reads" 
            help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
                <param format="fastqsanger,fastq,fasta" name="input2" type="data" label="RNA-Seq FASTQ file, reverse reads"
            help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
            </when>
        </conditional>

               </action>
             </when>
             </conditional>
          </actions>
       </data>
       <data format="bam" name="chimeric_reads" label="${jobName}_starmappedchim.bam" 
                    from_work_dir="ChimericSorted.bam">
         <filter>(params['settingsType'] == 'full' and params['chim_segment_min'] > 0)</filter>
          <actions>
             <conditional name="refGenomeSource.genomeSource">
             <when value="indexed">

               </action>
             </when>
             </conditional>
          </actions>
        </data>
        <data format="interval" name="splice_junctions" label="${jobName}_starsplicejunct.bed" 
                   from_work_dir="SJ.out.tab">
          <actions>
             <conditional name="refGenomeSource.genomeSource">
             <when value="indexed">
               <action type="metadata" name="dbkey">

               </action>
             </when>
             </conditional>
          </actions>
        </data>
        <data format="bam" name="mapped_reads" label="${jobName}_starmapped.bam" 
                    from_work_dir="AlignedSorted.bam">
          <actions>
             <conditional name="refGenomeSource.genomeSource">
             <when value="indexed">
               <action type="metadata" name="dbkey">

--outFilterIntronMotifs RemoveNoncanonicalUnannotated
filter out alignments that contain non-canonical unannotated junctions
when using annotated splice junctions database. The annotated non-
canonical junctions will be kept.
 
    
**Attributions**

Note that each component has its own license. Good luck with figuring out your obligations.

rna_star - see the web site at rna_star_

For details, please see the rna_starMS_
"STAR: ultrafast universal RNA-seq aligner"
A. Dobin et al, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts635

Galaxy_ (that's what you are using right now!) for gluing everything together 

Most of the work for this wrapper XML is Jeremy Goecks' original STAR_ wrapper 

Minor tweaks to output names to suit our downstream purposes, toolshed automated dependencies 
and odds and ends of other code and documentation comprising this tool was 
written by Ross Lazarus and that part is licensed_ the same way as other rgenetics artefacts

.. _STAR: https://bitbucket.org/jgoecks/jeremys-code/raw/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml
.. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/
.. _rna_star: http://code.google.com/p/rna-star/

35:e2dd4a5fad65

    <description>Gapped-read mapper for RNA-seq data</description>
    <requirements>
        <requirement type="package" version="2.4.0d">rnastar</requirement>
        <requirement type="package" version="0.1.19">samtools</requirement>
    </requirements>
    <stdio>
        <regex match=".*" source="both" level="warning" description="Some stderr/stdout text"/>
    </stdio>

    <command>
    ##
    ## Run STAR.
    ##
    #if str($refGenomeSource.genomeSource) == 'history':

    ## Can adjust this as appropriate for the system.
    --genomeLoad NoSharedMemory
    #if str($refGenomeSource.genomeSource) == 'history':
        --genomeDir "tempstargenomedir"
    #else
        --genomeDir "$refGenomeSource.index.fields.path"
    #end if
    --readFilesIn $singlePaired.input1
    #if str($singlePaired.sPaired) == "paired"
            $singlePaired.input2
    #end if
        --runThreadN 4
    #if str($params.settingsType) == "full":

    ##
    ## BAM conversion.
    ##

    ## Convert aligned reads.
    samtools view -Shb Aligned.out.sam | samtools sort - AlignedSorted 2>/dev/null

    ## Convert chimeric reads.
    #if str($params.settingsType) == "full" and $params.chim_segment_min > 0:
        ; samtools view -Shb Chimeric.out.sam | samtools sort - ChimericSorted 2>/dev/null
    #end if
    </command>

    <inputs>
        <param name="jobName" type="text" size="120" value="rna-star run" label="Job narrative (added to output names)"
          help="Only letters, numbers and underscores (_) will be retained in this field">
           <sanitizer invalid_char="">
              <valid initial="string.letters,string.digits"><add value="_" /> </valid>
           </sanitizer>
        </param>

            </param>
            <when value="single">
                <param format="fastqsanger,fastq,fasta" name="input1" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33"/>
            </when>
            <when value="paired">
                <param format="fastqsanger,fastq,fasta" name="input1" type="data" label="RNA-Seq FASTQ file, forward reads"
            help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
                <param format="fastqsanger,fastq,fasta" name="input2" type="data" label="RNA-Seq FASTQ file, reverse reads"
            help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
            </when>
        </conditional>

               </action>
             </when>
             </conditional>
          </actions>
       </data>
       <data format="bam" name="chimeric_reads" label="${jobName}_starmappedchim.bam"
                    from_work_dir="ChimericSorted.bam">
         <filter>(params['settingsType'] == 'full' and params['chim_segment_min'] > 0)</filter>
          <actions>
             <conditional name="refGenomeSource.genomeSource">
             <when value="indexed">

               </action>
             </when>
             </conditional>
          </actions>
        </data>
        <data format="interval" name="splice_junctions" label="${jobName}_starsplicejunct.bed"
                   from_work_dir="SJ.out.tab">
          <actions>
             <conditional name="refGenomeSource.genomeSource">
             <when value="indexed">
               <action type="metadata" name="dbkey">

               </action>
             </when>
             </conditional>
          </actions>
        </data>
        <data format="bam" name="mapped_reads" label="${jobName}_starmapped.bam"
                    from_work_dir="AlignedSorted.bam">
          <actions>
             <conditional name="refGenomeSource.genomeSource">
             <when value="indexed">
               <action type="metadata" name="dbkey">

--outFilterIntronMotifs RemoveNoncanonicalUnannotated
filter out alignments that contain non-canonical unannotated junctions
when using annotated splice junctions database. The annotated non-
canonical junctions will be kept.


**Attributions**

Note that each component has its own license. Good luck with figuring out your obligations.

rna_star - see the web site at rna_star_

For details, please see the rna_starMS_
"STAR: ultrafast universal RNA-seq aligner"
A. Dobin et al, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts635

Galaxy_ (that's what you are using right now!) for gluing everything together

Most of the work for this wrapper XML is Jeremy Goecks' original STAR_ wrapper

Minor tweaks to output names to suit our downstream purposes, toolshed automated dependencies
and odds and ends of other code and documentation comprising this tool was
written by Ross Lazarus and that part is licensed_ the same way as other rgenetics artefacts

.. _STAR: https://bitbucket.org/jgoecks/jeremys-code/raw/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml
.. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/
.. _rna_star: http://code.google.com/p/rna-star/