changeset 35:e2dd4a5fad65 draft default tip

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

--- a/rg_rnaStar.xml	Tue Apr 28 22:56:01 2015 -0400
+++ b/rg_rnaStar.xml	Mon May 04 22:46:43 2015 -0400
@@ -4,6 +4,10 @@
         <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.
@@ -24,9 +28,9 @@
     #if str($refGenomeSource.genomeSource) == 'history':
         --genomeDir "tempstargenomedir"
     #else
-        --genomeDir "$refGenomeSource.index.fields.path" 
+        --genomeDir "$refGenomeSource.index.fields.path"
     #end if
-    --readFilesIn $singlePaired.input1 
+    --readFilesIn $singlePaired.input1
     #if str($singlePaired.sPaired) == "paired"
             $singlePaired.input2
     #end if
@@ -45,20 +49,16 @@
     ##
 
     ## Convert aligned reads.
-    samtools view -Shb Aligned.out.sam | samtools sort - AlignedSorted 2&gt;/dev/null 
+    samtools view -Shb Aligned.out.sam | samtools sort - AlignedSorted 2&gt;/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&gt;/dev/null 
+        ; samtools view -Shb Chimeric.out.sam | samtools sort - ChimericSorted 2&gt;/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)" 
+        <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>
@@ -74,7 +74,7 @@
                 <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" 
+                <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" />
@@ -152,7 +152,7 @@
              </conditional>
           </actions>
        </data>
-       <data format="bam" name="chimeric_reads" label="${jobName}_starmappedchim.bam" 
+       <data format="bam" name="chimeric_reads" label="${jobName}_starmappedchim.bam"
                     from_work_dir="ChimericSorted.bam">
          <filter>(params['settingsType'] == 'full' and params['chim_segment_min'] > 0)</filter>
           <actions>
@@ -173,7 +173,7 @@
              </conditional>
           </actions>
         </data>
-        <data format="interval" name="splice_junctions" label="${jobName}_starsplicejunct.bed" 
+        <data format="interval" name="splice_junctions" label="${jobName}_starsplicejunct.bed"
                    from_work_dir="SJ.out.tab">
           <actions>
              <conditional name="refGenomeSource.genomeSource">
@@ -193,7 +193,7 @@
              </conditional>
           </actions>
         </data>
-        <data format="bam" name="mapped_reads" label="${jobName}_starmapped.bam" 
+        <data format="bam" name="mapped_reads" label="${jobName}_starmapped.bam"
                     from_work_dir="AlignedSorted.bam">
           <actions>
              <conditional name="refGenomeSource.genomeSource">
@@ -287,8 +287,8 @@
 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.
@@ -299,12 +299,12 @@
 "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 
+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 
+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 
+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