diff rsem_prepare_reference.xml @ 1:73a9e9df80da draft

Uploaded

--- a/rsem_prepare_reference.xml	Wed May 25 08:35:34 2016 -0400
+++ b/rsem_prepare_reference.xml	Wed May 25 10:08:02 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="rsem_prepare_reference" name="RSEM prepare reference" version="1.1.17">
+<tool id="rsem_prepare_reference" name="RSEM prepare reference" version="EBA2016-v1">
   <description></description>
   <requirements>
     <requirement type="package" version="1.2.28">rsem</requirement>
@@ -23,13 +23,19 @@
       --no-polyA
     #end if
     $ntog
+    $bowtie
+    $bowtietwo
     #if $transcript_to_gene_map:
       --transcript-to-gene-map $transcript_to_gene_map
     #end if
     #if $reference.ref_type == 'transcripts':
       $reference.reference_fasta_file
     #else:
+     #if $reference.gtf.extension == 'gtf':
       --gtf $reference.gtf
+     #elif $reference.gtf.extension == 'gff3':
+      --gff3 $reference.gtf
+     #end if
       $reference.reference_fasta_file
     #end if
     $reference_name
@@ -48,8 +54,8 @@
       <when value="genomic">
         <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file" 
                help="The file should contain the sequence of an entire genome."/>
-        <param name="gtf" type="data" format="gtf" label="gtf" 
-               help="extract transcript reference sequences using the gene annotations specified in this GTF" />
+        <param name="gtf" type="data" format="gtf,gff3" label="gtf or gff3 file" 
+               help="extract transcript reference sequences using the gene annotations specified in this GTF or GFF3 file" />
       </when>
     </conditional>
     <param name="transcript_to_gene_map" type="data" format="tabular" optional="true" label="Map of gene ids to transcript (isoform) ids" >
@@ -86,6 +92,8 @@
       </when>
       <when value="none"/>
     </conditional>
+    <param name="bowtie" type="boolean" truevalue="--bowtie" falsevalue="" checked="false" label="Use bowtie" />
+    <param name="bowtietwo" type="boolean" truevalue="--bowtie2" falsevalue="" checked="false" label="Use bowtie2" />
     <param name="ntog" type="boolean" truevalue="--no-ntog" falsevalue="" checked="false" label="Disable the conversion of 'N' characters to 'G' characters in the reference sequences" help="Bowite uses the automatic N to G conversion to to align against all positions in the reference."/>
   </inputs>
   <stdio>