# HG changeset patch
# User yboursin
# Date 1464185282 14400
# Node ID 73a9e9df80da9234ff0ea4d96635fc52159f4bbe
# Parent  7146e81bc8861acf09e82d178c0cc6f1c3605c44
Uploaded

diff -r 7146e81bc886 -r 73a9e9df80da rsem_calculate_expression.xml
--- a/rsem_calculate_expression.xml	Wed May 25 08:35:34 2016 -0400
+++ b/rsem_calculate_expression.xml	Wed May 25 10:08:02 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="rsem_calculate_expression" name="RSEM calculate expression" version="1.1.17">
+<tool id="rsem_calculate_expression" name="RSEM calculate expression" version="EBA2016-v1">
   <description>RNA-Seq by Expectation-Maximization</description>
   <requirements>
     <requirement type="package" version="1.2.28">rsem</requirement>
@@ -34,26 +34,32 @@
         #end if
       #end if
       ## Calculate 95% credibility intervals and posterior mean estimates. 
-      #if $rsem_options.useci.ci == 'yes':
+      #if $rsem_options.ci == 'yes':
         --calc-ci
-        #if $rsem_options.useci.cimem:
-          --ci-memory $rsem_options.useci.cimem
-        #end if
+        --ci-memory 2048
       #end if
     #end if
-    ## --num-threads $GALAXY_SLOTS
-    #if $input.format != 'bam' and $input.bowtie_options.fullparams == 'fullset':
+    ## Calculate PME
+    $rsem_options.pme
+    --num-threads \${GALAXY_SLOTS:-4}
+    #if str($input.usebowtie.bowtie) == "one":
+     #if $input.format != 'bam' and $input.usebowtie.bowtie_options.fullparams == 'fullset':
       ## Bowtie params
-      #if $bowtie_options.bowtie_e:
-      --bowtie-e $bowtie_options.bowtie_e
+      #if $input.usebowtie.bowtie_options.bowtie_e:
+      --bowtie-e $input.usebowtie.bowtie_options.bowtie_e
       #end if
-      #if $bowtie_options.bowtie_m:
-      --bowtie-m $bowtie_options.bowtie_m
+      #if $input.usebowtie.bowtie_options.bowtie_m:
+      --bowtie-m $input.usebowtie.bowtie_options.bowtie_m
+      #end if
+      #if $input.usebowtie.bowtie_options.bowtie_n:
+      --bowtie-n $input.usebowtie.bowtie_options.bowtie_n
       #end if
-      #if $bowtie_options.bowtie_n:
-      --bowtie-n $bowtie_options.bowtie_n
-      #end if
+     #end if
+
+    #elif str($input.usebowtie.bowtie) == "two":
+      --bowtie2
     #end if
+    
     ## Outputs
     #if $rsem_outputs.result_bams == 'none':
       --no-bam-output
@@ -143,21 +149,23 @@
                 </param>
               </when>
             </conditional>
-            <conditional name="useci">
               <param name="ci" type="select" label="Calculate 95% Credibility Intervals">
                 <option value="no" selected="true">no</option>
                 <option value="yes">yes</option>
               </param>
-              <when value="no"/>
-              <when value="yes">
-                <param name="cimem" size="4" type="text" value="1024" label="Amount of memory in (MB) for computing CI" />
-              </when>
-            </conditional>
+            
+            <param name="pme" type="boolean" truevalue="--calc-pme" falsevalue="" label="Calculate posterior mean estimates ? (collapsed Gibbs sampler)" />
           </when>
         </conditional>
     </macro>
     <macro name="bowtie_options">
-        <conditional name="bowtie_options">
+        <conditional name="usebowtie">
+         <param name="bowtie" type="select" label="Use bowtie 1 or 2 ?">
+          <option value="one" selected="true">Bowtie 1</option>
+          <option value="two">Bowtie 2</option>
+         </param>
+         <when value="one">
+         <conditional name="bowtie_options">
           <param name="fullparams" type="select" label="bowtie settings">
             <option value="default">use bowtie defaults</option>
             <option value="fullset">set bowtie options</option>
@@ -173,6 +181,9 @@
             </param>
           </when>
         </conditional>
+        </when>
+        <when value="two" />
+       </conditional>
     </macro>
     <macro name="sampling_for_bam">
         <param name="sampling_for_bam" type="boolean" truevalue="--sampling-for-bam" falsevalue="" checked="false" label="Use sampling for BAM">
diff -r 7146e81bc886 -r 73a9e9df80da rsem_prepare_reference.xml
--- 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>