# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1386262468 21600
# Node ID 1ff2fc8da32813e05adff157300bba37ca3ed9b2
# Parent  64d45f9593038d400c26fff91e46d38f03be07bb
Updates to rsem_calculate_expression.xml

diff -r 64d45f959303 -r 1ff2fc8da328 extract_transcript_to_gene_map_from_trinity.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_transcript_to_gene_map_from_trinity.xml	Thu Dec 05 10:54:28 2013 -0600
@@ -0,0 +1,35 @@
+<tool id="extract_transcript_to_gene_map_from_trinity" name="RSEM trinity fasta to gene map" version="1.1.17">
+  <description>extract transcript to gene map from trinity</description>
+  <requirements>
+    <requirement type="package" version="1.1.17">rsem</requirement>
+  </requirements>
+  <command>
+    extract-transcript-to-gene-map-from-trinity $trinity_fasta_file $map_file
+  </command>
+
+  <inputs>
+    <param name="trinity_fasta_file" type="data" format="fasta" label="Trinity fasta file" />
+  </inputs>
+  <stdio>
+    <exit_code range="1:"  level="fatal" description="Error Running RSEM" />
+  </stdio>
+  <outputs>
+    <data format="tabular" name="map_file" label="${sample} gene map file"/>
+  </outputs>
+  <help>
+  
+
+RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/
+
+NAME
+    extract-transcript-to-gene-map-from-trinity
+
+SYNOPSIS
+    extract-transcript-to-gene-map-from-trinity trinity_fasta_file map_file
+
+DESCRIPTION
+    generates a gene_mp_file from a trinity fasta file
+ 
+
+  </help> 
+</tool> 
diff -r 64d45f959303 -r 1ff2fc8da328 rsem.py
--- a/rsem.py	Mon Nov 11 13:54:43 2013 -0500
+++ b/rsem.py	Thu Dec 05 10:54:28 2013 -0600
@@ -1,5 +1,5 @@
 """
-SnpEff datatypes
+RSEM datatypes
 """
 import os,os.path,re,sys
 import galaxy.datatypes.data
@@ -8,7 +8,7 @@
 
 class RsemReference( Html ):
     """Class describing an RSEM reference"""
-    MetadataElement( name='reference_name', default='galaxy_generated_bowtie_index', desc='RSEM Reference Name', readonly=True, visible=True, no_value=None )
+    MetadataElement( name='reference_name', default=None, desc='RSEM Reference Name', readonly=True, visible=True, no_value=None )
 
     file_ext = 'rsem_ref'
     is_binary = True
@@ -69,7 +69,6 @@
         extra_files_path/<reference_name>.rev.2.ebwt
         extra_files_path/<reference_name>.rev.1.ebwt
         """
-        log.info( "RSEM reference set_meta %s %s" % (dataset,dataset.extra_files_path))
         pat = '^(.*)\.grp$'
         efp = dataset.extra_files_path
         flist = os.listdir(efp)
diff -r 64d45f959303 -r 1ff2fc8da328 rsem_calculate_expression.xml
--- a/rsem_calculate_expression.xml	Mon Nov 11 13:54:43 2013 -0500
+++ b/rsem_calculate_expression.xml	Thu Dec 05 10:54:28 2013 -0600
@@ -5,179 +5,289 @@
     <requirement type="package" version="0.1.19">samtools</requirement>
     <requirement type="package" version="1.0.0">bowtie</requirement>
   </requirements>
-  <command interpreter="perl">
+  <command>
     rsem-calculate-expression 
-    --calc-ci $useci.ci
-    --fragment-length-mean $fraglenmean
-    --fragment-length-min $fraglenmin
-    --fragment-length-sd $fraglensd
-    --fragment-length-max $fraglenmax
-    --bowtie-e $bowtie_e
-    --bowtie-m $bowtie_m
-
-   #if $input.format=="fastq"
-        ## IF FASTQ AND SINGLE END READS (DEFAULTS)
-	#if $input.fastqmatepair.matepair=="single" #rsem-wrapper-1.1.17.pl --bam_genome $bam_genome --bamtype $bamtype 
-	--seed-length $seedlength $input.fastq_select --estimate-rspd $rspd --forward-prob 
-	$fprob -p $cpus --bowtie-n $bowtie_mis --output-genome-bam --single_fastq $singlefastq 
-	--output $output --isoformfile $isoforms --bamfile $bam_res --log $log 
-	--sampling-for-bam $sampling_for_bam --reference ${index.fields.path}
-    	#end if
-        ## IF FASTQ AND PAIRED END READS (DEFAULTS)
-        #if $input.fastqmatepair.matepair=="paired" #rsem-wrapper-1.1.17.pl --bam_genome $bam_genome --bamtype $bamtype 
-	--paired-end --seed-length $seedlength --estimate-rspd $rspd $input.fastq_select --forward-prob $fprob -p $cpus 
-        --bowtie-n $bowtie_mis --output-genome-bam --fastq1 $fastq1 --fastq2 $fastq2 --output 
-        $output --isoformfile $isoforms --bamfile $bam_res --log $log --sampling-for-bam 
-        $sampling_for_bam --reference ${index.fields.path} 
-	#end if
-   #end if 
-   #if $input.format=="fasta"
-        ## IF FASTA AND SINGLE END READS (DEFAULTS)
-	#if $input.fastamatepair.matepair=="single" #rsem-wrapper-1.1.17.pl --bam_genome $bam_genome --bamtype $bamtype
-	--no-qualities --seed-length $seedlength --estimate-rspd $rspd --forward-prob $fprob -p $cpus --bowtie-n $bowtie_mis 
-	--output-genome-bam --single_fasta $single_fasta --output $output --isoformfile 
-	$isoforms --bamfile $bam_res --log $log --sampling-for-bam $sampling_for_bam --reference 
-	${index.fields.path}
+    ## --tag string
+    #if $seedlength:
+      --seed-length $seedlength 
+    #end if
+    --forward-prob $forward_prob
+    #if $rsem_options.fullparams == 'fullset':
+      ## Fragment info
+      #if $rsem_options.fragment_length_mean:
+        --fragment-length-mean $rsem_options.fragment_length_mean
+      #end if
+      #if $rsem_options.fragment_length_min:
+        --fragment-length-min $rsem_options.fragment_length_min
+      #end if
+      #if $rsem_options.fragment_length_sd:
+        --fragment-length-sd $rsem_options.fragment_length_sd
+      #end if
+      #if $rsem_options.fragment_length_max:
+        --fragment-length-max $rsem_options.fragment_length_max
+      #end if
+      ## RSPD
+      #if $rsem_options.rspd.estimate == 'yes':
+        --estimate-rspd
+        #if $rsem_options.rspd.num_rspd_bins:
+          --num-rspd-bins $rsem_options.rspd.num_rspd_bins
+        #end if
+      #end if
+      ## Calculate 95% credibility intervals and posterior mean estimates. 
+      #if $rsem_options.useci.ci == 'yes':
+        --calc-ci
+        #if $rsem_options.useci.cimem:
+          --ci-memory $rsem_options.useci.cimem
         #end if
-        ## IF FASTA AND PAIRED END READS (DEFAULTS)
-        #if $input.fastamatepair.matepair=="paired" #rsem-wrapper-1.1.17.pl --bam_genome $bam_genome --bamtype $bamtype
-	--no-qualities --paired-end --seed-length $seedlength --estimate-rspd $rspd --forward-prob $fprob -p $cpus 
-        --bowtie-n $bowtie_mis --output-genome-bam --fasta1 $fasta1 --fasta2 $fasta2 --output 
-        $output --isoformfile $isoforms --bamfile $bam_res --log $log --sampling-for-bam 
-        $sampling_for_bam --reference ${index.fields.path} 
-	#end if
+      #end if
+    #end if
+    ## --num-threads $GALAXY_SLOTS
+    #if $input.format != 'bam' and $input.bowtie_options.fullparams == 'fullset':
+      ## Bowtie params
+      #if $bowtie_options.bowtie_e:
+      --bowtie-e $bowtie_options.bowtie_e
+      #end if
+      #if $bowtie_options.bowtie_m:
+      --bowtie-m $bowtie_options.bowtie_m
+      #end if
+      #if $bowtie_options.bowtie_n:
+      --bowtie-n $bowtie_options.bowtie_n
+      #end if
+    #end if
+    ## Outputs
+    #if $rsem_outputs.result_bams == 'none':
+      --no-bam-output
+    #else
+      #if $rsem_outputs.result_bams == 'both':
+        --output-genome-bam
+      #end if
+      $rsem_outputs.sampling_for_bam
+    #end if
+    ## Input data
+    #if $input.format=="fastq"
+      $input.fastq_select
+      #if $input.fastq.matepair=="single": 
+        $input.fastq.singlefastq
+      #elif $input.fastq.matepair=="paired":
+        --paired-end
+        $input.fastq.fastq1
+        $input.fastq.fastq2
+      #end if
+    #elif $input.format=="fasta"
+      --no-qualities
+      #if $input.fasta.matepair=="single": 
+        $input.fasta.singlefasta
+      #elif $input.fasta.matepair=="paired":
+        --paired-end
+        $input.fasta.fasta1
+        $input.fasta.fasta2
+      #end if
+    #elif $input.format=="sam"
+      #if $input.matepair=="paired":
+        --paired-end
+      #end if
+      #if $input.rsem_sam._extension == 'sam':
+        --sam
+      #elif $input.rsem_sam._extension == 'bam':
+        --bam
+      #end if
+      $input.rsem_sam
+    #end if
+    ## RSEM reference
+    #if $reference.refSrc == 'history':
+      ${reference.rsem_ref.extra_files_path}/${reference.rsem_ref.metadata.reference_name}
+    #elif $reference.refSrc == 'cached':
+      ${reference.index.fields.path}
     #end if
-
- </command>
-
- <inputs>
- <param name="sample" type="text" format="txt" label="Sample label" />
- <conditional name="input">
-	<param name="format" type="select" label="Input file type">
-		<option value="fastq">FASTQ</option>
-		<option value="fasta">FASTA</option>
-	</param>
- 	<when value="fastq">
-                   <param name="fastq_select" size="15" type="select" label="FASTQ type" >
-						<option value="--phred33-quals">phred33 qualities</option>
-						<option value="--solexa-quals">solexa qualities</option>
-						<option value="--phred64-quals">phred64 qualities</option>
-		 </param>
+    ## sample_name: use a hard coded name so we can pull out galaxy outputs
+    rsem_output
+    ## direct output into logfile
+    > $log
+  </command>
+  <macros>
+    <macro name="rsem_options">
+        <param name="seedlength" type="integer" value="25" optional="true" label="Seed length used by the read aligner" help="Providing the correct value for this parameter is important for RSEM's accuracy if the data are single-end reads. RSEM uses this value for Bowtie's seed length parameter. The minimum value is 25. (Default:25)">
+        </param>
+        <param name="forward_prob" type="select" label="Is the library strand specific?">
+          <option value="0.5" selected="true">No</option>
+          <option value="1">Yes, the reads (or first reads from paired-end libraries) are only in the forward orientation</option>
+          <option value="0">Yes, the reads (or first reads from paired-end libraries) are only in the reverse orientation</option>
+        </param>
+        <conditional name="rsem_options">
+          <param name="fullparams" type="select" label="Additional RSEM options">
+            <option value="default">Use RSEM Defaults</option>
+            <option value="fullset">Set Additional RSEM Options</option>
+          </param>
+          <when value="default"/>
+          <when value="fullset">
+            <param name="fragment_length_min" type="integer" value="1" optional="true" label="Minimum read/insert length." help=" This is also the value for the bowtie -I option">
+              <validator type="in_range" message="0 or greater" min="0" />
+            </param>
+            <param name="fragment_length_max" type="integer" value="1000" optional="true" label="Maximum read/insert length." help=" This is also the value for the bowtie -X option">
+              <validator type="in_range" message="0 or greater" min="0" max="1000000"/>
+            </param>
+            <param name="fragment_length_mean" type="float" value="" optional="true" label="Fragment length mean (single-end data only)" help="The mean of the fragment length distribution, which is assumed to be a Gaussian. (Default: -1, which disables use of the fragment length distribution)">
+            </param>
+            <param name="fragment_length_sd" type="float" value="" optional="true" label="The standard deviation of the fragment length distribution (single-end data only)" help="Default 0, which assumes that all fragments are of the same length, given by the rounded value of fragment length mean. ">
+            </param>
+            <conditional name="rspd">
+              <param name="estimate" type="select" lanel="Read Start Position Distribution (RSPD)" 
+                  help="Set this option if you want to estimate the read start position distribution (RSPD) from data. Otherwise, RSEM will use a uniform RSPD.">
+                <option value="no" selected="true">Use a uniform RSPD</option>
+                <option value="yes">Estimate and correct for a non-uniform RSPD</option>
+              </param>
+              <when value="no"/>
+              <when value="yes"> 
+                <param name="num_rspd_bins" type="integer" value="20" optional="true" label="Number of bins in the RSPD." help="Use of the default setting of 20 is recommended.">
+                   <validator type="in_range" message="" min="0" max="100"/>
+                </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>
+          </when>
+        </conditional>
+    </macro>
+    <macro name="bowtie_options">
+        <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>
+          </param>
+          <when value="default"/>
+          <when value="fullset">
+            <param name="bowtie_n" type="integer" value="2" optional="true" label="Bowtie mismatches" help="Bowtie parameter max # of mismatches in the seed. (Range: 0-3, Default: 2) ">
+              <validator type="in_range" message="max # of mismatches in the seed between 0 and 3" min="0" max="3"/>
+            </param>
+            <param name="bowtie_e" type="integer" value="99999999" label="Maximum sum of quality scores at mismatched positions in read alignments.  This is also the value for the Bowtie -e option">
+            </param>
+            <param name="bowtie_m" type="integer" value="200" label="Discard alignments for reads with number of alignments greater than">
+            </param>
+          </when>
+        </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">
+          <help> When RSEM generates a BAM file, instead of outputing all alignments a read has with their posterior probabilities, one alignment is sampled according to the posterior probabilities. The sampling procedure includes the alignment to the "noise" transcript, which does not appear in the BAM file. Only the sampled alignment has a weight of 1. All other alignments have weight 0. If the "noise" transcript is sampled, all alignments appeared in the BAM file should have weight 0. (Default: off)
+          </help>
+        </param>
+    </macro>
+  </macros>
 
-	<conditional name="fastqmatepair">
-        	<when value="single">
-            	<param name="singlefastq" type="data" checked="yes" format="fastq" label="FASTQ file" />
-			</when>
-        	<when value="paired">
-             	<param name="fastq1" type="data" format="fastq" label="Read 1 fastq file" />
-                 <param name="fastq2" type="data" format="fastq" label="Read 2 fastq file" />
- 			</when>
-    		<param name="matepair" type="select" label="Library type">
-			<option value="single">Single End Reads</option>
-			<option value="paired">Paired End Reads</option>
-		</param>
- 	</conditional>
-	</when>
- 	<when value="fasta">
-	<conditional name="fastamatepair">
-    	<param name="matepair" type="select" label="Library Type">
-			<option value="single">Single End Reads</option>
-			<option value="paired">Paired End Reads</option>
-		</param>
-    	<when value="single">
-    		<param name="single_fasta" type="data" checked="yes" format="fasta" label="fasta file" />
-		</when>
-    	<when value="paired">
-    		<param name="fasta1" type="data" format="fasta" label="Read 1 fasta file" />
-        	<param name="fasta2" type="data" format="fasta" label="Read 2 fasta file" />
- 		</when>
- 	</conditional>
-	</when>
-	<when>
-	<conditional name="fastamatepair">
-    	<param name="matepair" type="select" label="Library Type" >
-			<option value="single">Single End Reads</option>
-			<option value="paired">Paired End Reads</option>
-		</param>
-        <when value="single">
-        	<param name="singlefastq" type="data" checked="yes" format="fastq" label="FASTQ	file" />
-		</when>
-        <when value="paired">
-        	<param name="fastq1" type="data" format="fastq" label="Read 1 FASTQ file" />
-            <param name="fastq2" type="data" format="fastq" label="Read 2 FASTQ file" />
- 		</when>
- 	</conditional>
-	</when>
-	</conditional>
-    <param name="fprob" type="select" >
-    	<label>Is the library strand specific?</label>
-		<option value="0.5">No</option>
-		<option value="1">Yes, the reads (or first reads from paired-end libraries) are only in the forward orientation</option>
-		<option value="0">Yes, the reads (or first reads from paired-end libraries) are only in the reverse orientation</option>
-    </param>
-
-	<param name="index" type="select" label="Select RSEM reference" help="Select from a list of pre-indexed references. If you don't see anything consult the wrapper's documentation on how to create or download a reference">
-		<options from_data_table="rsem_indexes">
-			<filter type="sort_by" column="2" />
-				<validator type="no_options" message="No indexes are available" />
-		</options>
-	</param>
-	<param name="fraglenmean" size="4" type="text" value="-1" label="Fragment length mean (single-end data only)" help="The mean of the fragment length distribution, which is assumed to be a Gaussian. (Default: -1, which disables use of the fragment length distribution)" />
-	<param name="fraglensd" size="4" type="text" value="0" label="The standard deviation of the fragment length distribution (single-end data only)" help="Default 0, which assumes that all fragments are of the same length, given by the rounded value of fragment length mean. " />
-
-    <param name="bamtype" type="select" label="Create genome bam file" help="In addition to the transcript-coordinate-based BAM file output, also output a BAM file with the read alignments in genomic coordinates" >
-      <option value="no">no</option>
-      <option value="yes">yes</option>
-   </param>
-    <param name="sampling_for_bam" type="select" format="text" help="When RSEM generates a BAM file, instead of outputing all alignments a read has with their posterior probabilities, one alignment is sampled and outputed according to the posterior probabilities. If the sampling result is that the read comes from the noise transcript, nothing is outputed. (Default: off)">
-  		<label>Sample Bam File</label>
-			<option value="no">no</option>
-			<option value="yes">yes</option>
-    </param>
-    <param name="rspd" type="select" format="text" help="Set this option if you want to estimate the read start position distribution (RSPD) from data. Otherwise, RSEM will use a uniform RSPD.  (Default: off)">
-  		<label>Estimate and correct for a non-uniform read start position distribution (RSPD)</label>
-			<option value="no">no</option>
-			<option value="yes">yes</option>
-    </param>
-    
-<!-- <conditional name="fullpar">
-		<param name="fullpar" type="select" label="Full list of parameters" help="use 
-full list for linting all the parameters in RSEM">
-			<option value="default">Default</option>
-			<option value="fullset">Full Set</option>
-		</param>
-	<when value="fullset"> -->
-	 <!-- <param name="testing" size="4" type="text" value="" label="Advanced Parameters" /> 
--->
-	<conditional name="useci">
-		<param name="ci" type="select" label="Calculate 95% Credibility Intervals">
-	   		<option value="no">no</option>
-	   		<option value="yes">yes</option>
-	   </param>
-       <when value="yes">
-	   	<param name="cimem" size="4" type="text" value="1024" label="Amount of memory in (MB) for computing CI" />
-       </when>
+  <inputs>
+    <param name="sample" type="text" value="rsem_sample" label="Sample name" />
+    <conditional name="reference">
+      <param name="refSrc" type="select" label="RSEM Reference">
+        <option value="cached">Locally cached</option>
+        <option value="history">From your history</option>
+      </param>
+      <when value="cached">
+        <param name="index" type="select" label="Select RSEM reference" help="Select from a list of pre-indexed references. If you don't see anything consult the wrapper's documentation on how to create or download a reference">
+          <options from_data_table="rsem_indexes">
+            <filter type="sort_by" column="2" />
+            <validator type="no_options" message="No indexes are available" />
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="rsem_ref" type="data" format="rsem_ref" label="RSEM reference" />
+      </when>
     </conditional>
-	<param name="fraglenmin" size="4" type="text" value="1" label="Minimum read/insert length. Minimum read/insert length allowed. This is also the value for the bowtie -X option" />
-	<param name="fraglenmax" size="4" type="text" value="1000" label="Maximum read/insert length. Minimum read/insert length allowed. This is also the value for the bowtie -l option" />
-        <param name="bowtie_mis" size="2" type="text" value="2" label="Bowtie mismatches" help="Bowtie parameter max # of mismatches in the seed. (Range: 0-3, Default: 2) "/>
-	<param name="bowtie_e" size="4" type="text" value="99999999" label="Maximum sum of quality scores at mismatched positions in read alignments.  This is also the value for the Bowtie -e option" />
-	<param name="bowtie_m" size="4" type="text" value="200" label="Discard alignments for reads with number of alignments greater than" />
-        <param name="seedlength" size="2" type="text" value="25" label="Seed length used by the read aligner" help="Providing the correct value for this parameter is important for RSEM's accuracy if the data are single-end reads. RSEM uses this value for Bowtie's seed length parameter. The minimum value is 25. (Default:25)" />
-        <param name="cpus" size="2" type="integer" value="1" label="Number of threads to use" help="Number of threads to use. Both Bowtie and expression estimation will use this many threads.  (Default: 1)" />
-   <!-- </when> --> <!-- </conditional> -->
+    <conditional name="input">
+      <param name="format" type="select" label="RSEM Input file type">
+        <option value="fastq">FASTQ</option>
+        <option value="fasta">FASTA</option>
+        <option value="sam">SAM/BAM</option>
+      </param>
+      <when value="fastq">
+        <param name="fastq_select" size="15" type="select" label="FASTQ type" >
+          <option value="--phred33-quals">phred33 qualities (default for sanger)</option>
+          <option value="--solexa-quals">solexa qualities</option>
+          <option value="--phred64-quals">phred64 qualities</option>
+        </param>
+        <conditional name="fastq">
+          <param name="matepair" type="select" label="Library type">
+            <option value="single">Single End Reads</option>
+            <option value="paired">Paired End Reads</option>
+          </param>
+          <when value="single">
+            <param name="singlefastq" type="data" format="fastq" label="FASTQ file" />
+          </when>
+          <when value="paired">
+            <param name="fastq1" type="data" format="fastq" label="Read 1 fastq file" />
+            <param name="fastq2" type="data" format="fastq" label="Read 2 fastq file" />
+          </when>
+        </conditional>
+        <expand macro="bowtie_options"/>
+      </when>
+      <when value="fasta">
+        <conditional name="fasta">
+          <param name="matepair" type="select" label="Library Type">
+            <option value="single">Single End Reads</option>
+            <option value="paired">Paired End Reads</option>
+          </param>
+          <when value="single">
+            <param name="singlefasta" type="data" format="fasta" label="fasta file" />
+          </when>
+          <when value="paired">
+            <param name="fasta1" type="data" format="fasta" label="Read 1 fasta file" />
+            <param name="fasta2" type="data" format="fasta" label="Read 2 fasta file" />
+          </when>
+        </conditional>
+        <expand macro="bowtie_options"/>
+      </when>
+      <when value="sam">
+          <!-- convert-sam-for-rsem /ref/mouse_125 input.sam -o input_for_rsem.sam -->
+          <param name="matepair" type="select" label="Library Type">
+            <option value="single">Single End Reads</option>
+            <option value="paired">Paired End Reads</option>
+          </param>
+          <param name="rsem_sam" type="data" format="rsem_sam" label="RSEM formatted SAM file" />
+      </when>
+    </conditional>
+    <expand macro="rsem_options"/>
+    <conditional name="rsem_outputs">
+      <param name="result_bams" type="select" label="Create bam results files" 
+             help="In addition to the transcript-coordinate-based BAM file output, also output a BAM file with the read alignments in genomic coordinates" >
+        <option value="none">No BAM results files</option>
+        <option value="default" selected="true">Transcript BAM results file</option>
+        <option value="both">Transcript and genome BAM results files</option>
+      </param>
+      <when value="none"/>
+      <when value="default">
+        <expand macro="sampling_for_bam"/>
+      </when>
+      <when value="both">
+        <expand macro="sampling_for_bam"/>
+      </when>
+    </conditional>
   </inputs>
   <stdio>
     <exit_code range="1:"  level="fatal" description="Error Running RSEM" />
   </stdio>
   <outputs>
-    <data format="tabular" name="output" label="${sample}.gene_abundances"/>
-    <data format="tabular" name="isoforms" label="${sample}.isoform_abundances"/>
-    <data format="bam" name="bam_res" label="${sample}.transcript.bam"/>
-    <data format="bam" name="bam_genome" label="${sample}.genome.bam">
-    	<filter>bamtype == "yes"</filter>
+    <data format="tabular" name="output" label="${sample}.gene_abundances" from_work_dir="rsem_output.genes.results"/>
+    <data format="tabular" name="isoforms" label="${sample}.isoform_abundances" from_work_dir="rsem_output.isoforms.results"/>
+    <data format="bam" name="transcript_bam" label="${sample}.transcript.bam" from_work_dir="rsem_output.transcript.bam" >
+      <filter>rsem_outputs['result_bams'] != "none"</filter>
     </data>
-
+    <data format="bam" name="transcript__sorted_bam" label="${sample}.transcript.bam" from_work_dir="rsem_output.transcript.sorted.bam" >
+      <filter>rsem_outputs['result_bams'] != "none"</filter>
+    </data>
+    <data format="bam" name="genome_bam" label="${sample}.genome.bam" from_work_dir="rsem_output.genome.bam">
+      <filter>rsem_outputs['result_bams'] == "both"</filter>
+    </data>
+    <data format="bam" name="genome_sorted_bam" label="${sample}.genome.bam" from_work_dir="rsem_output.genome.sorted.bam">
+      <filter>rsem_outputs['result_bams'] == "both"</filter>
+    </data>
     <data format="txt" name="log" label="${sample}.rsem_log"/>
   </outputs>
   <help>
diff -r 64d45f959303 -r 1ff2fc8da328 rsem_prepare_reference.xml
--- a/rsem_prepare_reference.xml	Mon Nov 11 13:54:43 2013 -0500
+++ b/rsem_prepare_reference.xml	Thu Dec 05 10:54:28 2013 -0600
@@ -5,6 +5,8 @@
     <requirement type="package" version="1.0.0">bowtie</requirement>
   </requirements>
   <command>
+    mkdir $reference_file.extra_files_path &amp;&amp; 
+    cd $reference_file.extra_files_path &amp;&amp; 
     rsem-prepare-reference 
     #if $polya.polya_use == 'add':
       #if $polya.polya_length:
diff -r 64d45f959303 -r 1ff2fc8da328 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Nov 11 13:54:43 2013 -0500
+++ b/tool_dependencies.xml	Thu Dec 05 10:54:28 2013 -0600
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="rsem" version="1.1.17">
-        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_rsem_1_1_17" owner="jjohnson" changeset_revision="9fa1826ae6d4" />
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_rsem_1_1_17" owner="jjohnson" changeset_revision="7d060ea51c6f" />
     </package>
     <package name="samtools" version="0.1.19">
         <repository changeset_revision="54195f1d4b0f" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />