# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1385153319 21600
# Node ID 8d546ef8cfea234a8fe0cb53536c649582a17232
# Parent  a67c0a0d24aceff3bf60db61ebeb0e9289737d81
Add RSEM_abundance_estimation

diff -r a67c0a0d24ac -r 8d546ef8cfea RSEM_abundance_estimation.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RSEM_abundance_estimation.xml	Fri Nov 22 14:48:39 2013 -0600
@@ -0,0 +1,91 @@
+<tool id="RSEM_abundance_estimation" name="RSEM abundance estimation" version="0.0.2">
+    <description>run RSEM to estimate transcript abundances</description>
+    <requirements>
+        <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
+        <requirement type="package" version="1.1.17">rsem</requirement>
+    </requirements>
+    <command>
+        \$TRINITY_HOME/util/RSEM_util/run_RSEM_align_n_estimate.pl  --transcripts $transcripts 
+        ## Inputs.
+        #if str($read_type.paired_or_single) == "single":
+            #if  $read_type.single_reads.extension.startswith( "fastq"):
+                --seqType fq
+            #else
+                --seqType fa
+            #end if
+            --single $read_type.single_reads
+        #else
+            #if  $read_type.left_reads.extension.startswith( "fastq"):
+                --seqType fq
+            #else
+                --seqType fa
+            #end if
+            --left $read_type.left_reads
+            --right $read_type.right_reads
+        #end if
+        #if $transcript.source == "other":
+            --no_group_by_component
+            --gene_trans_map $transcript.gene_trans_map
+        #end if         
+    </command>
+    <inputs>
+        <param name="transcripts" type="data" format="fasta" label="transcripts_fasta" help="Fasta sequences for which reads are aligned."  />
+        <conditional name="read_type">
+            <param name="paired_or_single" type="select" label="Paired or Single-end data?">
+                <option value="paired">Paired</option>
+                <option value="single">Single</option>
+            </param>
+            <when value="paired">
+                <param name="left_reads" type="data" format="fasta,fastq" label="left reads" help=""  />
+                <param name="right_reads" type="data" format="fasta,fastq" label="right reads" help=""  />
+                <param name="ss_lib_type" type="select" label="strand-specific library type">
+                    <option value="RF">RF</option>
+                    <option value="FR">FR</option>
+                </param>
+            </when>
+            <when value="single">
+                <param name="single_reads" type="data" format="fasta,fastq" label="single reads" help=""  />
+                <param name="ss_lib_type" type="select" label="strand-specific library type">
+                    <option value="F">F</option>
+                    <option value="R">R</option>
+                </param>
+            </when>
+        </conditional>
+        <conditional name="transcript">
+            <param name="source" type="select" label="Transcripts Source">
+                <option value="trinity">Trinity</option>
+                <option value="other">NOT trinity</option>
+            </param>
+            <when value="trinity"/>
+            <when value="other">
+                <param name="gene_trans_map" type="data" format="tabular" optional="true" label="Map of gene ids to transcript (isoform) ids" >
+                  <help>
+                    Each line of should be of the form: gene_id transcript_id ( with the two fields separated by a tab character )
+                  </help>
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+    <stdio>
+        <exit_code range="1:"  level="fatal" description="Error Running RSEM" />
+    </stdio>
+    <outputs>
+        <data format="text" name="transcript_counts" label="${tool.name} on ${on_string}: Isoform Counts" from_work_dir="RSEM.isoforms.results"/>
+        <data format="text" name="gene_counts" label="${tool.name} on ${on_string}: Gene counts" from_work_dir="RSEM.genes.results"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="target" value="trinity/Trinity.fasta" />
+            <param name="aligner" value="bowtie" />
+            <param name="paired_or_single" value="single" />
+            <param name="library_type" value="None" />
+            <param name="input" value="trinity/reads.left.fq" />
+        </test>
+    </tests>
+    <help>
+        .. _Trinity: http://trinityrnaseq.sourceforge.net
+
+        $TRINITY_HOME/util/RSEM_util/run_RSEM_align_n_estimate.pl --transcripts Trinity.fasta \
+        --seqType fq --left left.reads.fq --right right.reads.fq
+    </help>
+</tool>
diff -r a67c0a0d24ac -r 8d546ef8cfea tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Nov 11 11:15:53 2013 -0600
+++ b/tool_dependencies.xml	Fri Nov 22 14:48:39 2013 -0600
@@ -12,5 +12,8 @@
     <package name="hmmer" version="3.0">
         <repository changeset_revision="3bc37773c609" name="package_hmmer_3_0" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
+    <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" />
+    </package>
 </tool_dependency>