# HG changeset patch
# User gkumar09
# Date 1445616473 14400
# Node ID 9b159468135f0cf0b27d480d4accc3530a8d47e1
# Parent  0bb2b5dc3a539414acc6a513a1394c6fa3ed9757
Deleted selected files

diff -r 0bb2b5dc3a53 -r 9b159468135f trinityrnaseq_protocol/align_and_estimate_abundance.xml~
--- a/trinityrnaseq_protocol/align_and_estimate_abundance.xml~	Fri Oct 23 12:07:36 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,89 +0,0 @@
-<tool id="RSEM_abundance_estimation" name="RSEM_abundance_estimation" version="0.0.1">
-
-    <description>run RSEM to estimate transcript abundances</description>
-    <requirements>
-        <requirement type="package">trinity</requirement>
-    </requirements>
-    <command interpreter="python">
-
-        trinityToolWrapper.py util/align_and_estimate_abundance.pl --transcripts $transcripts --est_method RSEM --aln_method bowtie --trinity_mode --prep_reference
-
-        ## Inputs.
-        #if str($inputs.paired_or_single) == "paired":
-            --left $inputs.left_input --right $inputs.right_input
-            #if  $inputs.left_input.ext == 'fa':
-                --seqType fa
-            #else:
-                --seqType fq
-            #end if
-            #if str($inputs.library_type) != "None":
-                --SS_lib_type $inputs.library_type
-            #end if
-            
-        #else:
-            --single $inputs.input
-            #if  str($inputs.input.ext) == 'fa':
-                --seqType fa
-            #else:
-                --seqType fq
-            #end if
-            #if str($inputs.library_type) != "None":
-                --SS_lib_type $inputs.library_type
-            #end if
-        #end if
-
-
-    </command>
-    <inputs>
-		<param format="fasta" name="transcripts" type="data" label="transcripts_fasta" help="Fasta sequences for which reads are aligned."  />
-
-		<conditional name="inputs">
-                    <param name="paired_or_single" type="select" label="Paired or Single-end data?">
-                <option value="paired">Paired</option>
-                <option value="single">Single</option>
-            </param>
-            <when value="paired">
-                <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
-                <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
-                <param name="library_type" type="select" label="Strand-specific Library Type">
-                    <option value="None">None</option>
-                    <option value="FR">FR</option>
-                    <option value="RF">RF</option>
-                </param>
-
-            </when>
-            <when value="single">
-                <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
-                <param name="library_type" type="select" label="Strand-specific Library Type">
-                    <option value="None">None</option>
-                    <option value="F">F</option>
-                    <option value="R">R</option>
-                </param>
-
-            </when>
-        </conditional>
-
-	
-    </inputs>
-    <outputs>
-        <data format="text" name="transcript_counts" label="${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="transcript_file" value="fasta" />
-			<param name="input" value="reads.left.fq" />
-			<output name="transcripts_counts" value="text" />
-		
-        </test>
-	
-
-    </tests>
-    <help>
-        .. _Trinity: http://trinityrnaseq.sourceforge.net
-    </help>
-</tool>