# HG changeset patch
# User gkumar09
# Date 1443581639 14400
# Node ID 4eaf6b15b1b233b820c4a971c5282e6cc536ed5c
# Parent  1c37a800375581a6bc9313a98956f92b3cb7e96e
Deleted selected files

diff -r 1c37a8003755 -r 4eaf6b15b1b2 trinityrnaseq_protocol/EdgeR_differentialExpression.xml
--- a/trinityrnaseq_protocol/EdgeR_differentialExpression.xml	Mon Sep 28 22:44:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-<tool id="EdgeR_differentialExpression" name="EdgeR_differentialExpression" version="0.0.1">
-
-    <description>Identify Differentially Expressed Transcripts Using EdgeR</description>
-    <requirements>
-        <requirement type="package">trinity</requirement>
-    </requirements>
-    <command interpreter="python">
-
- 		EdgeR_differentialExpression_wrapper.py 
-			$counts_matrix 
-			$dispersion
-			
-    </command>
-    <inputs>
-		
-		<param type="data" format="txt" name="counts_matrix" label="Matrix of RNA-Seq fragment counts for transcripts per condition" />
-		<param type="data" format="fasta" name="transcripts_fasta_file" label="Transcripts fasta file corresponding to matrix" />
-		<param type="float" name="dispersion" value="0.1" min="0" label="dispersion value" help="Dispersion value to be used in the negative binomial" />
-	
-    </inputs>
-    <outputs>
-        
-        <data format="tar.gz" name="EdgeR_Archive" label="${tool.name} on ${on_string}: EdgeR_Results.tar.gz" from_work_dir="edgeR_results.tar.gz" />
-			
-	</outputs>
-    <tests>
-
-		<test>
-			<param name="myname" value="This is just a simple test" />
-
-        </test>
-	
-
-    </tests>
-    <help>
-         help info here.
-    </help>
-</tool>
diff -r 1c37a8003755 -r 4eaf6b15b1b2 trinityrnaseq_protocol/EdgeR_differentialExpression_wrapper.py
--- a/trinityrnaseq_protocol/EdgeR_differentialExpression_wrapper.py	Mon Sep 28 22:44:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,40 +0,0 @@
-import sys, os, subprocess
-
-TRINITY_BASE_DIR = ""
-if os.environ.has_key('TRINITY_HOME'):
-    TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
-else:
-    sys.stderr.write("You must set the environmental variable TRINITY_BASE_DIR to the base installation directory of Trinity before running this");
-    sys.exit(1)
-
-usage= "usage: " + " $counts_matrix" + " $dispersion"
-
-if len(sys.argv)<2:
-    print "Require atleast two parameters"
-else:
-    print "All good- command going ahead"
-print " "
-
-def run_command(cmd):
-    print "The command used: " + cmd
-    pipe=subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE)
-    pipe.wait()
-    ret= pipe.returncode
-    if ret:
-        print "command died: " + str(ret)
-        print pipe.stderr.readlines()
-        sys.exit(1)
-    else:
-        return
-print " "
-
-countmatrix= "counts_matrix"
-
-cmd= "cp " + sys.argv[1] + " " + countmatrix 
-run_command(cmd)
-
-cmd= TRINITY_BASE_DIR + "/Analysis/DifferentialExpression/run_DE_analysis.pl "+ " --matrix "+ countmatrix + " --method edgeR " + " --output edgeR_results "+ " --dispersion " + sys.argv[2] + " --tar_gz_outdir"
-
-run_command(cmd)
-
-sys.exit(0)
diff -r 1c37a8003755 -r 4eaf6b15b1b2 trinityrnaseq_protocol/RSEM_estimates_to_matrix.xml
--- a/trinityrnaseq_protocol/RSEM_estimates_to_matrix.xml	Mon Sep 28 22:44:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,51 +0,0 @@
-<tool id="RSEM_estimates_to_matrix" name="RSEM_estimates_to_matrix" version="0.0.1">
-
-    <description>Join RSEM estimates from multiple samples into a single matrix</description>
-    <requirements>
-        <requirement type="package">trinity</requirement>
-    </requirements>
-    <command interpreter="python">
-
-        trinityToolWrapper.py util/RSEM_util/merge_RSEM_counts_and_labels_single_table.pl
-
-		--labels
-        #for $entry in $RSEM_samples:
-        	${entry.column_label}
-        #end for
-
-		--RSEM_counts
-        #for $entry in $RSEM_samples:
-        	${entry.file}
-        #end for
-
-        > RSEM.counts.matrix
-
-    </command>
-    <inputs>
-
-       <repeat name="RSEM_samples" title="RSEM abundance estimates for samples">
-              <param name="file" label="Add file" type="data" format="text"/>
-              <param name="column_label" label="column label" type="text" />
-       </repeat>
-
-    </inputs>
-    <outputs>
-        <data format="text" name="counts_matrix" label="${tool.name} on ${on_string}: Counts Matrix" from_work_dir="RSEM.counts.matrix"/>
-	</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
-    </help>
-</tool>
diff -r 1c37a8003755 -r 4eaf6b15b1b2 trinityrnaseq_protocol/abundance_estimation_to_matrix.xml
--- a/trinityrnaseq_protocol/abundance_estimation_to_matrix.xml	Mon Sep 28 22:44:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,42 +0,0 @@
-<tool id="abundance_estimation_to_matrix" name="abundance_estimation_to_matrix" version="0.0.1">
-
-    <description>Join RSEM estimates from multiple samples into a single matrix</description>
-    <requirements>
-        <requirement type="package">trinity</requirement>
-    </requirements>
-    <command interpreter="python">
-
-        abundance_estimation_to_matrix_wrapper.py 
-		#for $q in $RSEM_samples
-			${q.file} "${q.column_label}"
-		#end for
-
-    </command>
-    <inputs>
-
-       <repeat name="RSEM_samples" title="RSEM abundance estimates for samples">
-              <param name="file" label="Add file" type="data" format="text"/>
-              <param name="column_label" label="column label" type="text" />
-       </repeat>
-
-    </inputs>
-    <outputs>
-        <data format="text" name="counts_matrix" label="${tool.name} on ${on_string}: Counts Matrix" from_work_dir="matrix.counts.matrix"/>
-	</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
-    </help>
-</tool>
diff -r 1c37a8003755 -r 4eaf6b15b1b2 trinityrnaseq_protocol/abundance_estimation_to_matrix_wrapper.py
--- a/trinityrnaseq_protocol/abundance_estimation_to_matrix_wrapper.py	Mon Sep 28 22:44:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,40 +0,0 @@
-#!/usr/bin/env python
-
-import sys, os, string, subprocess
-
-#aliasing the filenames using the labels
-
-
-def run_command(command):
-    print "Running command: " + command
-    
-    err_capture_file = open("my.stderr", 'w') # writing stderr to a file
-    cmd_run = subprocess.Popen(args=command, shell=True, stderr=err_capture_file, stdout=sys.stdout)
-    err = cmd_run.wait() # get exit code from command execution
-    err_capture_file.close()
-
-    if err:
-        # report the error messages we captured, and exit non-zero
-        sys.stderr.write("Error, cmd: " + command + " died with ret: " + `err`)
-        for line in open(err_capture_file):
-            sys.stderr.write(line)
-        sys.exit(err)
-    return
-
-label_list = []  # symlink files to the labels
-for i in range(1, len(sys.argv), 2):
-    filename=sys.argv[i]
-    label= sys.argv[i+1]
-    cmd= "ln -sf " + filename + " " + label
-    label_list.append(label)
-    run_command(cmd)
-
-
-# run the abundance estimation script
-
-cmd = os.path.dirname(sys.argv[0]) + "/trinityToolWrapper.py " + " util/abundance_estimates_to_matrix.pl --est_method RSEM --cross_sample_fpkm_norm TMM " + " ".join(label_list) 
-
-run_command(cmd)
-
-sys.exit(0)
-
diff -r 1c37a8003755 -r 4eaf6b15b1b2 trinityrnaseq_protocol/align_and_estimate_abundance.xml
--- a/trinityrnaseq_protocol/align_and_estimate_abundance.xml	Mon Sep 28 22:44:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,90 +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="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
-    </help>
-</tool>
diff -r 1c37a8003755 -r 4eaf6b15b1b2 trinityrnaseq_protocol/alignreads.xml
--- a/trinityrnaseq_protocol/alignreads.xml	Mon Sep 28 22:44:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,138 +0,0 @@
-<tool id="alignreads" name="alignReads" version="0.0.1">
-
-    <description>alignReads: short read alignment tool wrapper</description>
-    <requirements>
-        <requirement type="package">trinity</requirement>
-    </requirements>
-    <command interpreter="python">
-
-        trinityToolWrapper.py util/alignReads.pl --target $target -o alignment --aligner $aligner_selection.aligner
-
-
-        ## Inputs.
-        #if str($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
-			--max_dist_between_pairs $inputs.max_dist_between_pairs
-        #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 $inputs.library_type
-            #end if
-        #end if
-
-        ## Additional parameters.
-	    ##if str($inputs.use_additional) == "yes":
-		##	-- $inputs.additional_params
-        ##end if
-	
-                
-        ## direct to output
-	    > outCapture.txt  
-
-
-    </command>
-    <inputs>
-		<param format="fasta" name="target" type="data" label="target" help="Fasta sequences targeted for short-read alignment"  />
-
-        <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>
-                <param name="max_dist_between_pairs" type="integer" value="2000" min="1" label="max_dist_between_pairs" help="Maximum length expected between fragment pairs as aligned to the target, including introns where relevant."/>
-
-
-            </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>
-
-		<conditional name="aligner_selection">
-			<param name="aligner" type="select" label="Select alignment tool to run">
-				<option value="bowtie">bowtie</option>
-				<option value="bwa">bwa</option>
-				<option value="blat">blat</option>
-			</param>
-			<when value="blat">
-				<param name="max_intron_length" type="integer" value="10000" min = "1" label="maximum intron length" help="" />
-				<param name="min_percent_identity" type="integer" value="95" min="1" label="minimum percent identity" help="" />
-			</when>
-			<when value="bwa">
-			</when>
-			<when value="bowtie">
-			</when>
-		</conditional>
-
-
-	<!--	    	
-		<conditional name="use_additional_params">
-            <param name="use_additional" type="select" label="Use Additional Params?">
-                <option value="no">No</option>
-                <option value="yes">Yes</option>
-            </param>
-            <when value="no">
-            </when>
-            <when value="yes">            
-				<param name="additional_params" type="text" value="" label="Additional command-line parameters to aligner" help="" />
-            </when>
-        </conditional>
-    
-	-->
-
-    </inputs>
-    <outputs>
-        <data format="bam" name="coordSortedBam" label="${tool.name} on ${on_string}: COORD-sorted read alignments" from_work_dir="alignment/alignment.coordSorted.bam"/>
-		<data format="bam" name="nameSortedBam" label="${tool.name} on ${on_string}: NAME-sorted read alignments" from_work_dir="alignment/alignment.nameSorted.bam"/>
-
-		<!-- notes: need to retain:
-			 -the sample name for the alignment
-			 -coordinate-sorted vs. name-sorted bam file
-			 -paired vs. unpaired vs. strictly proper pairs (for RSEM)
-			 -strand-specific or not
-		-->
-
-	</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
-    </help>
-</tool>
diff -r 1c37a8003755 -r 4eaf6b15b1b2 trinityrnaseq_protocol/analyze_diff_exp.xml
--- a/trinityrnaseq_protocol/analyze_diff_exp.xml	Mon Sep 28 22:44:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,41 +0,0 @@
-<tool id="Analyze_Diff_Exp" name="Analyze_Differential_Expression" version="0.0.1">
-
-    <description>Analyze differential expression</description>
-    <requirements>
-        <requirement type="package">trinity</requirement>
-    </requirements>
-    <command interpreter="python">
-
-        analyze_diff_exp_wrapper.py $EdgeRTarGz $TMM_Matrix_FPKM $Pvalue $Cvalue 
-	
-    </command>
-    <inputs>
-              <param name="EdgeRTarGz" label="EdgeR tar gz file" type="data" format="file"/>
-              <param name="TMM_Matrix_FPKM" label="TMM Normalized FPKM matrix" type="data" format="file" />
-	      <param name="Pvalue" label="P-value" value="0.05" type="float" />
-	      <param name="Cvalue" label="C-value" value="0" type="float" />
-      
-    </inputs>
-    <outputs>
-        <data format="data" name="diffExpr_matrix" label="${tool.name} on ${on_string}: Matrix" from_work_dir="diffExpr.matrix"/>
-	<data format="data" name="diffExpr_correlation_matrix" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix" from_work_dir="diffExpr.matrix.log2.sample_cor.dat"/>
-	<data format="data" name="diffExpr_correlation_matrix_pdf" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix_PDF" from_work_dir="diffExpr.matrix.log2.sample_cor_matrix.pdf"/>
-	<data format="data" name="Heatmap" label="${tool.name} on ${on_string}: Heatmap" from_work_dir="diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/>
-    </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
-    </help>
-</tool>
diff -r 1c37a8003755 -r 4eaf6b15b1b2 trinityrnaseq_protocol/analyze_diff_exp_wrapper.py
--- a/trinityrnaseq_protocol/analyze_diff_exp_wrapper.py	Mon Sep 28 22:44:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,63 +0,0 @@
-import sys, os, subprocess
-
-TRINITY_BASE_DIR = ""
-if os.environ.has_key('TRINITY_HOME'):
-    TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
-else:
-    sys.stderr.write("You must set the environmental variable TRINITY_BASE_DIR to the base installation directory of Trinity before running this");
-    sys.exit()
-
-usage= "usage: " + sys.argv[0] + " " + "edgeR.tar.gz " + "TMM_normalized_FPKM_matrix " + "P-value " + "C-value"
-print sys.argv 
-print usage 
-print " "
-
-if len(sys.argv)<5:
-	print "Require atleast two parameters"
-else:
-	print "All good- command going ahead"
-print " "
-
-Normalized_Matrix=sys.argv[2]
-Pvalue=sys.argv[3]
-Cvalue=sys.argv[4]
-
-def run_command(cmd):
-	print "The command used: " + cmd
-	pipe= subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE)
-        pipe.wait()
-	ret= pipe.returncode
-	if ret:
-		print "command died: " + str(ret)
-                print pipe.stderr.readlines()
-                sys.exit(1)
-	else:
-		return
-print " "
-
-Final_tar_gz= "edgeR.tar.gz"
-run_command("cp "+ sys.argv[1] + " " + "Final_tar_gz")
-run_command("tar -xvf " + "Final_tar_gz")
-run_command("mv " + "edgeR_results" + "/* ." )
-
-# run the analyze command
-cmd= TRINITY_BASE_DIR + "/Analysis/DifferentialExpression/analyze_diff_expr.pl "+ "--matrix " +  Normalized_Matrix + " -P " +  Pvalue + " -C " + Cvalue
-run_command(cmd)
-
-origMatrixName= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix"
-# diffExpr.P0.001_C2.0.matrix
-run_command("mv " + origMatrixName + " diffExpr.matrix")
-
-SampleCorName= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.sample_cor.dat"
-# diffExpr.P0.001_C2.0.matrix.log2.sample_cor.dat
-run_command("mv " + SampleCorName + " diffExpr.matrix.log2.sample_cor.dat")
-
-CorMatrix= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.sample_cor_matrix.pdf"
-# diffExpr.P0.001_C2.0.matrix.log2.sample_cor_matrix.pdf
-run_command("mv " + CorMatrix + " diffExpr.matrix.log2.sample_cor_matrix.pdf")
-
-Heatmap= "diffExpr.P" + Pvalue + "_" + "C" + Cvalue + ".matrix.log2.centered.genes_vs_samples_heatmap.pdf"
-#diffExpr.P0.001_C2.0.matrix.log2.centered.genes_vs_samples_heatmap.pdf
-run_command("mv " + Heatmap + " diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf")
-
-sys.exit(0)
diff -r 1c37a8003755 -r 4eaf6b15b1b2 trinityrnaseq_protocol/cat.xml
--- a/trinityrnaseq_protocol/cat.xml	Mon Sep 28 22:44:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,41 +0,0 @@
-<tool id="catbash" name="Concatenate datasets">
-    <description>tail-to-head</description>
-    <command interpreter="python">
-        bash_command_executer.py cat
-        $input1
-        #for $q in $queries
-            ${q.input2}
-        #end for
-        > $out_file1 
-    </command>
-    <inputs>
-        <param name="input1" type="data" label="Concatenate Dataset"/>
-        <repeat name="queries" title="Dataset">
-            <param name="input2" type="data" label="Select" />
-        </repeat>
-    </inputs>
-    <outputs>
-        <data name="out_file1" format="input" metadata_source="input1"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input1" value="1.bed"/>
-            <param name="input2" value="2.bed"/>
-            <output name="out_file1" file="cat_wrapper_out1.bed"/>
-        </test>
-        <!--TODO: if possible, enhance the underlying test code to handle this test
-            the problem is multiple params with the same name "input2"
-        <test>
-            <param name="input1" value="1.bed"/>
-            <param name="input2" value="2.bed"/>
-            <param name="input2" value="3.bed"/>
-            <output name="out_file1" file="cat_wrapper_out2.bed"/>
-        </test>
-        -->
-    </tests>
-    <help>
-
-    no help
-
-    </help>
-</tool>
diff -r 1c37a8003755 -r 4eaf6b15b1b2 trinityrnaseq_protocol/diffExpress_edgeR.xml
--- a/trinityrnaseq_protocol/diffExpress_edgeR.xml	Mon Sep 28 22:44:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,47 +0,0 @@
-<tool id="diffExpress_edgeR" name="diffExpress_edgeR" version="0.0.1">
-
-    <description>Identify Differentially Expressed Transcripts Using EdgeR</description>
-    <requirements>
-        <requirement type="package">edgeR</requirement>
-    </requirements>
-    <command interpreter="python">
-
- 		trinityToolWrapper.py Analysis/DifferentialExpression/run_EdgeR.pl 
-			--matrix $counts_matrix 
-			--transcripts $transcripts_fasta_file
-			--output edgeR_results
-			--dispersion $dispersion
-
-		> stdout.txt
-
-
-    </command>
-    <inputs>
-		
-		<param type="data" format="txt" name="counts_matrix" label="Matrix of RNA-Seq fragment counts for transcripts per condition" />
-		<param type="data" format="fasta" name="transcripts_fasta_file" label="Transcripts fasta file corresponding to matrix" />
-		<param type="float" name="dispersion" value="0.1" min="0" label="dispersion value" help="Dispersion value to be used in the negative binomial" />
-	
-    </inputs>
-    <outputs>
-        
-        <data format="txt" name="diff_expressed_edgeR_results"  label="${tool.name} on ${on_string}: differentially expressed transcripts per pair of conditions"  from_work_dir="edgeR_results/all_diff_expression_results.txt" />
-
-        <data format="txt" name="matrix_FPKM" label="${tool.name} on ${on_string}: matrix.TMM_normalized.FPKM" from_work_dir="edgeR_results/matrix.TMM_normalized.FPKM" />
-
-		<data format="txt" name="TMM_info" label="${tool.name} on ${on_string}: TMM library size estimates" from_work_dir="edgeR_results/TMM_info.txt" />
-	
-	</outputs>
-    <tests>
-
-		<test>
-			<param name="myname" value="This is just a simple test" />
-
-        </test>
-	
-
-    </tests>
-    <help>
-         help info here.
-    </help>
-</tool>
diff -r 1c37a8003755 -r 4eaf6b15b1b2 trinityrnaseq_protocol/trinityToolWrapper.py
--- a/trinityrnaseq_protocol/trinityToolWrapper.py	Mon Sep 28 22:44:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,82 +0,0 @@
-#!/usr/bin/env python
-
-
-# borrowed from: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr and modified for use with Trinity tools.
-
-"""
-Wrapper that execute a program and its arguments but reports standard error
-messages only if the program exit status was not 0
-Example: ./stderr_wrapper.py myprog arg1 -f arg2
-"""
-
-import sys, subprocess, os
-
-assert sys.version_info[:2] >= ( 2, 4 )
-
-TRINITY_BASE_DIR = ""
-if os.environ.has_key('TRINITY_HOME'):
-    TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
-else:
-    sys.stderr.write("You must set the environmental variable TRINITY_BASE_DIR to the base installation directory of Trinity before running this");
-    sys.exit()
-
-
-
-# get bindir
-bindir = sys.argv[0]
-bindir = bindir.split("/")
-if len(bindir) > 1:
-    bindir.pop()
-    bindir = "/".join(bindir)
-else:
-    bindir = "."
-
-
-## add locations of tools to path setting.
-TOOL_PATHS_FILE = bindir + "/__add_to_PATH_setting.txt";
-for line in open(TOOL_PATHS_FILE):
-    line = line.rstrip()
-    os.environ['PATH'] += ":" + line
-
-
-def stop_err( msg ):
-    sys.stderr.write( "%s\n" % msg )
-    sys.exit()
-
-def __main__():
-    # Get command-line arguments
-    args = sys.argv
-    # Remove name of calling program, i.e. ./stderr_wrapper.py
-    args.pop(0)
-    # If there are no arguments left, we're done
-    if len(args) == 0:
-        return
-
-    # If one needs to silence stdout 
-    #args.append( ">" )
-    #args.append( "/dev/null" )
-
-    args[0] = "".join([TRINITY_BASE_DIR, '/', args[0]]);
-
-    cmdline = " ".join(args)
-
-    
-
-    try:
-        # Run program
-        err_capture = open("stderr.txt", 'w')
-        proc = subprocess.Popen( args=cmdline, shell=True, stderr=err_capture, stdout=sys.stdout )
-        returncode = proc.wait()
-        err_capture.close()
-
-        
-        if returncode != 0:
-            raise Exception
-
-    except Exception:
-        # Running Grinder failed: write error message to stderr
-        err_text = open("stderr.txt").readlines()
-        stop_err( "ERROR:\n" + "\n".join(err_text))
-
-
-if __name__ == "__main__": __main__()