# HG changeset patch
# User gkumar09
# Date 1443492190 14400
# Node ID 9be8023b486a281dc5acb12575e21441685e5fa1
# Parent  0845cefc6cfe0b1f592a438e1d894270d750ace0
Deleted selected files

diff -r 0845cefc6cfe -r 9be8023b486a Final/EdgeR_differentialExpression.xml
--- a/Final/EdgeR_differentialExpression.xml	Mon Sep 28 22:02:36 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 0845cefc6cfe -r 9be8023b486a Final/EdgeR_differentialExpression_wrapper.py
--- a/Final/EdgeR_differentialExpression_wrapper.py	Mon Sep 28 22:02:36 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 0845cefc6cfe -r 9be8023b486a Final/RSEM_estimates_to_matrix.xml
--- a/Final/RSEM_estimates_to_matrix.xml	Mon Sep 28 22:02:36 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 0845cefc6cfe -r 9be8023b486a Final/abundance_estimation_to_matrix.xml
--- a/Final/abundance_estimation_to_matrix.xml	Mon Sep 28 22:02:36 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 0845cefc6cfe -r 9be8023b486a Final/abundance_estimation_to_matrix_wrapper.py
--- a/Final/abundance_estimation_to_matrix_wrapper.py	Mon Sep 28 22:02:36 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 0845cefc6cfe -r 9be8023b486a Final/align_and_estimate_abundance.xml
--- a/Final/align_and_estimate_abundance.xml	Mon Sep 28 22:02:36 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>