# HG changeset patch
# User gkumar09
# Date 1443492156 14400
# Node ID 0845cefc6cfe0b1f592a438e1d894270d750ace0
# Parent ecf8be6538f84485d498cc22cb44714e33d779dc
Deleted selected files
diff -r ecf8be6538f8 -r 0845cefc6cfe Final/alignreads.xml
--- a/Final/alignreads.xml Mon Sep 28 22:02:25 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,138 +0,0 @@
-
-
- alignReads: short read alignment tool wrapper
-
- trinity
-
-
-
- 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
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- .. _Trinity: http://trinityrnaseq.sourceforge.net
-
-
diff -r ecf8be6538f8 -r 0845cefc6cfe Final/analyze_diff_exp.xml
--- a/Final/analyze_diff_exp.xml Mon Sep 28 22:02:25 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,41 +0,0 @@
-
-
- Analyze differential expression
-
- trinity
-
-
-
- analyze_diff_exp_wrapper.py $EdgeRTarGz $TMM_Matrix_FPKM $Pvalue $Cvalue
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- .. _Trinity: http://trinityrnaseq.sourceforge.net
-
-
diff -r ecf8be6538f8 -r 0845cefc6cfe Final/analyze_diff_exp_wrapper.py
--- a/Final/analyze_diff_exp_wrapper.py Mon Sep 28 22:02:25 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 ecf8be6538f8 -r 0845cefc6cfe Final/cat.xml
--- a/Final/cat.xml Mon Sep 28 22:02:25 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,41 +0,0 @@
-
- tail-to-head
-
- bash_command_executer.py cat
- $input1
- #for $q in $queries
- ${q.input2}
- #end for
- > $out_file1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- no help
-
-
-
diff -r ecf8be6538f8 -r 0845cefc6cfe Final/diffExpress_edgeR.xml
--- a/Final/diffExpress_edgeR.xml Mon Sep 28 22:02:25 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,47 +0,0 @@
-
-
- Identify Differentially Expressed Transcripts Using EdgeR
-
- edgeR
-
-
-
- trinityToolWrapper.py Analysis/DifferentialExpression/run_EdgeR.pl
- --matrix $counts_matrix
- --transcripts $transcripts_fasta_file
- --output edgeR_results
- --dispersion $dispersion
-
- > stdout.txt
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- help info here.
-
-