# HG changeset patch
# User vipints
# Date 1340825711 14400
# Node ID 8ab01cc29c4b4b0bc72a03e014d17abae31efcdc
# Parent  94a108763d9e96cbbc8c780e362c7cba527d9eca
Uploaded

diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/._README
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/._setup_deseq-hts.sh
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/README
--- a/deseq-hts_1.0/README	Wed May 09 20:43:47 2012 -0400
+++ b/deseq-hts_1.0/README	Wed Jun 27 15:35:11 2012 -0400
@@ -1,5 +1,5 @@
 ---------------------------------------------------
-DESeq-hts: A Galaxy wrapper for DESeq version 1.6.0
+DESeq-hts: A Galaxy wrapper for DESeq version 1.6.1
 ---------------------------------------------------
 
 Description:
diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/bin/._deseq_config.sh
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/bin/._genarglist.sh
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/bin/._genes_cell2struct
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/bin/._get_read_counts
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/bin/._start_interpreter.sh
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/galaxy/._deseq.xml
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/galaxy/deseq.xml
--- a/deseq-hts_1.0/galaxy/deseq.xml	Wed May 09 20:43:47 2012 -0400
+++ b/deseq-hts_1.0/galaxy/deseq.xml	Wed Jun 27 15:35:11 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="deseq-hts" name="DESeq" version="1.6.0">
+<tool id="deseq-hts" name="DESeq" version="1.6.1">
   <description>Determines differentially expressed transcripts from read alignments</description>
   <command> 
 deseq-hts/src/deseq-hts.sh $anno_input_selected $deseq_out $deseq_out.extra_files_path/gene_map.mat 
@@ -6,6 +6,7 @@
 #for $j in $i.replicates
 $j.bam_alignment:#slurp
 #end for
+
 #end for
     >> $Log_File </command>
   <inputs>
diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/mex/._Makefile
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/mex/._get_bam_properties.cpp
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/mex/._get_reads.cpp
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/mex/._get_reads_direct.cpp
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/mex/._get_reads_direct.h
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/mex/._interval_overlap.cpp
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/mex/._mex_input.cpp
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/mex/._mex_input.h
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/mex/._read.cpp
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/mex/._read.h
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/src/._deseq-hts.sh
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/src/._deseq_config.m
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/src/._difftest_deseq.R
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/src/._genes_cell2struct.m
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/src/._get_read_counts.m
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/src/._mask_dubl.m
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/src/._remove_reads_from_other_genes.m
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/src/deseq-hts.sh
--- a/deseq-hts_1.0/src/deseq-hts.sh	Wed May 09 20:43:47 2012 -0400
+++ b/deseq-hts_1.0/src/deseq-hts.sh	Wed Jun 27 15:35:11 2012 -0400
@@ -68,7 +68,7 @@
 tmpfile=`mktemp --tmpdir=/tmp`
 
 echo "${DIR}/../bin/get_read_counts ${GENES_FN} $tmpfile $@"
-${DIR}/../bin/get_read_counts ${GENES_FN} $tmpfile $@ 2>&1
+${DIR}/../bin/get_read_counts ${GENES_FN} $tmpfile "$@" 2>&1
 
 echo
 echo %%%%%%%%%%%%%%%%%%%%%%%%%%%
diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/test_data/._deseq_c_elegans_WS200-I-regions-SRX001872.bam
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/test_data/._deseq_c_elegans_WS200-I-regions-SRX001872.bam.bai
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/test_data/._deseq_c_elegans_WS200-I-regions-SRX001875.bam
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/test_data/._deseq_c_elegans_WS200-I-regions-SRX001875.bam.bai
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/test_data/._deseq_c_elegans_WS200-I-regions.gff3
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/test_data/._deseq_c_elegans_WS200-I-regions.info
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/test_data/._deseq_c_elegans_WS200-I-regions_deseq.txt
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/test_data/._genes.mat
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/tools/._ParseGFF.py
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/tools/._determine_engine.m
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/tools/._separate.m
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diff -r 94a108763d9e -r 8ab01cc29c4b deseq-hts_1.0/tools/ParseGFF.py
--- a/deseq-hts_1.0/tools/ParseGFF.py	Wed May 09 20:43:47 2012 -0400
+++ b/deseq-hts_1.0/tools/ParseGFF.py	Wed Jun 27 15:35:11 2012 -0400
@@ -342,7 +342,7 @@
 
 def __main__():
     """This function provides a best way to extract genome feature 
-       information from a GFF3 file for the rQuant downstream processing.
+       information from a GFF3 file for the downstream processing.
     """
     try:
         gff_file = sys.argv[1]