# HG changeset patch
# User mytest
# Date 1440768353 14400
# Node ID afd60bca5f67684264bb484688a36612bedee8b9
# Parent 04df17578afd015990c0cf25190c5b01bbee3005
Deleted selected files
diff -r 04df17578afd -r afd60bca5f67 NGSAP-Workflow-Denovo_workflow.ga
--- a/NGSAP-Workflow-Denovo_workflow.ga Fri Aug 28 09:25:16 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,792 +0,0 @@
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diff -r 04df17578afd -r afd60bca5f67 NGSAP-Workflow-Denovo_workflow.ga~
--- a/NGSAP-Workflow-Denovo_workflow.ga~ Fri Aug 28 09:25:16 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,792 +0,0 @@
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diff -r 04df17578afd -r afd60bca5f67 NGSAP-Workflow-Reference_based_workflow.ga
--- a/NGSAP-Workflow-Reference_based_workflow.ga Fri Aug 28 09:25:16 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1364 +0,0 @@
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diff -r 04df17578afd -r afd60bca5f67 NGSAP-Workflow-Reference_based_workflow.ga~
--- a/NGSAP-Workflow-Reference_based_workflow.ga~ Fri Aug 28 09:25:16 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1364 +0,0 @@
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diff -r 04df17578afd -r afd60bca5f67 README.rst
--- a/README.rst Fri Aug 28 09:25:16 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-Introduction
-============
-
-Next Generation Sequence Analysis Pipelines (NGSAP) is to provide a user friendly platform for NGS analysis to support researchers working on myriad aspects of life sciences with post processing of the next generation sequencing data. It has beed designed specifically for transcriptomics tools available through Galaxy for data analysis which can be translated into meaningful scientific publications. NGSAP is an initiative of NGSAP team working in School of Computational and Integrative Sciences at Jawaharlal Nehru University, Delhi
-
-NGSAP provides two worlflows
-
-
-Denovo Assembly and differential gene analysis workflow
-========================================================
-
-details of the workflow
-
-
-Reference based assembly and differential gene analysis workflow
-=================================================================
-details of the workflow
-
diff -r 04df17578afd -r afd60bca5f67 abundance_estimates_to_matrix.xml
--- a/abundance_estimates_to_matrix.xml Fri Aug 28 09:25:16 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-
- Generates combined Matrix for abundance estimates
-
-
- trinityrnaseq
- edgeR
- TRINITY_HOME
-
-
-\$TRINITY_HOME/util/abundance_estimates_to_matrix.pl
- --est_method $est_method
- #for $i in $isoform_sample:
- $i.isoform_sample_matrix
- #end for
- > $output_log 2>&1;
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff -r 04df17578afd -r afd60bca5f67 align_and_estimate_abundance.xml
--- a/align_and_estimate_abundance.xml Fri Aug 28 09:25:16 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,150 +0,0 @@
-
-
-align_and_estimate_abundance
-
-
- trinityrnaseq
- rsem
- eXpress
- bowtie2
- bowtie
- samtools
- TRINITY_HOME
-
-
-perl \$TRINITY_HOME/util/align_and_estimate_abundance.pl
- --transcripts $transcripts
- --est_method $est_method
- --aln_method $aln_method
- --prep_reference
-
- ## Inputs.
- #if str($reads.paired_or_single) == "paired":
-
- --left $reads.left_input --right $reads.right_input
-
- #if $reads.left_input.ext == 'fa':
- --seqType fa
- #else:
- --seqType fq
- #end if
-
- ## Additional parameters.
- #if str($reads.optional.use_options) == "yes":
-
- #if str($reads.optional.library_type) != "None":
- --SS_lib_type $reads.optional.library_type
- #end if
-
-
-
- #end if
-
- #else:
- --single $reads.input
-
- #if str($reads.input.ext) == 'fa':
- --seqType fa
- #else:
- --seqType fq
- #end if
-
- ## Additional parameters.
- #if str($reads.optional.use_option) == "yes":
-
- #if str($reads.additional_params.library_type) != "None":
- --SS_lib_type $reads.optional.library_type
- #end if
-
- #end if
- #end if
-
-## direct to output
-> $align_and_estimate_abundance_log 2>&1;samtools sort bowtie.bam bowtie_sorted
-
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diff -r 04df17578afd -r afd60bca5f67 all_de_steps.xml
--- a/all_de_steps.xml Fri Aug 28 09:25:16 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,94 +0,0 @@
-
-Generates results for DE
-
-
- trinityrnaseq
- TRINITY_HOME
-
-
-
-
-echo -e "Differential Expression Log File" > $output_log 2>&1;
-
-## Step 0: preprocess input_file preparaton
-
- #for $i in $isoform_sample:
- cp -s $i.isoform_sample_matrix $i.sample_name;
- #end for;
-
-
-## Step 1: abundance_estimates_to_matrix
-echo -e "" >> $output_log 2>&1;
-echo -e "\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#" >> $output_log 2>&1;
-echo -e "\#\# Step 1: abundance_estimates_to_matrix" >> $output_log 2>&1;
-echo -e "" >> $output_log 2>&1;
-
-
-perl \$TRINITY_HOME/util/abundance_estimates_to_matrix.pl
- --est_method $est_method
- #for $i in $isoform_sample:
- $i.sample_name
- #end for
- >> $output_log 2>&1;
-
-
-## Step 2: run_DE_analysis
-echo -e "" >> $output_log 2>&1;
-echo -e "\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#" >> $output_log 2>&1;
-echo -e "\#\# Step 2: run_DE_analysis" >> $output_log 2>&1;
-echo -e "" >> $output_log 2>&1;
-
-perl \$TRINITY_HOME/Analysis/DifferentialExpression/run_DE_analysis.pl
- --matrix matrix.counts.matrix
- --method $method
- --output result_dir
- >> $output_log 2>&1;
-
-## Step 3: analyze_diff_expr
-echo -e "" >> $output_log 2>&1;
-echo -e "\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#" >> $output_log 2>&1;
-echo -e "\#\# Step 3: analyze_diff_expr" >> $output_log 2>&1;
-echo -e "" >> $output_log 2>&1;
-
-cd result_dir && perl \$TRINITY_HOME/Analysis/DifferentialExpression/analyze_diff_expr.pl
-
- --matrix ../matrix.TMM.fpkm.matrix
-
- >> $output_log 2>&1;
-
-pwd;
-cd .. && zip -r results.zip result_dir;
-
-
-
-
-
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-
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diff -r 04df17578afd -r afd60bca5f67 blast_parser.xml
--- a/blast_parser.xml Fri Aug 28 09:25:16 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,59 +0,0 @@
-
-
-
-parses Blast Output File
-
-
- /bin/awk
- 'BEGIN {FS="\t"} {if($11 <= $evalue && $13 >= $qcovs) print $0 }'
- $blastoutfile
- > $parsed_blastfile_above_cutoff;
-
- /bin/awk
- '{FS="\t"} {if($11 > $evalue || $13 < $qcovs) print $0 }'
- $blastoutfile
- > $parsed_blastfile_below_cutoff;
-
- /bin/sed -e '/^>/s/$/@@@@/' -e 's/^>/#/' $trinityassembledfile
- | tr -d '\n'
- | tr "#" '\n'
- | sed -e 's/^/>/' -e 's/@@@@/\n/'
- | sed -e "1d"
- > $oneline_file;
-
- /bin/awk
- 'BEGIN {FS="|"} {print "grep -w -A 1 \""$1"\" $oneline_file >> $blastfile_below_cutoff"}'
- $parsed_blastfile_below_cutoff
- > pick_below_sh;
-
- /bin/sh pick_below_sh;
-
- /bin/awk
- 'BEGIN {FS="|"} {print "grep -w -A 1 \""$1"\" $oneline_file >> $blastfile_above_cutoff"}'
- $parsed_blastfile_above_cutoff
- > pick_above_sh;
-
- /bin/sh pick_above_sh;
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-blast output parser tool
-
-
-
diff -r 04df17578afd -r afd60bca5f67 gtf2fasta.xml
--- a/gtf2fasta.xml Fri Aug 28 09:25:16 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-
-
-
- Converts gtf to fasta
-
-
- tophat2
-
-
-gtf_to_fasta $gtf $genome $fasta
-
-
-
-
-
-
-
-
-
-
-
-
-
-**What it does**
- Converts gtf file to fasta using reference genome
-
-
-
-
-
diff -r 04df17578afd -r afd60bca5f67 insilico_read_normalization.xml
--- a/insilico_read_normalization.xml Fri Aug 28 09:25:16 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,152 +0,0 @@
-
-
-
-Read Normalization
-
- trinityrnaseq
- TRINITY_HOME
-
-
- \$TRINITY_HOME/util/insilico_read_normalization.pl
---JM $JM
---max_cov $maximum_coverage
-
-## Inputs.
-#if str($inputs.paired_or_single) == "paired":
-
- --left $inputs.left_input --right $inputs.right_input
-
- #if $inputs.left_input.ext == 'fa':
- --seqType fa
- #else:
- --seqType fq
- #end if
-
- ## Additional parameters.
- #if str($inputs.additional_params.use_additional) == "yes":
-
- #if str($inputs.additional_params.library_type) != "None":
- --SS_lib_type $inputs.additional_params.library_type
- #end if
-
- $inputs.additional_params.pairs_together
- --CPU $inputs.additional_params.CPU
- $inputs.additional_params.PARALLEL_STATS
- --KMER_SIZE $inputs.additional_params.KMER_SIZE
- --max_pct_stdev $inputs.additional_params.max_pct_stdev
-
- #end if
-
-
-#else:
-
- --single $inputs.input
-
- #if str($inputs.input.ext) == 'fa':
- --seqType fa
- #else:
- --seqType fq
- #end if
-
- ## Additional parameters.
- #if str($inputs.additional_params.use_additional) == "yes":
-
- #if str($inputs.additional_params.library_type) != "None":
- --SS_lib_type $inputs.additional_params.library_type
- #end if
-
- ##$inputs.additional_params.pairs_together
- --CPU $inputs.additional_params.CPU
- ##$inputs.additional_params.PARALLEL_STATS
- --KMER_SIZE $inputs.additional_params.KMER_SIZE
- --max_pct_stdev $inputs.additional_params.max_pct_stdev
-
- #end if
-
-#end if
-
-
-
-## direct to output
-> $insilico_read_normalization_log 2>&1
-
-
-
-
-
-
-
-
-
-
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-Insilico Read Normalization
-
-
diff -r 04df17578afd -r afd60bca5f67 pfam_db.loc.sample
--- a/pfam_db.loc.sample Fri Aug 28 09:25:16 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-
-###1_name ###2_date ###2_path_to_db
-pfam_db.hmm july 2014 /home/username/galaxy-dist/tool-data/pfam_db.hmm
diff -r 04df17578afd -r afd60bca5f67 tool_dependencies.xml
--- a/tool_dependencies.xml Fri Aug 28 09:25:16 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,336 +0,0 @@
-
-
-
-
-
- http://ngsaptools.osdd.jnu.ac.in/ngsap/trinityrnaseq_r20140717.tar.gz
- make
-
- .
- $INSTALL_DIR
-
-
- $INSTALL_DIR
-
-
- $INSTALL_DIR
-
-
-
-
-
-
-
-
-
-
- http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.18-linux-i386.tgz
-
- .
- $INSTALL_DIR
-
-
-
- http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.18-linux-x86_64.tgz
-
- .
- $INSTALL_DIR
-
-
-
- http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.18-Darwin-i386.tgz
-
- .
- $INSTALL_DIR
-
-
-
- http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.18-Darwin-x86_64.tgz
-
- .
- $INSTALL_DIR
-
-
-
- http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.18.tar.bz2
- sed -i.bak 's/-lcurses/-lncurses/' Makefile
- make
-
- samtools
- $INSTALL_DIR/bin
-
-
- libbam.a
- $INSTALL_DIR/lib
-
-
- .
- $INSTALL_DIR/include/bam
-
-
-
- $INSTALL_DIR/bin
- $INSTALL_DIR/lib
- $INSTALL_DIR
-
-
-
-
-
-
-
-
-
- http://deweylab.biostat.wisc.edu/rsem/src/rsem-1.1.17.tar.gz
- make
- $INSTALL_DIR/bin/sam
-
- sam/samtools
- $INSTALL_DIR/bin/sam
-
-
- convert-sam-for-rsem
- $INSTALL_DIR/bin
-
-
- extract-transcript-to-gene-map-from-trinity
- $INSTALL_DIR/bin
-
-
- rsem-bam2readdepth
- $INSTALL_DIR/bin
-
-
- rsem-bam2wig
- $INSTALL_DIR/bin
-
-
- rsem-build-read-index
- $INSTALL_DIR/bin
-
-
- rsem-calculate-credibility-intervals
- $INSTALL_DIR/bin
-
-
- rsem-calculate-expression
- $INSTALL_DIR/bin
-
-
- rsem-extract-reference-transcripts
- $INSTALL_DIR/bin
-
-
- rsem-gen-transcript-plots
- $INSTALL_DIR/bin
-
-
- rsem-get-unique
- $INSTALL_DIR/bin
-
-
- rsem-parse-alignments
- $INSTALL_DIR/bin
-
-
- rsem-plot-model
- $INSTALL_DIR/bin
-
-
- rsem-plot-transcript-wiggles
- $INSTALL_DIR/bin
-
-
- rsem-prepare-reference
- $INSTALL_DIR/bin
-
-
- rsem-preref
- $INSTALL_DIR/bin
-
-
- rsem-run-em
- $INSTALL_DIR/bin
-
-
- rsem-run-gibbs
- $INSTALL_DIR/bin
-
-
- rsem-simulate-reads
- $INSTALL_DIR/bin
-
-
- rsem-synthesis-reference-transcripts
- $INSTALL_DIR/bin
-
-
- rsem-tbam2gbam
- $INSTALL_DIR/bin
-
-
- $INSTALL_DIR/bin
-
-
-
-
-
-
-
-
-
-
- http://bio.math.berkeley.edu/eXpress/downloads/express-1.5.1/express-1.5.1-linux_x86_64.tgz
-
- .
- $INSTALL_DIR/bin
-
-
-
- http://bio.math.berkeley.edu/eXpress/downloads/express-1.5.1/express-1.5.1-macosx_x86_64.tgz
-
- .
- $INSTALL_DIR/bin
-
-
-
- http://bio.math.berkeley.edu/eXpress/downloads/express-1.5.1/express-1.5.1-src.tgz
- cmake src -DCMAKE_INSTALL_PREFIX:PATH=$INSTALL_DIR
- make && make install
-
-
- $INSTALL_DIR/bin
-
-
-
-
-
-
-
-
-
- http://depot.galaxyproject.org/package/linux/x86_64/bowtie/bowtie-0.12.7-linux-x86_64.tgz
-
- .
- $INSTALL_DIR
-
-
-
- http://depot.galaxyproject.org/package/darwin/x86_64/bowtie/bowtie-0.12.7-macos-10.5-x86_64.tgz
-
- .
- $INSTALL_DIR
-
-
-
- http://depot.galaxyproject.org/package/linux/i386/bowtie/bowtie-0.12.7-linux-i386.tgz
-
- .
- $INSTALL_DIR
-
-
-
- http://depot.galaxyproject.org/package/darwin/i386/bowtie/bowtie-0.12.7-macos-10.5-i386.tgz
-
- .
- $INSTALL_DIR
-
-
-
- http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.7/bowtie-0.12.7-src.zip
- make
-
- bowtie
- $INSTALL_DIR
-
-
- bowtie-build
- $INSTALL_DIR
-
-
- bowtie-inspect
- $INSTALL_DIR
-
-
-
- $INSTALL_DIR
-
-
-
-
-
-
-
-
-
- http://depot.galaxyproject.org/package/linux/x86_64/bowtie2/bowtie2-2.1.0-linux-x86_64.tgz
-
- .
- $INSTALL_DIR
-
-
-
- http://depot.galaxyproject.org/package/darwin/x86_64/bowtie2/bowtie2-2.1.0-macos-x86_64.tgz
-
- .
- $INSTALL_DIR
-
-
-
- http://depot.galaxyproject.org/package/linux/i386/bowtie2/bowtie2-2.1.0-linux-i386.tgz
-
- .
- $INSTALL_DIR
-
-
-
- http://depot.galaxyproject.org/package/darwin/i386/bowtie2/bowtie2-2.1.0-macos-i386.tgz
-
- .
- $INSTALL_DIR
-
-
-
- http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.1.0/bowtie2-2.1.0-source.zip
- make
-
- bowtie2
- $INSTALL_DIR
-
-
- bowtie2-align
- $INSTALL_DIR
-
-
- bowtie2-build
- $INSTALL_DIR
-
-
- bowtie2-inspect
- $INSTALL_DIR
-
-
-
- $INSTALL_DIR
-
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diff -r 04df17578afd -r afd60bca5f67 transDecoder.xml
--- a/transDecoder.xml Fri Aug 28 09:25:16 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,120 +0,0 @@
-
- coding region
-
-
- trinityrnaseq
- TRINITY_HOME
-
-
-perl \$TRINITY_HOME/trinity-plugins/transdecoder/TransDecoder
-
- -t $transcript
-
- #if str($optional.parameters) == 'yes':
- #if ($train):
- --train $train
- #end if
-
- #if ($min_protein_length):
- -m $min_protein_length
- #end if
-
- #if ($genetic_code):
- -G $genetic_code
- #end if
-
- #if ($strand-specific):
- $strand-specific
- #end if
-
- #if ($lottmn):
- -T $lottmm
- #end if
-
- #if ($retain_long_orfs):
- --retain_long_orfs $retain_long_orfs
- #end if
- #end if
-
- #if str($pfam.options) == 'yes':
- #if ($pfam_db):
- --search_pfam $pfam_db
- #end if
-
- #if ($CPU):
- --CPU $CPU
- #end if
- #end if
-
- ##log file
- > $transdecoder_log 2>&1;
-
-
- ## output renaming
-
- cp -s dataset_*.dat.transdecoder.pep transcript.transdecoder.pep;
- cp -s dataset_*.dat.transdecoder.cds transcript.transdecoder.cds;
- cp -s dataset_*.dat.transdecoder.bed transcript.transdecoder.bed;
- cp -s dataset_*.dat.transdecoder.gff3 transcript.transdecoder.gff3;
- cp -s dataset_*.dat.transdecoder.mRNA transcript.transdecoder.mRNA;
-
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diff -r 04df17578afd -r afd60bca5f67 trinityStats.xml
--- a/trinityStats.xml Fri Aug 28 09:25:16 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-
- check stats...
-
-
- trinityrnaseq
- TRINITY_HOME
-
-
-perl \$TRINITY_HOME/util/TrinityStats.pl $fastafile
-> $statsfile 2>&1;
-
-
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diff -r 04df17578afd -r afd60bca5f67 trinityrnaseq.xml
--- a/trinityrnaseq.xml Fri Aug 28 09:25:16 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,129 +0,0 @@
-
-
-
- De novo assembly of RNA-Seq data Using Trinity
-
- trinityrnaseq
- TRINITY_HOME
-
-
-
- \$TRINITY_HOME/Trinity --JM $JM --CPU $CPU
-
- ## Inputs.
- #if str($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
- --group_pairs_distance $inputs.group_pairs_distance
- #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 $inputs.library_type
- #end if
- #end if
-
- ## Additional parameters.
- #if str($additional_params.use_additional) == "yes":
- --min_kmer_cov $inputs.min_kmer_cov --max_reads_per_graph $inputs.max_reads_per_graph --bflyHeapSpaceMax $input.bflyHeapSpaceMax
- #if $inputs.bfly_opts != 'None':
- --bfly_opts " $inputs.bfly_opts "
- #end if
- #end if
-
-
- ## direct to output
- > $trinity_log 2>&1
-
-
-
-
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- Trinity is a de novo transcript assembler that uses RNA-seq data as input. This tool runs all Trinity_ commands--Inchworm, Chrysalis, and Butterfly--in a single pass.
-
- .. _Trinity: http://trinityrnaseq.sourceforge.net
-
-