Mercurial > repos > mytest > ngsap
changeset 0:0dedb6ecf305 draft default tip
Uploaded
| author | mytest |
|---|---|
| date | Sat, 01 Aug 2015 08:08:50 -0400 |
| parents | |
| children | |
| files | NGSAP-Workflow-Denovo_workflow.ga NGSAP-Workflow-Reference_based_workflow.ga NGSAP-Workflow-Reference_based_workflow.ga~ README.rst README.rst~ abundance_estimates_to_matrix.xml align_and_estimate_abundance.xml all_de_steps.xml blast_parser.xml gtf2fasta.xml insilico_read_normalization.xml pfam_db.loc.sample tool_dependencies.xml tool_dependencies.xml~ transDecoder.xml trinityStats.xml trinityrnaseq.xml |
| diffstat | 17 files changed, 5029 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Sat Aug 01 08:08:50 2015 -0400 @@ -0,0 +1,18 @@ +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 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst~ Sat Aug 01 08:08:50 2015 -0400 @@ -0,0 +1,18 @@ +Introduction +============ + +Welcome to the Home of Next Generation Sequence Analysis Pipelines (NGSAP). Our mission is to provide a user friendly platform for NGS analysis to support Indian researchers working on myriad aspects of life sciences with post processing of the next generation sequencing data. Present portal introduces readers to the 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 + +Two workflows in NGSAP +======================== + +Denovo Assembly and differential gene analysis workflow +======================================================== + +details of the workflow + + +Reference based assembly and differential gene analysis workflow +================================================================= +details of the workflow +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abundance_estimates_to_matrix.xml Sat Aug 01 08:08:50 2015 -0400 @@ -0,0 +1,39 @@ +<tool id='abundance_estimates_to_matrix' name='abundance estimates to matrix' version='1.0'> +<description> Generates combined Matrix for abundance estimates </description> +<!--requirement></requirement--> +<requirements> + <requirement type="package" version="2013_08_14">trinityrnaseq</requirement> + <requirement type="R-module">edgeR</requirement> + <requirement type="set_environment">TRINITY_HOME</requirement> + +</requirements> +<command interpreter='perl'>\$TRINITY_HOME/util/abundance_estimates_to_matrix.pl + --est_method $est_method + #for $i in $isoform_sample: + $i.isoform_sample_matrix + #end for + > $output_log 2>&1; +</command> + +<inputs> + <!-- Required --> + + <param name='est_method' type='select' display="radio" label='Select est_method'> + <option value="RSEM" selected='true'>RSEM</option> + <option value="eXpress">eXpress</option> + </param> + + + <repeat name="isoform_sample" title="Isoform Sample" min="2"> + <param name="isoform_sample_matrix" type="data" label="Isoform Sample Matrix"/> + </repeat> + + <!-- Optional --> + +</inputs> +<outputs> + <data name='matrix_count' format='tabular' label="${tool.name} on ${on_string}: matrix_count" from_work_dir="matrix.counts.matrix"/> + <data name='matrix_fpkm' format='tabular' label="${tool.name} on ${on_string} : matrix_fpkm" from_work_dir="matrix.TMM.fpkm.matrix"/> + <data name='output_log' format='txt' label="${tool.name} on ${on_string} : matrix_log"/> +</outputs> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align_and_estimate_abundance.xml Sat Aug 01 08:08:50 2015 -0400 @@ -0,0 +1,150 @@ +<tool id='id_align_and_estimate_abundance' name='align_and_estimate_abundance' version='1.0'> + +<description>align_and_estimate_abundance</description> + +<requirements> + <requirement type="package" version="2013_08_14">trinityrnaseq</requirement> + <requirement type="package" version="1.1.17">rsem</requirement> + <requirement type="package" version="1.5.1">eXpress</requirement> + <requirement type="package" version="2.1.0">bowtie2</requirement> + <requirement type="package" version="0.12.7">bowtie</requirement> + <requirement type="package" version="0.1.18">samtools</requirement> + <requirement type="set_environment">TRINITY_HOME</requirement> + +</requirements> +<command >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 + +</command> + +<inputs> + +<!-- Required --> +<param name="transcripts" type="data" format="fasta" label="Transcripts [ in fasta format ]" help="--transcripts < string > ; transcript fasta file"/> + +<param name="est_method" type="select" display="radio" label="Choose abundance estimation method" help=""> + <option value="RSEM" selected="True">RSEM</option> + <option value="eXpress">eXpress</option> +</param> + +<param name="aln_method" type="select" display="radio" label="Choose alignment method" help=""> + <option value="bowtie" selected="True">bowtie</option> + <option value="bowtie2">bowtie2</option> +</param> + +<conditional name="reads"> + <param name="paired_or_single" type="select" label="Paired or Single-end reads?"> + <option value="paired">Paired</option> + <option value="single">Single</option> + </param> + + + <when value="paired"> + <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/> + <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/> + + <param name="seqtype" type="select" label="--seqType" help=""> + <option value='fq' selected='true'>fastq</option> + <option value='fa'>fasta</option> + </param> + + <conditional name='optional'> + <param name='use_options' type='select' label='Use Optional parameters?'> + <option value='no'>NO</option> + <option value='yes'>YES</option> + </param> + <when value='no'/> + <when value='yes'> + <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> + </conditional> + </when> + + <when value="single"> + <param format="fastq" name="input" type="data" label="Single-end reads" help=""/> + <param name="seqtype" type="select" label="--seqType" help=""> + <option value='fq' selected='true'>fastq</option> + <option value='fa'>fasta</option> + </param> + + <conditional name='optional'> + <param name='use_options' type='select' label='Use Optional parameters?'> + <option value='no'>NO</option> + <option value='yes'>YES</option> + </param> + <when value='no'/> + <when value='yes'> + <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> + </when> +</conditional> + +</inputs> + +<outputs> + <data format="txt" name="align_and_estimate_abundance_log" label="${tool.name} on ${on_string}: log" /> + <data format="bam" name="bowtie_bam" label="${tool.name} on ${on_string}: bam" from_work_dir="bowtie.bam" /> + <data format="tabular" name="rsem_isoforms" label="${tool.name} on ${on_string}: isoforms" from_work_dir="RSEM.isoforms.results"/> + <data format="tabular" name="rsem_genes" label="${tool.name} on ${on_string}: genes" from_work_dir="RSEM.genes.results"/> +</outputs> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all_de_steps.xml Sat Aug 01 08:08:50 2015 -0400 @@ -0,0 +1,94 @@ +<tool id='differential_expression' name='Differential Expression' version='1.0'> +<description>Generates results for DE </description> +<!--requirement></requirement--> +<requirements> + <requirement type="package" version="2013_08_14">trinityrnaseq</requirement> + <requirement type="set_environment">TRINITY_HOME</requirement> + +</requirements> +<command> + +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 + + >> $output_log 2>&1; + +pwd; +cd .. && zip -r results.zip result_dir; +</command> + +<inputs> + <!-- Required --> + + <param name='est_method' type='select' display="radio" label='Select est_method'> + <option value="RSEM" selected='true'>RSEM</option> + <option value="eXpress">eXpress</option> + </param> + + + <repeat name="isoform_sample" title="Isoform Sample" min="2"> + <param name="sample_name" type="text" label="Sample Name" help="Only alpha-numerical name without space."> + <validator type="empty_field" message="don't leave the field empty!"/> + </param> + <param format="tabular" name="isoform_sample_matrix" type="data" label="Isoform Sample Matrix"/> + </repeat> + + <param name='method' type="select" label="Select Method" > + <option value="edgeR">edgeR</option> + <option value="DESeq">DESeq</option> + <option value="DESeq2">DESeq2</option> + </param> + + + + <!-- Optional --> + +</inputs> +<outputs> + <data name='de_output' format='zip' label="${tool.name} on ${on_string}: compressed_output" from_work_dir="results.zip"/> + <data name='output_log' format='txt' label="${tool.name} on ${on_string} : matrix_log"/> +</outputs> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/blast_parser.xml Sat Aug 01 08:08:50 2015 -0400 @@ -0,0 +1,59 @@ +<?xml version="1.0"?> +<tool id="blast_parser_using_awk" name="BLAST OUTPUT PARSER" version="0.0.1"> + +<description>parses Blast Output File</description> + +<command> + /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; + +</command> + +<inputs> + <param name="blastoutfile" type="data" format="tabular" label="blast output file"/> + <param name="trinityassembledfile" type="data" format="fasta" label="Trinity Assembled [fasta file]" /> + <param name="evalue" type="float" value='1e-05' label="EVALUE" help="default (evalue < = 1e-05)"/> + <param name="qcovs" type="integer" value='95' label="Query Coverage" help="default (qcovs > = 95)"/> +</inputs> + +<outputs> + <data name="parsed_blastfile_above_cutoff" format="tabular" label="parsed_blastfile (Above Cutoff Value)" /> + <data name="parsed_blastfile_below_cutoff" format="tabular" label="parsed_blastfile (Below cutoff Value)" /> + <data name="oneline_file" format="fasta" label="parsed_trinity_assembled_file (oneline_file)" /> + <data name="blastfile_below_cutoff" format="fasta" label="blast fasta file (Below cutoff Value)" /> + <data name="blastfile_above_cutoff" format="fasta" label="blast fasta file (Above cutoff Value)" /> +</outputs> + +<tests/> +<help>blast output parser tool</help> + + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gtf2fasta.xml Sat Aug 01 08:08:50 2015 -0400 @@ -0,0 +1,30 @@ +<tool id='id_gtf2fasta' name='gtf2fasta' version='1.0'> + +<description> + Converts gtf to fasta +</description> + <requirements> + <requirement type="package" version="2.0.9">tophat2</requirement> + </requirements> + +<command >gtf_to_fasta $gtf $genome $fasta</command> + +<inputs> + <param name='gtf' type='data' format="gtf" optional='false' label='gtf_file' help='input gtf file'/> + <param name='genome' type='data' format="fasta" optional='false' label='genome_file' help='input genome'/> +</inputs> + + +<outputs> + <data format='fasta' name='fasta' label='fasta file'/> +</outputs> + + +<help> +**What it does** + Converts gtf file to fasta using reference genome + +</help> + +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/insilico_read_normalization.xml Sat Aug 01 08:08:50 2015 -0400 @@ -0,0 +1,152 @@ +<?xml version="1.0"?> +<tool id="insilico_read_nomalization" name="Insilico Read Normalization" version="0.0.1"> + +<description>Read Normalization</description> +<requirements> + <requirement type="package" version="2013_08_14">trinityrnaseq</requirement> + <requirement type="set_environment">TRINITY_HOME</requirement> + +</requirements> +<command interperter="perl"> \$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 + +</command> + +<inputs> + <param name="JM" type="select" label="JM" help="--JM < string > ; Amount of memory to allocate to Jellyfish for Kmer catalog construction"> + <option value="1G">1G</option> + <option value="10G">10G</option> + <option value="20G">20G</option> + <option value="50G">50G</option> + </param> + + <param name="maximum_coverage" type="integer" value="25" label="Maximum Coverage" help="--max_cov < int > ; targeted maximum coverage for reads"/> + + <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=""/> + + <conditional name="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 value="yes"> + <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="pairs_together" type="boolean" label="--pairs_together" help="process paired reads by averaging stats between pairs and retaining linking info" truevalue="--pairs_together" falsevalue="" checked="true" /> + <param name="CPU" type="integer" value="2" min="1" max="30" label="CPU" help="--CPU < int > ; Number of CPUs to use (Maximum limit is 30 core)" /> + <param name="PARALLEL_STATS" type="boolean" label="--PARALLEL_STATS" help="Generate read stats in parallel for paired reads" truevalue="--PARALLEL_STATS" falsevalue="" checked="true" /> + <param name="KMER_SIZE" type="integer" value="25" label="--KMER SIZE" help="Default is 25" /> + <param name="max_pct_stdev" type="integer" value="200" label="--max_pct_stdev" help="maximum pct of mean for stdev of kmer coverage across read"/> + </when> + </conditional> + </when> + + <when value="single"> + <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/> + + <conditional name="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 value="yes"> + <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> + <param name="CPU" type="integer" value="2" min="1" max="30" label="CPU" help="--CPU < int > ; Number of CPUs to use (Maximum limit is 30 core)" /> + <param name="KMER_SIZE" type="integer" value="25" label="--KMER SIZE" help="Default is 25" /> + <param name="max_pct_stdev" type="integer" value="200" label="--max_pct_stdev" help="maximum pct of mean for stdev of kmer coverage across read"/> + </when> + </conditional> + </when> + </conditional> + + +</inputs> + +<outputs> +<data format="txt" name="insilico_read_normalization_log" label="${tool.name} on ${on_string}: log" /> +<data format="fastq" name="left_normalized_read" label="${tool.name} on ${on_string}: Left Read" from_work_dir="left.norm.fq"/> +<data format="fastq" name="right_normalized_read" label="${tool.name} on ${on_string}: Right Read" from_work_dir="right.norm.fq"/> +</outputs> + + +<tests/> +<help>Insilico Read Normalization</help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pfam_db.loc.sample Sat Aug 01 08:08:50 2015 -0400 @@ -0,0 +1,3 @@ + +###1_name ###2_date ###2_path_to_db +pfam_db.hmm july 2014 /home/username/galaxy-dist/tool-data/pfam_db.hmm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sat Aug 01 08:08:50 2015 -0400 @@ -0,0 +1,336 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="trinityrnaseq" version="2013_08_14"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://ngsaptools.osdd.jnu.ac.in/ngsap/trinityrnaseq_r20140717.tar.gz</action> + <action type="shell_command">make</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + </action> + <action type="set_environment"> + <environment_variable name="TRINITY_HOME" action="set_to">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> + </readme> + </package> + <package name="samtools" version="0.1.18"> + <install version="1.0"> + <actions_group> + <actions os="linux" architecture="i386"> + <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.18-linux-i386.tgz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <actions os="linux" architecture="x86_64"> + <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.18-linux-x86_64.tgz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <actions os="darwin" architecture="i386"> + <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.18-Darwin-i386.tgz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <actions os="darwin" architecture="x86_64"> + <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.18-Darwin-x86_64.tgz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <actions> + <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.18.tar.bz2</action> + <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>samtools</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>libbam.a</source> + <destination>$INSTALL_DIR/lib</destination> + </action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR/include/bam</destination_directory> + </action> + </actions> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable> + <environment_variable name="BAM_ROOT" action="set_to">$INSTALL_DIR</environment_variable> + </action> + </actions_group> + </install> + <readme> + </readme> + </package> +<package name="rsem" version="1.1.17"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://deweylab.biostat.wisc.edu/rsem/src/rsem-1.1.17.tar.gz</action> + <action type="shell_command">make</action> + <action type="make_directory">$INSTALL_DIR/bin/sam</action> + <action type="move_file"> + <source>sam/samtools</source> + <destination>$INSTALL_DIR/bin/sam</destination> + </action> + <action type="move_file"> + <source>convert-sam-for-rsem</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>extract-transcript-to-gene-map-from-trinity</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-bam2readdepth</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-bam2wig</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-build-read-index</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-calculate-credibility-intervals</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-calculate-expression</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-extract-reference-transcripts</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-gen-transcript-plots</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-get-unique</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-parse-alignments</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-plot-model</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-plot-transcript-wiggles</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-prepare-reference</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-preref</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-run-em</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-run-gibbs</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-simulate-reads</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-synthesis-reference-transcripts</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-tbam2gbam</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> + </readme> + </package> + <package name="eXpress" version="1.5.1"> + <install version="1.0"> + <actions_group> + <actions os="linux" architecture="x86_64"> + <action 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type="shell_command">make</action> + <action type="move_file"> + <source>bowtie2</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>bowtie2-align</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>bowtie2-build</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>bowtie2-inspect</source> + <destination>$INSTALL_DIR</destination> + </action> + </actions> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + </action> + </actions_group> + </install> + <readme></readme> + </package> +<package name="tophat2" version="2.0.9"> +<repository toolshed="http://toolshed.g2.bx.psu.edu" name="tophat2" owner="devteam" changeset_revision="ae06af1118dc" /> +</package> +<package name="fastq_groomer" version="1.0.0"> +<repository toolshed="http://toolshed.g2.bx.psu.edu" name="fastq_groomer" owner="devteam" changeset_revision="1298445c852b" /> +</package> +<package name="blast+" version="2.2.29"> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="ncbi_blast_plus" owner="devteam" changeset_revision="2fe07f50a41e" /> + </package> +<package name="cufflinks" version="2.1.1"> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="cufflinks" owner="devteam" changeset_revision="9aab29e159a7" /> + </package> +<package name="cufflinks" version="2.2.1"> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="cuffmerge" owner="devteam" changeset_revision="b6e3849293b1" /> + </package> +</tool_dependency> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/transDecoder.xml Sat Aug 01 08:08:50 2015 -0400 @@ -0,0 +1,120 @@ +<tool id='id_transDecoder' name='transDecoder' version='1.0'> +<description> coding region </description> +<!--requirement></requirement--> +<requirements> + <requirement type="package" version="2013_08_14">trinityrnaseq</requirement> + <requirement type="set_environment">TRINITY_HOME</requirement> + +</requirements> +<command interpreter='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; +</command> + +<inputs> + <!-- Required --> + + <param name='transcript' type='data' label='Transcripts [ in fasta format ]' help=' -t < string > ; Assembled reads in fasta file format'/> + + <!-- Optional --> + + <conditional name='optional'> + <param name='parameters' type='select' label='Use Optional Parameters'> + <option value='no'>NO</option> + <option value='yes'>YES</option> + </param> + <when value='no'/> + <when value='yes'> + <param name='train' type='data' optional='true' label='FASTA file with ORFs to train Markov Mod for protein identification' help='--train < string > ; FASTA file with ORFs to train Markov Mod for protein identification; otherwise longest non-redundant ORFs used' /> + <param name='min_protein_length' type='integer' optional='true' value='100' label='Minimum Protein Length' help='-m < int > ;minimum protein length (default: 100)'/> + <param name='genetic_code' type='select' optional='true' label='Select Genetic Code' help=' -G < string > ; genetic code (default is "universal")'> + <option value='universal' selected='true'>Universal</option> + <option value='Euplotes'>Euplotes</option> + <option value='Tetrahymena'>Tetrahymena</option> + <option value='Candida'>Candida</option> + <option value='Acetabularia'>Acetabularia</option> + </param> + <param name='strand-specific' type='boolean' truevalue='-S' falsevalue='' optional='true' label='Strand-Specific [ -S ]' help='strand-specific (only analyzes top strand)'/> + <param name='lottmm' type='integer' optional='true' value='500' label=' -T ; Needs a label ??? ' help='-T < int > ; If no --train, top longest ORFs to train Markov Model (hexamer stats) (default: 500)'/> + <param name='retain_long_orfs' type="integer" optional='true' value="900" label=' --retain_long_orfs ; Needs a label ??? ' help='--retain_long_orfs < int > ; Retain all ORFs found that are equal or longer than these many nucleotides even if no other evidence marks it as coding (default: 900 bp => 300aa)' /> + </when> + </conditional> + + + <!-- Pfam Options --> + + <conditional name='pfam'> + <param name='options' type='select' label='Use Pfam Options [ Optional ]'> + <option value='no'>NO</option> + <option value='yes'>YES</option> + </param> + <when value='no'/> + <when value='yes'> + <param name='pfam_db' type='select' label='Search pfam database' help=' --search_pfam < pfam_db.hmm > ; /path/to/pfam_db.hmm to search using hmmscan'> + <options from_file="pfam_db.loc"> + <column name="name" index="0"/> + <column name="value" index="2"/> + </options> + </param> + <param name='CPU' type='integer' value='2' label='CPU' help='--CPU < int > Number of CPU for the job'/> + </when> + </conditional> + +</inputs> +<outputs> + <data name='transdecoder_pep' format='fasta' label="${tool.name} on ${on_string}: pep" from_work_dir="transcript.transdecoder.pep"/> + <data name='transdecoder_cds' format='fasta' label="${tool.name} on ${on_string}: cds" from_work_dir="transcript.transdecoder.cds"/> + <data name='transdecoder_bed' format='bed' label="${tool.name} on ${on_string}: bed" from_work_dir="transcript.transdecoder.bed"/> + <data name='transdecoder_gff3' format='tabular' label="${tool.name} on ${on_string}: gff3" from_work_dir="transcript.transdecoder.gff3"/> + <data name='transdecoder_mRNA' format='fasta' label="${tool.name} on ${on_string}: mRNA" from_work_dir="transcript.transdecoder.mRNA"/> + <data name='transdecoder_log' format='txt' label="${tool.name} on ${on_string}: log" /> +</outputs> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trinityStats.xml Sat Aug 01 08:08:50 2015 -0400 @@ -0,0 +1,25 @@ +<tool id='id_trinity_stats' name='Trinity Stats' version='1.0'> +<description> check stats... </description> + +<requirements> + <requirement type="package" version="2013_08_14">trinityrnaseq</requirement> + <requirement type="set_environment">TRINITY_HOME</requirement> + +</requirements> +<command >perl \$TRINITY_HOME/util/TrinityStats.pl $fastafile +> $statsfile 2>&1; +</command> + +<inputs> + <!-- Required --> + + <param name='fastafile' type="data" format="fasta" label='fastafile' help='Assembled fasta file'> + </param> + + <!-- Optional --> + +</inputs> +<outputs> +<data name='statsfile' format='text' label="${tool.name} on ${on_string}: "/> +</outputs> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trinityrnaseq.xml Sat Aug 01 08:08:50 2015 -0400 @@ -0,0 +1,129 @@ +<tool id="trinityrnaseq" name="Trinity" version="0.0.1"> + + <!-- Written by Jeremy Goecks, now maintained here by bhaas --> + <description>De novo assembly of RNA-Seq data Using Trinity</description> + <requirements> + <requirement type="package" version="2013_08_14">trinityrnaseq</requirement> + <requirement type="set_environment">TRINITY_HOME</requirement> + +</requirements> + <command> + \$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 + + </command> + <inputs> + <param name="JM" type="select" label="JM" help="Amount of memory to allocate to Jellyfish for Kmer catalog construction"> + <option value="1G">1G</option> + <option value="10G">10G</option> + <option value="50G">50G</option> + <option value="100G">100G</option> + <option value="200G">200G</option> + <option value="500G">500G</option> + </param> + + <param name="CPU" type="integer" value="2" min="1" label="CPU" help="Number of CPUs to use by Trinity" /> + + + <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="group_pairs_distance" type="integer" value="500" min="1" label="Group pairs distance" help="Maximum length expected between fragment pairs"/> + <param name="path_reinforcement_distance" type="integer" value="75" min="1" label="Path reinforcement distance" help="Minimum read overlap required for path extension in the graph" /> + + </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> + <param name="path_reinforcement_distance" type="integer" value="40" min="1" label="Path reinforcement distance" help="Minimum read overlap required for path extension in the graph" /> + </when> + </conditional> + + <conditional name="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="min_kmer_cov" type="integer" value="1" min="1" label="inchworm_min_kmer_cov" help="Minimum kmer coverage required by Inchworm for initial contig construction" /> + <param name="max_reads_per_graph" type="integer" value="20000000" min="10000" label="chrysalis_max_reads_per_graph" help="Maximum number of reads to be anchored within each transcript graph by Chrysalis" /> + + + <param name="bfly_opts" type="text" value="None" label="bfly_opts" help="Options to pass on to Butterfly" /> + <param name="bflyHeapSpaceMax" type="select" label="bflyHeapSpaceMax" help="Java heap space maximum value for Butterfly"> + <option value="1G">1G</option> + <option value="2G">2G</option> + <option value="4G" selected="true">4G</option> + <option value="10G">10G</option> + <option value="20G">20G</option> + </param> + + <param name="min_contig_length" type="integer" value="200" min="1" label="Minimum Contig Length" help=""/> + </when> + </conditional> + + + </inputs> + <outputs> + <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /> + <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/> + </outputs> + <tests> + </tests> + <help> + 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 + </help> +</tool>