Mercurial > repos > gkumar09 > trinityrnaseq_protocol
changeset 26:9af2f4621bb1 draft
Uploaded
| author | gkumar09 |
|---|---|
| date | Fri, 23 Oct 2015 12:02:09 -0400 |
| parents | 3f4a1c58e722 |
| children | 0bb2b5dc3a53 |
| files | trinityrnaseq_protocol/._RSEM_estimates_to_matrix.xml trinityrnaseq_protocol/EdgeR_differentialExpression.xml trinityrnaseq_protocol/EdgeR_differentialExpression_wrapper.py trinityrnaseq_protocol/abundance_estimation_to_matrix.xml trinityrnaseq_protocol/abundance_estimation_to_matrix_wrapper.py trinityrnaseq_protocol/align_and_estimate_abundance.xml trinityrnaseq_protocol/align_and_estimate_abundance.xml~ trinityrnaseq_protocol/analyze_diff_exp.xml trinityrnaseq_protocol/analyze_diff_exp_wrapper.py trinityrnaseq_protocol/concatanate.xml trinityrnaseq_protocol/trinityToolWrapper.py trinityrnaseq_protocol/trinityrnaseq.xml |
| diffstat | 12 files changed, 698 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trinityrnaseq_protocol/EdgeR_differentialExpression.xml Fri Oct 23 12:02:09 2015 -0400 @@ -0,0 +1,40 @@ +<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="counts_matrix" value="matrix_text_file" /> + <param name="transcript_fasta_file" value="fasta_file" /> + <param name="dispersion" value="0.1" /> + <output name="EdgeR_Archive" file="EdgeR_Results.tar.gz" /> + </test> + + + </tests> + <help> + help info here. + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trinityrnaseq_protocol/EdgeR_differentialExpression_wrapper.py Fri Oct 23 12:02:09 2015 -0400 @@ -0,0 +1,40 @@ +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)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trinityrnaseq_protocol/abundance_estimation_to_matrix.xml Fri Oct 23 12:02:09 2015 -0400 @@ -0,0 +1,39 @@ +<tool id="abundance_estimation_to_matrix" name="abundance_estimation_to_matrix" version="0.0.1"> + + <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="file" value="text" /> + <param name="column_label" value="text" /> + <output name="counts_matrix" file="text" /> + </test> + + + </tests> + <help> + .. _Trinity: http://trinityrnaseq.sourceforge.net + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trinityrnaseq_protocol/abundance_estimation_to_matrix_wrapper.py Fri Oct 23 12:02:09 2015 -0400 @@ -0,0 +1,40 @@ +#!/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) +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trinityrnaseq_protocol/align_and_estimate_abundance.xml Fri Oct 23 12:02:09 2015 -0400 @@ -0,0 +1,89 @@ +<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="transcript_file" value="fasta" /> + <param name="input" value="reads.left.fq" /> + <output name="transcripts_counts" file="text" /> + + </test> + + + </tests> + <help> + .. _Trinity: http://trinityrnaseq.sourceforge.net + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trinityrnaseq_protocol/align_and_estimate_abundance.xml~ Fri Oct 23 12:02:09 2015 -0400 @@ -0,0 +1,89 @@ +<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="transcript_file" value="fasta" /> + <param name="input" value="reads.left.fq" /> + <output name="transcripts_counts" value="text" /> + + </test> + + + </tests> + <help> + .. _Trinity: http://trinityrnaseq.sourceforge.net + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trinityrnaseq_protocol/analyze_diff_exp.xml Fri Oct 23 12:02:09 2015 -0400 @@ -0,0 +1,44 @@ +<tool id="Analyze_Diff_Exp" name="Analyze_Differential_Expression" version="0.0.1"> + + <description>Analyze differential expression</description> + <requirements> + <requirement type="package">trinity</requirement> + </requirements> + <command interpreter="python"> + + analyze_diff_exp_wrapper.py $EdgeRTarGz $TMM_Matrix_FPKM $Pvalue $Cvalue + + </command> + <inputs> + <param name="EdgeRTarGz" label="EdgeR tar gz file" type="data" format="file"/> + <param name="TMM_Matrix_FPKM" label="TMM Normalized FPKM matrix" type="data" format="file" /> + <param name="Pvalue" label="P-value" value="0.05" type="float" /> + <param name="Cvalue" label="C-value" value="0" type="float" /> + + </inputs> + <outputs> + <data format="data" name="diffExpr_matrix" label="${tool.name} on ${on_string}: Matrix" from_work_dir="diffExpr.matrix"/> + <data format="data" name="diffExpr_correlation_matrix" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix" from_work_dir="diffExpr.matrix.log2.sample_cor.dat"/> + <data format="data" name="diffExpr_correlation_matrix_pdf" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix_PDF" from_work_dir="diffExpr.matrix.log2.sample_cor_matrix.pdf"/> + <data format="data" name="Heatmap" label="${tool.name} on ${on_string}: Heatmap" from_work_dir="diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/> + </outputs> + <tests> + + + <test> + <param name="EdgeRtargz" value="EdgeR.tar.gz" /> + <param name="TMM_matrix" value="matrix_file" /> + <param name="P_value" value="float" /> + <param name="C_value" value="float" /> + <output name="diffExpr_matrix" file="diffExp.matrix" /> + <output name="SampleCorrelation_matrix" file="diffExp.matrix.log2.dat" /> + <output name="Correlation_matrix" file="diffExp_matrix.pdf" /> + <output name="heatmap" file="heatmap.pdf" /> + </test> + + + </tests> + <help> + .. _Trinity: http://trinityrnaseq.sourceforge.net + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trinityrnaseq_protocol/analyze_diff_exp_wrapper.py Fri Oct 23 12:02:09 2015 -0400 @@ -0,0 +1,63 @@ +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)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trinityrnaseq_protocol/concatanate.xml Fri Oct 23 12:02:09 2015 -0400 @@ -0,0 +1,41 @@ +<tool id="catbash" name="Concatenate datasets"> + <description>tail-to-head</description> + <command interpreter="python"> + bash_command_executer.py cat + $input1 + #for $q in $queries + ${q.input2} + #end for + > $out_file1 + </command> + <inputs> + <param name="input1" type="data" label="Concatenate Dataset"/> + <repeat name="queries" title="Dataset"> + <param name="input2" type="data" label="Select" /> + </repeat> + </inputs> + <outputs> + <data name="out_file1" format="input" metadata_source="input1"/> + </outputs> + <tests> + <test> + <param name="input1" value="1.bed"/> + <param name="input2" value="2.bed"/> + <output name="out_file1" file="cat_wrapper_out1.bed"/> + </test> + <!--TODO: if possible, enhance the underlying test code to handle this test + the problem is multiple params with the same name "input2" + <test> + <param name="input1" value="1.bed"/> + <param name="input2" value="2.bed"/> + <param name="input2" value="3.bed"/> + <output name="out_file1" file="cat_wrapper_out2.bed"/> + </test> + --> + </tests> + <help> + + no help + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trinityrnaseq_protocol/trinityToolWrapper.py Fri Oct 23 12:02:09 2015 -0400 @@ -0,0 +1,82 @@ +#!/usr/bin/env python + + +# borrowed from: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr and modified for use with Trinity tools. + +""" +Wrapper that execute a program and its arguments but reports standard error +messages only if the program exit status was not 0 +Example: ./stderr_wrapper.py myprog arg1 -f arg2 +""" + +import sys, subprocess, os + +assert sys.version_info[:2] >= ( 2, 4 ) + +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() + + + +# get bindir +bindir = sys.argv[0] +bindir = bindir.split("/") +if len(bindir) > 1: + bindir.pop() + bindir = "/".join(bindir) +else: + bindir = "." + + +## add locations of tools to path setting. +TOOL_PATHS_FILE = bindir + "/__add_to_PATH_setting.txt"; +for line in open(TOOL_PATHS_FILE): + line = line.rstrip() + os.environ['PATH'] += ":" + line + + +def stop_err( msg ): + sys.stderr.write( "%s\n" % msg ) + sys.exit() + +def __main__(): + # Get command-line arguments + args = sys.argv + # Remove name of calling program, i.e. ./stderr_wrapper.py + args.pop(0) + # If there are no arguments left, we're done + if len(args) == 0: + return + + # If one needs to silence stdout + #args.append( ">" ) + #args.append( "/dev/null" ) + + args[0] = "".join([TRINITY_BASE_DIR, '/', args[0]]); + + cmdline = " ".join(args) + + + + try: + # Run program + err_capture = open("stderr.txt", 'w') + proc = subprocess.Popen( args=cmdline, shell=True, stderr=err_capture, stdout=sys.stdout ) + returncode = proc.wait() + err_capture.close() + + + if returncode != 0: + raise Exception + + except Exception: + # Running Grinder failed: write error message to stderr + err_text = open("stderr.txt").readlines() + stop_err( "ERROR:\n" + "\n".join(err_text)) + + +if __name__ == "__main__": __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trinityrnaseq_protocol/trinityrnaseq.xml Fri Oct 23 12:02:09 2015 -0400 @@ -0,0 +1,131 @@ +<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">trinity</requirement> + </requirements> + <command interpreter="python"> + trinityToolWrapper.py Trinity --max_memory $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 + + </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> + <param name="JM" value="1G" /> + <param name="paired_or_single" value="Single" /> + <output name="txt" file="trinity_log" /> + <output name="fasta" file="assembled_transcripts" /> + </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>