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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
| author | artbio |
|---|---|
| date | Mon, 16 Mar 2020 06:15:02 -0400 |
| parents | |
| children | 02861b32a62f |
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<tool id="SigProfiler" name="SigProfiler" version="@VERSION@"> <description>SigProfiler performs the mutational signature characterization from VCF files.</description> <macros> <import>sigmut_macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <command detect_errors="exit_code"><![CDATA[ @VERSION@ @pipefail@ #import os #import random #import datetime #set job_dir=os.getcwd() #set run_dir = job_dir + (' ' + str(random.randint(1,100000))).strip() + '/' #set job_num = "Job_" + (' ' + str(random.randint(1,500))).strip() mkdir $run_dir && #if str( $set_analysis.choices ) == "install_genome": ln -s -f '$__tool_directory__/install.log' '${logref}' && #else if str( $set_analysis.choices ) == "get_sigmut": #set err_file = $run_dir + "logs/SigProfilerMatrixGenerator_" + $job_num + "_" + str($set_analysis.refgendat) + str(datetime.date.today()) + ".err" #set log_file = $run_dir + "logs/SigProfilerMatrixGenerator_" + $job_num + "_" + str($set_analysis.refgendat) + str(datetime.date.today()) + ".out" #set plot1 = $run_dir + "output/plots/SBS_6_plots_" + $job_num + ".pdf" #set plot2 = $run_dir + "output/plots/SBS_24_plots_" + $job_num + ".pdf" #set plot3 = $run_dir + "output/plots/SBS_78_plots_" + $job_num + ".pdf" #set plot4 = $run_dir + "output/plots/SBS_96_plots_" + $job_num + ".pdf" #set plot5 = $run_dir + "output/plots/SBS_384_plots_" + $job_num + ".pdf" #set plot6 = $run_dir + "output/plots/SBS_1536_plots_" + $job_num + ".pdf" #set plot7 = $run_dir + "output/plots/DBS_78_plots_" + $job_num + ".pdf" #set plot8 = $run_dir + "output/plots/DBS_186_plots_" + $job_num + ".pdf" #set plot9 = $run_dir + "output/plots/ID_simple_plots_" + $job_num + ".pdf" #set plot10 = $run_dir + "output/plots/ID_TSB_plots_" + $job_num + ".pdf" #set plot11 = $run_dir + "output/plots/ID_83_plots_" + $job_num + ".pdf" #set plot12 = $run_dir + "output/plots/ID_94_plots_" + $job_num + ".pdf" #set plot13 = $run_dir + "output/plots/ID_96_plots_" + $job_num + ".pdf" #set exo1 = $run_dir + "output/DBS/" + $job_num + ".DBS78" + ".exome" #set exo2 = $run_dir + "output/DBS/" + $job_num + ".DBS186" + ".exome" #set exo3 = $run_dir + "output/DBS/" + $job_num + ".DBS1248" + ".exome" #set exo4 = $run_dir + "output/DBS/" + $job_num + ".DBS2976" + ".exome" #set exo5 = $run_dir + "output/SBS/" + $job_num + ".SBS6" + ".exome" #set exo6 = $run_dir + "output/SBS/" + $job_num + ".SBS24" + ".exome" #set exo7 = $run_dir + "output/SBS/" + $job_num + ".SBS96" + ".exome" #set exo8 = $run_dir + "output/SBS/" + $job_num + ".SBS384" + ".exome" #set exo9 = $run_dir + "output/SBS/" + $job_num + ".SBS1536" + ".exome" #set exo10 = $run_dir + "output/SBS/" + $job_num + ".SBS6144" + ".exome" #set exo11 = $run_dir + "output/vcf_files/DBS/" + $job_num + "_" + "DBS_exome.vcf" #set exo12 = $run_dir + "output/vcf_files/SNV/" + $job_num + "_" + "SNV_exome.vcf" #set tsb1 = $run_dir + "output/TSB/strandBiasTest_24.txt" #set tsb2 = $run_dir + "output/TSB/strandBiasTest_384.txt" #set tsb3 = $run_dir + "output/TSB/strandBiasTest_6144.txt" #set tsb4 = $run_dir + "output/TSB/significantResults_strandBiasTest.txt" #set seqinf1 = $run_dir + "output/DBS/" + $job_num + ".DBS78" + ".all" #set seqinf2 = $run_dir + "output/DBS/" + $job_num + ".DBS186" + ".all" #set seqinf3 = $run_dir + "output/DBS/" + $job_num + ".DBS1248" + ".all" #set seqinf4 = $run_dir + "output/DBS/" + $job_num + ".DBS2976" + ".all" #set seqinf5 = $run_dir + "output/SBS/" + $job_num + ".SBS6" + ".all" #set seqinf6 = $run_dir + "output/SBS/" + $job_num + ".SBS24" + ".all" #set seqinf7 = $run_dir + "output/SBS/" + $job_num + ".SBS96" + ".all" #set seqinf8 = $run_dir + "output/SBS/" + $job_num + ".SBS384" + ".all" #set seqinf9 = $run_dir + "output/SBS/" + $job_num + ".SBS1536" + ".all" #set seqinf10 = $run_dir + "output/SBS/" + $job_num + ".SBS6144" + ".all" #set seqinf11 = $run_dir + "output/ID/" + $job_num + ".ID28" + ".all" #set seqinf12 = $run_dir + "output/ID/" + $job_num + ".ID83" + ".all" #set seqinf13 = $run_dir + "output/ID/" + $job_num + ".ID94" + ".all" #set seqinf14 = $run_dir + "output/ID/" + $job_num + ".ID96" + ".all" #set seqinf15 = $run_dir + "output/ID/" + $job_num + ".ID415" + ".all" #set seqinf16 = $run_dir + "output/ID/" + $job_num + ".ID8628" + ".all" ln -s -f '$log_file' '${logsmt}' && #if str($set_analysis.plot) == "true": ln -s -f '$plot1' '${SBS6}' && ln -s -f '$plot2' '${SBS24}' && ln -s -f '$plot3' '${SBS78}' && ln -s -f '$plot4' '${SBS96}' && ln -s -f '$plot5' '${SBS384}' && ln -s -f '$plot6' '${SBS1536}' && ln -s -f '$plot7' '${DBS78}' && ln -s -f '$plot8' '${DBS186}' && ln -s -f '$plot9' '${ID_simple}' && ln -s -f '$plot10' '${ID_TSB}' && ln -s -f '$plot11' '${ID_83}' && ln -s -f '$plot12' '${ID_94}' && ln -s -f '$plot13' '${ID_96}' && ln -s -f '$seqinf1' '${SeqInf1}' && ln -s -f '$seqinf2' '${SeqInf2}' && ln -s -f '$seqinf3' '${SeqInf3}' && ln -s -f '$seqinf4' '${SeqInf4}' && ln -s -f '$seqinf5' '${SeqInf5}' && ln -s -f '$seqinf6' '${SeqInf6}' && ln -s -f '$seqinf7' '${SeqInf7}' && ln -s -f '$seqinf8' '${SeqInf8}' && ln -s -f '$seqinf9' '${SeqInf9}' && ln -s -f '$seqinf10' '${SeqInf10}' && ln -s -f '$seqinf11' '${SeqInf11}' && ln -s -f '$seqinf12' '${SeqInf12}' && ln -s -f '$seqinf13' '${SeqInf13}' && ln -s -f '$seqinf14' '${SeqInf14}' && ln -s -f '$seqinf15' '${SeqInf15}' && ln -s -f '$seqinf16' '${SeqInf16}' && #end if #if str($set_analysis.exome) == "true": ln -s -f '$exo1' '${Exo1}' && ln -s -f '$exo2' '${Exo2}' && ln -s -f '$exo3' '${Exo3}' && ln -s -f '$exo4' '${Exo4}' && ln -s -f '$exo5' '${Exo5}' && ln -s -f '$exo6' '${Exo6}' && ln -s -f '$exo7' '${Exo7}' && ln -s -f '$exo8' '${Exo8}' && ln -s -f '$exo9' '${Exo9}' && ln -s -f '$exo10' '${Exo10}' && ln -s -f '$exo11' '${Exo11}' && ln -s -f '$exo12' '${Exo12}' && #end if #if str($set_analysis.tsb_stat) == "true": ln -s -f '$tsb1' '${TSB24}' && ln -s -f '$tsb2' '${TSB384}' && ln -s -f '$tsb3' '${TSB6144}' && ln -s -f '$tsb4' '${sigRes}' && #end if #if str($set_analysis.seqInfo) == "true": ln -s -f '$seqinf1' '${SeqInf1}' && ln -s -f '$seqinf2' '${SeqInf2}' && ln -s -f '$seqinf3' '${SeqInf3}' && ln -s -f '$seqinf4' '${SeqInf4}' && ln -s -f '$seqinf5' '${SeqInf5}' && ln -s -f '$seqinf6' '${SeqInf6}' && ln -s -f '$seqinf7' '${SeqInf7}' && ln -s -f '$seqinf8' '${SeqInf8}' && ln -s -f '$seqinf9' '${SeqInf9}' && ln -s -f '$seqinf10' '${SeqInf10}' && ln -s -f '$seqinf11' '${SeqInf11}' && ln -s -f '$seqinf12' '${SeqInf12}' && ln -s -f '$seqinf13' '${SeqInf13}' && ln -s -f '$seqinf14' '${SeqInf14}' && ln -s -f '$seqinf15' '${SeqInf15}' && ln -s -f '$seqinf16' '${SeqInf16}' && #end if #if str( $set_analysis.vcfile_input.vcfile ) == "maf": #set $infile = $run_dir + 'snps.maf' ln -s -f '$set_analysis.vcfile_input.maf_file' '$infile' && #else if str( $set_analysis.vcfile_input.vcfile ) == "icgc": #set $infile = $run_dir + 'snps.txt' ln -s -f '$set_analysis.vcfile_input.icgc_file' '$infile' && #else if str( $set_analysis.vcfile_input.vcfile ) == "vcf": #set $infile = $run_dir + 'snps.vcf' ln -s -f '$set_analysis.vcfile_input.vcf_file' '$infile' && #end if #end if sigprofiler #if str( $set_analysis.choices ) == "install_genome": -ig $set_analysis.refgendwn #else if str( $set_analysis.choices ) == "get_sigmut": -n $job_num -g $set_analysis.refgendat -f $run_dir #if str( $set_analysis.exome ) == "true": -e #end if #if str( $set_analysis.chrom_based ) == "true": -c #end if #if str( $set_analysis.plot ) == "true": -p #end if #if str( $set_analysis.tsb_stat ) == "true": -t #end if #if str( $set_analysis.gs ) == "true": -s #end if ##-b $set_analysis.bed #end if ]]></command> <inputs> <conditional name="set_analysis"> <param name="choices" type="select" label="Which of the following jobs do you want perform?"> <option value="install_genome">Install 'de novo' a reference genome </option> <option value="get_sigmut">Obtain the mutational signatures from VCF files</option> </param> <when value="install_genome"> <param name="refgendwn" type="select" label="Reference genome" help="Get data from any of the following reference genomes:"> <option value="GRCh37">Homo sapiens, GRCh37.p13 [GCA_000001405.14] </option> <option value="GRCh38">Homo sapiens, GRCh38.p12 [GCA_000001405.27] </option> <option value="mm9">Mus musculus, GRCm37 [GCA_000001635.18]</option> <option value="mm10">Mus musculus, GRCm38.p6 [GCA_000001635.8]</option> <option value="rn6">Rattus norvegicus, Rnor_6.0 [GCA_000001895.4]</option> <option value="c_elegans">Caenorhabditis elegans</option> <option value="dog">Dog</option> </param> </when> <when value="get_sigmut"> <conditional name="vcfile_input"> <param name="vcfile" type="select" label="VC file" help="Select the format of your input data"> <option value="maf">Mutation Annotation Format</option> <option value="icgc">Tab-separated file</option> <option value="vcf">Variant Call Format</option> </param> <when value='maf'> <param name="maf_file" type="data" format="maf" label="select VC file" help="Select the input file in MAF format." /> </when> <when value='icgc'> <param name="icgc_file" type="data" format="txt" label="select VC file" help="Select the input file in ICGC format." /> </when> <when value='vcf'> <param name="vcf_file" type="data" format="vcf" label="select VC file" help="Select the input file in VCF format." /> </when> </conditional> <param name="refgendat" type="select" label="Reference genome to be analyzed" help="Use the following reference genome:"> <option value="GRCh37">Homo sapiens, GRCh37.p13 [GCA_000001405.14] </option> <option value="GRCh38">Homo sapiens, GRCh38.p12 [GCA_000001405.27] </option> <option value="mm9">Mus musculus, GRCm37 [GCA_000001635.18]</option> <option value="mm10">Mus musculus, GRCm38.p6 [GCA_000001635.8]</option> <option value="rn6">Rattus norvegicus, Rnor_6.0 [GCA_000001895.4]</option> <option value="c_elegans">Caenorhabditis elegans</option> <option value="dog">Dog</option> </param> <conditional name="bed_input"> <param name="bedfile" type="select" label="BED file" help="Input a BED file"> <option value="yes">Yes</option> <option value="no" selected="true">No</option> </param> <when value='yes'> <param name="bed_file" format="bed" type="data" label="Use a BED file containing the set of regions" help="Provide a BED file"/> </when> <when value='no'> </when> </conditional> <param name="plot" type="boolean" truevalue="true" label="Produce plot results?" checked="False" help="Show plots"/> <param name="exome" type="boolean" label="Use only the exome?" checked="False" help="Use exome"/> <param name="chrom_based" type="boolean" label="Create the matrices on a per chromosome basis?" checked="False" help="Show snvs"/> <param name="tsb_stat" type="boolean" truevalue="true" label="Performs a transcriptional strand bias test?" checked="False" help="Show snvs"/> <param name="seqInfo" type="boolean" truevalue="true" label="Export sequence information?" checked="False" help="Show sequence information"/> <param name="gs" type="boolean" label="Performs gene strand bias test?" checked="False" help="Show snvs"/> </when> </conditional> </inputs> <outputs> <data format="txt" name="logref" label="Log file: Install a Reference Genome"> <filter>set_analysis['choices'] == 'install_genome'</filter> </data> <data format="txt" name="logsmt" label="Log file: Calculate Mutational Signatures"> <filter>set_analysis['choices'] == 'get_sigmut'</filter> </data> <data format="pdf" name="SBS6" label="--> Plot SBS 6 Sig. Mut."> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter> </data> <data format="pdf" name="SBS24" label="--> Plot SBS 24 Sig. Mut."> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter> </data> <data format="pdf" name="SBS78" label="--> Plot SBS 78 Sig. Mut."> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter> </data> <data format="pdf" name="SBS96" label="--> Plot SBS 96 Sig. Mut."> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter> </data> <data format="pdf" name="SBS384" label="--> Plot SBS 384 Sig. Mut."> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter> </data> <data format="pdf" name="SBS1536" label="--> Plot SBS 1536 Sig. Mut."> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter> </data> <data format="pdf" name="DBS78" label="--> Plot DBS 78 Sig. Mut."> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter> </data> <data format="pdf" name="DBS186" label="--> Plot DBS 186 Sig. Mut."> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter> </data> <data format="pdf" name="ID_simple" label="--> Plot ID simple Sig. Mut."> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter> </data> <data format="pdf" name="ID_TSB" label="--> Plot ID TSB Sig. Mut."> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter> </data> <data format="pdf" name="ID_83" label="--> Plot ID 83 Sig. Mut."> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter> </data> <data format="pdf" name="ID_94" label="--> Plot ID 94 Sig. Mut."> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter> </data> <data format="pdf" name="ID_96" label="--> Plot ID 96 Sig. Mut."> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter> </data> <data format="txt" name="Exo11" label="--> DBS_exome.vcf"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter> </data> <data format="txt" name="Exo12" label="--> SNV_exome.vcf"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter> </data> <data format="txt" name="Exo1" label="--> DBS 78 Sig. Mut. EXOME"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter> </data> <data format="txt" name="Exo2" label="--> DBS 186 Sig. Mut. EXOME"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter> </data> <data format="txt" name="Exo3" label="--> DBS 1248 Sig. Mut. EXOME"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter> </data> <data format="txt" name="Exo4" label="--> DBS 2976 Sig. Mut. EXOME"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter> </data> <data format="txt" name="Exo5" label="--> SBS 6 Sig. Mut. EXOME"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter> </data> <data format="txt" name="Exo6" label="--> SBS 24 Sig. Mut. EXOME"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter> </data> <data format="txt" name="Exo7" label="--> SBS 96 Sig. Mut. EXOME"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter> </data> <data format="txt" name="Exo8" label="--> SBS 384 Sig. Mut. EXOME"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter> </data> <data format="txt" name="Exo9" label="--> SBS 1536 Sig. Mut. EXOME"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter> </data> <data format="txt" name="Exo10" label="--> SBS 6144 Sig. Mut. EXOME"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter> </data> <data format="txt" name="sigRes" label="--> TSB: Significant Results"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['tsb_stat'] is True</filter> </data> <data format="txt" name="TSB24" label="--> TSB: 24 Sig. Mut."> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['tsb_stat'] is True</filter> </data> <data format="txt" name="TSB384" label="--> TSB: 96 Sig. Mut."> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['tsb_stat'] is True</filter> </data> <data format="txt" name="TSB6144" label="--> TSB: 1536 Sig. Mut."> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['tsb_stat'] is True</filter> </data> <data format="txt" name="SeqInf1" label="--> DBS 78 Sig. Mut. ALL"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter> </data> <data format="txt" name="SeqInf2" label="--> DBS 186 Sig. Mut. ALL"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter> </data> <data format="txt" name="SeqInf3" label="--> DBS 1248 Sig. Mut. ALL"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter> </data> <data format="txt" name="SeqInf4" label="--> DBS 2976 Sig. Mut. ALL"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter> </data> <data format="txt" name="SeqInf5" label="--> SBS 6 Sig. Mut. ALL"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter> </data> <data format="txt" name="SeqInf6" label="--> SBS 24 Sig. Mut. ALL"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter> </data> <data format="txt" name="SeqInf7" label="--> SBS 96 Sig. Mut. ALL"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter> </data> <data format="txt" name="SeqInf8" label="--> SBS 384 Sig. Mut. ALL"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter> </data> <data format="txt" name="SeqInf9" label="--> SBS 1536 Sig. Mut. ALL"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter> </data> <data format="txt" name="SeqInf10" label="--> SBS 6144 Sig. Mut. ALL"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter> </data> <data format="txt" name="SeqInf11" label="--> ID 28 Sig. Mut. ALL"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter> </data> <data format="txt" name="SeqInf12" label="--> ID 83 Sig. Mut. ALL"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter> </data> <data format="txt" name="SeqInf13" label="--> ID 94 Sig. Mut. ALL"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter> </data> <data format="txt" name="SeqInf14" label="--> ID 96 Sig. Mut. ALL"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter> </data> <data format="txt" name="SeqInf15" label="--> ID 415 Sig. Mut. ALL"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter> </data> <data format="txt" name="SeqInf16" label="--> ID 8628 Sig. Mut. ALL"> <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter> </data> </outputs> <tests> <test> <conditional name="set_analysis"> <param name="choices" value="install_genome"/> <param name="refgendwn" ftype="fasta" value="c_elegans"/> </conditional> <output name="logref" file="c_elegans.log" lines_diff="5"/> </test> <test> <conditional name="set_analysis"> <param name="choices" value="get_sigmut"/> <param name="refgendat" ftype="fasta" value="c_elegans"/> <conditional name="vcfile_input"> <param name="vcfile" value="icgc"/> <param name="icgc_file" ftype="txt" value="test_matrix.txt"/> </conditional> <conditional name="bed_input"> <param name="bedfile" value="no"/> </conditional> <param name="plot" value="True"/> </conditional> <output name="ID_simple" file="ID_simple.pdf" lines_diff="5"/> <output name="ID_TSB" file="ID_TSB.pdf" lines_diff="5"/> <output name="ID_83" file="ID_83.pdf" lines_diff="5"/> </test> </tests> <help><![CDATA[ **SigProfiler** This script configures the SigProfiler analysis pipeline. You must specify a VCF file for at least one sample. **Options** --version show program's version number and exit -h, --help show this help message and exit --install_genome Install de novo any of the following reference genomes: 'GRCh37', 'GRCh38', 'mm9' or 'mm10'. --name=APPENDIX Provide a project name --genome=NAME Provide a reference genome (ex: GRCh37, GRCh38, mm9 or mm10). --files=Abs_path Path where the input vcf files are located --exome Use only the exome or not --bed=FILE BED file containing the set of regions to be used in generating the matrices --chrom Create the matrices on a per chromosome basis --plot Generate the plots for each context --tsb Performs a transcriptional strand bias test for the 24, 384, and 6144 contexts --gs Performs a gene strand bias test For further info see: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator ]]></help> <citations> <citation type="doi">10.1186/s12864-019-6041-2</citation> </citations> </tool>