Mercurial > repos > artbio > sigmut
diff sigmut.xml @ 1:02861b32a62f draft default tip
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
| author | artbio |
|---|---|
| date | Sun, 14 Jun 2020 20:27:29 -0400 |
| parents | 9f48c5d97be8 |
| children |
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--- a/sigmut.xml Mon Mar 16 06:15:02 2020 -0400 +++ b/sigmut.xml Sun Jun 14 20:27:29 2020 -0400 @@ -1,538 +1,377 @@ <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 + <description>performs mutational signature characterization from variant files</description> - #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' + <macros> + <import>sigmut_macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command detect_errors="exit_code"><![CDATA[ + @VERSION@ + @pipefail@ + BIN=`which sigprofiler | sed 's,/sigprofiler,,g'` && + echo \$BIN && + chmod -R 777 \$BIN && + mkdir run_dir && + #if str( $set_analysis.choices ) == "get_sigmut": + #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' + #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 + #end if + + sigprofiler + + #if str( $set_analysis.choices ) == "install_genome": + -ig $set_analysis.refgendwn > install.log + #else if str( $set_analysis.choices ) == "get_sigmut": + -g $set_analysis.refgendat + -f 'run_dir' + -n "project" + -p +## ! implement exome functionality when good test available +## #if str( $set_analysis.exome ) == "true": +## -e +## #end if +## ! implement per chromosome functionality when good test available +## #if str( $set_analysis.chrom_based ) == "true": +## -c +## #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 ### to be done + && pdfcombine -f -s -o blinder.pdf run_dir/output/plots/*.pdf + && ls run_dir/logs/ + #if str( $set_analysis.tsb_stat ) == "true": + && tail -n +1 run_dir/output/TSB/*.txt > transcriptional_strand_biases.txt + #end if + #if $set_analysis.seqInfo: + && tail -n +1 run_dir/output/*/*.all > information.txt + #end if + #end if + ]]></command> - #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> - <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> - <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> + <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> + </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> +<!-- implement bed when test available --> +<!-- <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> --> + <!-- implement exome functionality when test available --> + <!-- <param name="exome" type="boolean" label="Use only the exome?" checked="False" help="Use exome"/> --> + <!-- implement chrom_based functionality when test available --> + <!--<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> - <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> + <outputs> + <data format="txt" name="logref" label="Log file: Install a Reference Genome" + from_work_dir="./install.log"> + <filter>set_analysis['choices'] == 'install_genome'</filter> + </data> + <data format="txt" name="logsmt" label="Log file: Calculate Mutational Signatures" + from_work_dir="run_dir/logs/SigProfilerMatrixGenerator*.out"> + <filter>set_analysis['choices'] == 'get_sigmut'</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="blinder" label="SBS Mutational Signatures plots (pdf)" + from_work_dir="./blinder.pdf" > + <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> + <!-- implement exome outputs when test available --> + <!-- + <data format="txt" name="dbs_exome" label="DBS_exome.vcf"> + <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter> + </data> + <data format="txt" name="snv_exome" label="SNV_exome.vcf"> + <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter> + </data> + + <data format="txt" name="sig_exome" label="DBS 78 and so on Sig. Mut. EXOME"> + <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter> + </data> + --> + <data format="txt" name="tsb" label="Transcriptional Strand Biases" + from_work_dir="./transcriptional_strand_biases.txt" > + <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['tsb_stat'] 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="txt" name="seqinfo" label="Mutational Signature detailed infos" + from_work_dir="./information.txt" > + <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] 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> + </outputs> + <tests> + <test> + <param name="choices" value="install_genome"/> + <param name="refgendwn" value="GRCh38"/> + <output name="logref" file="hg38_install.log" lines_diff="5"/> + </test> + <test> + <param name="choices" value="get_sigmut"/> + <param name="refgendat" value="GRCh38"/> + <param name="vcfile" value="vcf"/> + <param name="vcf_file" ftype="vcf" value="hg38.vcf"/> + <param name="plot" value="True"/> + <output name="logsmt" ftype="txt" file="sigmut.log" lines_diff="5" /> + <output name="blinder" file="hg38_blinder.pdf" lines_diff="5" /> + </test> + </tests> - <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> + <help><![CDATA[ - <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> + **SigProfiler** - <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> + Background: - <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> + Cancer genomes evince somatic mutations, which are imprinted by + different mutational processes, that give rise to diverse + mutational signatures. Their analysis from single base + substitutions and their immediate sequencing context, allows the + classification of small mutational events (including + substitutions, insertions, deletions, and doublet substitutions) + for better understanding the mutational processes that have + shaped a cancer genome. - <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> + In this sense, SigProfiler constitutes a Galaxy-based wrapper of + a computational method developed by Ludmil B. Alexandrov, that + allow the exploration and visualization of mutational patterns + for all types of small mutational events. Specifically, the + following actions can be performed using SigProfiler wrapper: - <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> + 1. Identify and categorize the mutations based on possible + single nucleotide variants (SNVs), double base substitutions + (DBS), and insertions/deletions and provides further + transcriptional strand bias categorization. Afterwards, the + classification of these mutations are integrated into distinct + matrices. + SigProfiler provides matrix generation support for SBS-6, + SBS-96, SBS-1536, DBS-78 and DBS-1248. In addition, the + generation of mutational matrices of indels including + ID-28 and ID-83 are procured. Besides, an ID-8628 matrix that + extends the ID-83 classification is generated. + SigProfiler examines transcriptional strand bias for single base + substitutions, doublet base substitutions, and small indels. It + is evaluated whether a mutation occurs on the transcribed or the + non-transcribed strand of well-annotated protein coding genes of + a reference genome. Mutations found in the transcribed regions + of the genome are further subclassified as: (i) transcribed, + (ii) un-transcribed, (iii) bi-directional, or (iv) unknown. + + 2. Generation of plots of all types of mutational signatures as + well as all types of mutational patterns in cancer genomes. - <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> + Additional Information: - <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> + Classification of Single Base substitutions (SBSs): + Single base substitutions (SBSs) are single DNA base-pairs + substituted with another single DNA base-pairs. The most + basic classification catalogues SBSs into six distinct + categories, including: C:G > A:T, C:G > G:C, C:G > T:A, + T:A > A:T, T:A > C:G, and T:A > G:C. In practice, a C:G > A:T + substitution is denoted as either a C > A mutation using the + pyrimidine base or as a G > T mutation using the purine base. + In consequence, the most commonly used SBS-6 classification of + single base substitutions can be written as: C > A, C > G, + C > T, T > A, T > C, and T > G. + Additionally, the SBS-6 classification can be further + expanded by considering the base-pairs immediately + adjacent 5′ and 3′ to the somatic mutation. Therefore, an + extended classification for analysis of mutational signatures is + SBS-96, where each of the classes in SBS-6 is further elaborated + using one base adjacent at the 5′ of the mutation and one base + adjacent at the 3′ of the mutation. + Logically, SBS-96 can be further elaborated by including + additional 5′ and 3′ adjacent context. Each of the six single + base substitutions in SBS-6 has 256 possible pentanucleotides + resulting in a classification with 1536 possible channels. + + Classification of Doublet Base substitutions (DBSs): + Doublet base substitutions (DBSs) are somatic mutations in which + a set of two adjacent DNA base-pairs is simultaneously + substituted with another set of two adjacent DNA base-pairs. An + example of a DBS is a set of CT:GA base-pairs mutating to a set + of AA:TT base-pairs, which is usually denoted as CT:GA > AA:TT. + It should be noted that a CT:GA > AA:TT mutation can be + equivalently written as either a CT > AA mutation. Overall, the + basic classification catalogues DBSs into 78 distinct categories + denoted as the DBS-78 matrix. + Similarly, we can expand the characterization of DBS mutations + by considering the 5′ and 3′ adjacent contexts. With + seventy-eight possible DBS mutations having sixteen possible + tetranucleotides each, this context expansion results in 1248 + possible channels denoted as the DBS-1248 context. + + Classification of small insertions and deletions (IDs): + A somatic insertion is the incorporation of a set of base-pairs + that lengthens a chromosome, while a somatic deletion is the + removing of a set of existing base-pairs from a given location + of a chromosome. + Unfortunately, indel classification cannot be performed + analogously to SBS or DBS classifications, where the immediate + sequencing context flanking each mutation was + utilized to subclassify these mutational events. + Consequently, indels (IDs) are classified as single base-pair + or longer events. They can be further subclassified as either a + C:G or a T:A indel, while longer indels can also be + subclassified based on their lengths: 2 bp, 3 bp, 4 bp, and + 5 + bp. - <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> + Incorporation of transcription Strand Bias (TSB): + The mutational classifications described above allow the + characterization of mutational patterns of single base + substitutions, doublet base substitutions, and small insertions + and deletions. Nevertheless, these classifications can be + further elaborated by incorporating strand bias. Mutations + from the same type are expected to be equally distributed across the two + DNA strands. However, in many cases an asymmetric number of mutations are + observed due to either one of the strands being preferentially + repaired or one of the strands having a higher propensity for + being damaged. To sub-classify mutations based on their + transcriptional strand bias, the pyrimidine orientation with + respect to the locations of well-annotated protein coding genes + on a genome is considered. - <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> + Running SigProfiler: + + 1. Reference Genomes: + Before using SigProfiler, the installation of a reference genome + is demanded. By default, the tool supports the following + reference genomes: + Human: GRCh37 & GRCh38 + + Mouse: mm9 & mm10 + + Rat: rn6 + + Nematode: c_elegans + + A right command line should look like: - <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> + sigprofiler -ig GRCh37 - <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> + 2. Mutational signatures calculation: + + After successful installation of a reference genome, SigProfiler + can be applied to files containing somatic mutations in multiple + formats, for transforming these mutational catalogues into mutational + matrices. Specifically, the tool can read data formats such as + Variant Calling Format (VCF) and Mutation Annotation Format + (MAF) and the following parameters should be provided for + generating the diverse matrices and plots: + + --name | -n = Project name + --genome | -g = Reference Genome + -files | -f = Absolute path where the input mutation files are located - </tests> + A right command line should look like: - <help><![CDATA[ - - **SigProfiler** + sigprofiler -n MYPROJECT -g GRCh37 -f /path_to_folder_with_VCF_files/ -p - 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 - **Options** - --version show program's version number and exit + -h, --help show this help message 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'. - --install_genome Install de novo any of the following reference - genomes: 'GRCh37', 'GRCh38', 'mm9' or 'mm10'. - - --name=APPENDIX Provide a project name + --name=APPENDIX Provide a project name - --genome=NAME Provide a reference genome (ex: GRCh37, GRCh38, - mm9 or mm10). + --genome=NAME Provide a reference genome (ex: GRCh37, GRCh38, + mm9 or mm10). - --files=Abs_path Path where the input vcf files are located + --files=Abs_path Path where the input vcf files are located + + --exome Use only the exome or not - --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 - --bed=FILE BED file containing the set of regions to be used - in generating the matrices + --plot Generate the plots for each context - --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 - --tsb Performs a transcriptional strand bias test for the - 24, 384, and 6144 contexts + --gs Performs a gene strand bias test - --gs Performs a gene strand bias test + For further info see: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator - For further info see: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator - - ]]></help> + ]]></help> - <citations> - <citation type="doi">10.1186/s12864-019-6041-2</citation> - </citations> + <citations> + <citation type="doi">10.1186/s12864-019-6041-2</citation> + </citations> </tool>