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"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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
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1 <tool id="SigProfiler" name="SigProfiler" version="@VERSION@">
1
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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2 <description>performs mutational signature characterization from variant files</description>
0
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
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3
1
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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4 <macros>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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5 <import>sigmut_macros.xml</import>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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6 </macros>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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7 <expand macro="requirements"/>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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8 <expand macro="stdio"/>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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9 <command detect_errors="exit_code"><![CDATA[
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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10 @VERSION@
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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11 @pipefail@
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12 BIN=`which sigprofiler | sed 's,/sigprofiler,,g'` &&
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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13 echo \$BIN &&
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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14 chmod -R 777 \$BIN &&
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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15 mkdir run_dir &&
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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16 #if str( $set_analysis.choices ) == "get_sigmut":
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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17 #if str( $set_analysis.vcfile_input.vcfile ) == "maf":
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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18 #set $infile = 'run_dir/snps.maf'
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19 ln -s -f '$set_analysis.vcfile_input.maf_file' '$infile' &&
1
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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20 #else if str( $set_analysis.vcfile_input.vcfile ) == "icgc":
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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21 #set $infile = 'run_dir/snps.txt'
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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22 ln -s -f '$set_analysis.vcfile_input.icgc_file' '$infile' &&
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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23 #else if str( $set_analysis.vcfile_input.vcfile ) == "vcf":
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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24 #set $infile = 'run_dir/snps.vcf'
0
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
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25 ln -s -f '$set_analysis.vcfile_input.vcf_file' '$infile' &&
1
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26 #end if
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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27 #end if
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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28
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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29 sigprofiler
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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30
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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31 #if str( $set_analysis.choices ) == "install_genome":
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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32 -ig $set_analysis.refgendwn > install.log
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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33 #else if str( $set_analysis.choices ) == "get_sigmut":
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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34 -g $set_analysis.refgendat
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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35 -f 'run_dir'
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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36 -n "project"
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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37 -p
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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38 ## ! implement exome functionality when good test available
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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39 ## #if str( $set_analysis.exome ) == "true":
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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40 ## -e
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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41 ## #end if
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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42 ## ! implement per chromosome functionality when good test available
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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43 ## #if str( $set_analysis.chrom_based ) == "true":
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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44 ## -c
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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45 ## #end if
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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46 #if str( $set_analysis.tsb_stat ) == "true":
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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47 -t
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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48 #end if
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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49 #if str( $set_analysis.gs ) == "true":
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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50 -s
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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51 #end if
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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52 ##-b $set_analysis.bed ### to be done
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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53 && pdfcombine -f -s -o blinder.pdf run_dir/output/plots/*.pdf
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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54 && ls run_dir/logs/
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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55 #if str( $set_analysis.tsb_stat ) == "true":
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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56 && tail -n +1 run_dir/output/TSB/*.txt > transcriptional_strand_biases.txt
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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57 #end if
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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58 #if $set_analysis.seqInfo:
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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59 && tail -n +1 run_dir/output/*/*.all > information.txt
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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60 #end if
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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61 #end if
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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62 ]]></command>
0
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63
1
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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64 <inputs>
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65 <conditional name="set_analysis">
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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66 <param name="choices" type="select" label="Which of the following jobs do you want perform?">
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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67 <option value="install_genome">Install 'de novo' a reference genome </option>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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68 <option value="get_sigmut">Obtain the mutational signatures from VCF files</option>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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69 </param>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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70 <when value="install_genome">
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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71 <param name="refgendwn" type="select" label="Reference genome" help="Get data from any of the following reference genomes:">
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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72 <option value="GRCh37">Homo sapiens, GRCh37.p13 [GCA_000001405.14] </option>
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73 <option value="GRCh38">Homo sapiens, GRCh38.p12 [GCA_000001405.27] </option>
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74 <option value="mm9">Mus musculus, GRCm37 [GCA_000001635.18]</option>
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75 <option value="mm10">Mus musculus, GRCm38.p6 [GCA_000001635.8]</option>
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76 <option value="rn6">Rattus norvegicus, Rnor_6.0 [GCA_000001895.4]</option>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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77 <option value="c_elegans">Caenorhabditis elegans</option>
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78 <option value="dog">Dog</option>
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79 </param>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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80 </when>
0
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
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81
1
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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82 <when value="get_sigmut">
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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83 <conditional name="vcfile_input">
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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84 <param name="vcfile" type="select" label="VC file" help="Select the format of your input data">
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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85 <option value="maf">Mutation Annotation Format</option>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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86 <option value="icgc">Tab-separated file</option>
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87 <option value="vcf">Variant Call Format</option>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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88 </param>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
89 <when value='maf'>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
90 <param name="maf_file" type="data" format="maf" label="select VC file" help="Select the input file in MAF format." />
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
91 </when>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
92 <when value='icgc'>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
93 <param name="icgc_file" type="data" format="txt" label="select VC file" help="Select the input file in ICGC format." />
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
94 </when>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
95 <when value='vcf'>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
96 <param name="vcf_file" type="data" format="vcf" label="select VC file" help="Select the input file in VCF format." />
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
97 </when>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
98 </conditional>
0
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
99
1
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
100 <param name="refgendat" type="select" label="Reference genome to be analyzed" help="Use the following reference genome:">
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
101 <option value="GRCh37">Homo sapiens, GRCh37.p13 [GCA_000001405.14] </option>
0
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
102 <option value="GRCh38">Homo sapiens, GRCh38.p12 [GCA_000001405.27] </option>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
103 <option value="mm9">Mus musculus, GRCm37 [GCA_000001635.18]</option>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
104 <option value="mm10">Mus musculus, GRCm38.p6 [GCA_000001635.8]</option>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
105 <option value="rn6">Rattus norvegicus, Rnor_6.0 [GCA_000001895.4]</option>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
106 <option value="c_elegans">Caenorhabditis elegans</option>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
107 <option value="dog">Dog</option>
1
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
108 </param>
0
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
109
1
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
110 <!-- implement bed when test available -->
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
111 <!-- <conditional name="bed_input">
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
112 <param name="bedfile" type="select" label="BED file" help="Input a BED file">
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
113 <option value="yes">Yes</option>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
114 <option value="no" selected="true">No</option>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
115 </param>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
116 <when value='yes'>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
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117 <param name="bed_file" format="bed" type="data" label="Use a BED file containing the set of regions" help="Provide a BED file"/>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
118 </when>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
119 <when value='no'>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
120 </when>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
121 </conditional> -->
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
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122 <!-- implement exome functionality when test available -->
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
123 <!-- <param name="exome" type="boolean" label="Use only the exome?" checked="False" help="Use exome"/> -->
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
124 <!-- implement chrom_based functionality when test available -->
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
125 <!--<param name="chrom_based" type="boolean" label="Create the matrices on a per chromosome basis?" checked="False" help="Show snvs"/> -->
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
126 <param name="tsb_stat" type="boolean" truevalue="true" label="Performs a transcriptional strand bias test?" checked="False" help="Show snvs"/>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
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diff changeset
127 <param name="seqInfo" type="boolean" truevalue="true" label="Export sequence information?" checked="False" help="Show sequence information"/>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
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128 <param name="gs" type="boolean" label="Performs gene strand bias test?" checked="False" help="Show snvs"/>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
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diff changeset
129 </when>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
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130 </conditional>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
131 </inputs>
0
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
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132
1
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
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133 <outputs>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
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134 <data format="txt" name="logref" label="Log file: Install a Reference Genome"
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
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diff changeset
135 from_work_dir="./install.log">
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
136 <filter>set_analysis['choices'] == 'install_genome'</filter>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
137 </data>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
138 <data format="txt" name="logsmt" label="Log file: Calculate Mutational Signatures"
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
139 from_work_dir="run_dir/logs/SigProfilerMatrixGenerator*.out">
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
140 <filter>set_analysis['choices'] == 'get_sigmut'</filter>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
141 </data>
0
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
142
1
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
143 <data format="pdf" name="blinder" label="SBS Mutational Signatures plots (pdf)"
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
144 from_work_dir="./blinder.pdf" >
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
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145 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
146 </data>
0
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
147
1
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
148 <!-- implement exome outputs when test available -->
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
149 <!--
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
150 <data format="txt" name="dbs_exome" label="DBS_exome.vcf">
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
151 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
152 </data>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
153 <data format="txt" name="snv_exome" label="SNV_exome.vcf">
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
154 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
155 </data>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
156
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
157 <data format="txt" name="sig_exome" label="DBS 78 and so on Sig. Mut. EXOME">
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
158 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
159 </data>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
160 -->
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
161 <data format="txt" name="tsb" label="Transcriptional Strand Biases"
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
162 from_work_dir="./transcriptional_strand_biases.txt" >
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
163 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['tsb_stat'] is True</filter>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
164 </data>
0
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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165
1
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
166 <data format="txt" name="seqinfo" label="Mutational Signature detailed infos"
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
167 from_work_dir="./information.txt" >
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
168 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
169 </data>
0
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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170
1
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
171 </outputs>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
172 <tests>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
173 <test>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
174 <param name="choices" value="install_genome"/>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
parents: 0
diff changeset
175 <param name="refgendwn" value="GRCh38"/>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
artbio
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176 <output name="logref" file="hg38_install.log" lines_diff="5"/>
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177 </test>
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178 <test>
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179 <param name="choices" value="get_sigmut"/>
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180 <param name="refgendat" value="GRCh38"/>
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181 <param name="vcfile" value="vcf"/>
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182 <param name="vcf_file" ftype="vcf" value="hg38.vcf"/>
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183 <param name="plot" value="True"/>
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184 <output name="logsmt" ftype="txt" file="sigmut.log" lines_diff="5" />
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185 <output name="blinder" file="hg38_blinder.pdf" lines_diff="5" />
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186 </test>
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187 </tests>
0
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188
1
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189 <help><![CDATA[
0
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190
1
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191 **SigProfiler**
0
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192
1
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193 Background:
0
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194
1
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195 Cancer genomes evince somatic mutations, which are imprinted by
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196 different mutational processes, that give rise to diverse
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197 mutational signatures. Their analysis from single base
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198 substitutions and their immediate sequencing context, allows the
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199 classification of small mutational events (including
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200 substitutions, insertions, deletions, and doublet substitutions)
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201 for better understanding the mutational processes that have
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202 shaped a cancer genome.
0
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203
1
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204 In this sense, SigProfiler constitutes a Galaxy-based wrapper of
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205 a computational method developed by Ludmil B. Alexandrov, that
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206 allow the exploration and visualization of mutational patterns
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207 for all types of small mutational events. Specifically, the
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208 following actions can be performed using SigProfiler wrapper:
0
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209
1
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210 1. Identify and categorize the mutations based on possible
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211 single nucleotide variants (SNVs), double base substitutions
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212 (DBS), and insertions/deletions and provides further
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213 transcriptional strand bias categorization. Afterwards, the
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214 classification of these mutations are integrated into distinct
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215 matrices.
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216 SigProfiler provides matrix generation support for SBS-6,
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217 SBS-96, SBS-1536, DBS-78 and DBS-1248. In addition, the
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218 generation of mutational matrices of indels including
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219 ID-28 and ID-83 are procured. Besides, an ID-8628 matrix that
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220 extends the ID-83 classification is generated.
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221 SigProfiler examines transcriptional strand bias for single base
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222 substitutions, doublet base substitutions, and small indels. It
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223 is evaluated whether a mutation occurs on the transcribed or the
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224 non-transcribed strand of well-annotated protein coding genes of
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225 a reference genome. Mutations found in the transcribed regions
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226 of the genome are further subclassified as: (i) transcribed,
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227 (ii) un-transcribed, (iii) bi-directional, or (iv) unknown.
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228
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229 2. Generation of plots of all types of mutational signatures as
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230 well as all types of mutational patterns in cancer genomes.
0
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231
1
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232 Additional Information:
0
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233
1
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234 Classification of Single Base substitutions (SBSs):
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235 Single base substitutions (SBSs) are single DNA base-pairs
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236 substituted with another single DNA base-pairs. The most
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237 basic classification catalogues SBSs into six distinct
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238 categories, including: C:G > A:T, C:G > G:C, C:G > T:A,
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239 T:A > A:T, T:A > C:G, and T:A > G:C. In practice, a C:G > A:T
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240 substitution is denoted as either a C > A mutation using the
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241 pyrimidine base or as a G > T mutation using the purine base.
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242 In consequence, the most commonly used SBS-6 classification of
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243 single base substitutions can be written as: C > A, C > G,
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244 C > T, T > A, T > C, and T > G.
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245 Additionally, the SBS-6 classification can be further
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246 expanded by considering the base-pairs immediately
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247 adjacent 5′ and 3′ to the somatic mutation. Therefore, an
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248 extended classification for analysis of mutational signatures is
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249 SBS-96, where each of the classes in SBS-6 is further elaborated
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250 using one base adjacent at the 5′ of the mutation and one base
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251 adjacent at the 3′ of the mutation.
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252 Logically, SBS-96 can be further elaborated by including
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253 additional 5′ and 3′ adjacent context. Each of the six single
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254 base substitutions in SBS-6 has 256 possible pentanucleotides
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255 resulting in a classification with 1536 possible channels.
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256
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257 Classification of Doublet Base substitutions (DBSs):
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258 Doublet base substitutions (DBSs) are somatic mutations in which
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259 a set of two adjacent DNA base-pairs is simultaneously
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260 substituted with another set of two adjacent DNA base-pairs. An
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261 example of a DBS is a set of CT:GA base-pairs mutating to a set
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262 of AA:TT base-pairs, which is usually denoted as CT:GA > AA:TT.
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263 It should be noted that a CT:GA > AA:TT mutation can be
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264 equivalently written as either a CT > AA mutation. Overall, the
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265 basic classification catalogues DBSs into 78 distinct categories
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266 denoted as the DBS-78 matrix.
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267 Similarly, we can expand the characterization of DBS mutations
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268 by considering the 5′ and 3′ adjacent contexts. With
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269 seventy-eight possible DBS mutations having sixteen possible
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270 tetranucleotides each, this context expansion results in 1248
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271 possible channels denoted as the DBS-1248 context.
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272
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273 Classification of small insertions and deletions (IDs):
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274 A somatic insertion is the incorporation of a set of base-pairs
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275 that lengthens a chromosome, while a somatic deletion is the
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276 removing of a set of existing base-pairs from a given location
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277 of a chromosome.
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278 Unfortunately, indel classification cannot be performed
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279 analogously to SBS or DBS classifications, where the immediate
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280 sequencing context flanking each mutation was
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281 utilized to subclassify these mutational events.
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282 Consequently, indels (IDs) are classified as single base-pair
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283 or longer events. They can be further subclassified as either a
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284 C:G or a T:A indel, while longer indels can also be
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285 subclassified based on their lengths: 2 bp, 3 bp, 4 bp, and
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286 5 + bp.
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287
1
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288 Incorporation of transcription Strand Bias (TSB):
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289 The mutational classifications described above allow the
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290 characterization of mutational patterns of single base
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291 substitutions, doublet base substitutions, and small insertions
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292 and deletions. Nevertheless, these classifications can be
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293 further elaborated by incorporating strand bias. Mutations
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294 from the same type are expected to be equally distributed across the two
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295 DNA strands. However, in many cases an asymmetric number of mutations are
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296 observed due to either one of the strands being preferentially
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297 repaired or one of the strands having a higher propensity for
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298 being damaged. To sub-classify mutations based on their
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299 transcriptional strand bias, the pyrimidine orientation with
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300 respect to the locations of well-annotated protein coding genes
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301 on a genome is considered.
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302
1
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303 Running SigProfiler:
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304
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305 1. Reference Genomes:
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306 Before using SigProfiler, the installation of a reference genome
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307 is demanded. By default, the tool supports the following
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308 reference genomes:
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309
1
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310 Human: GRCh37 & GRCh38
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311
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312 Mouse: mm9 & mm10
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313
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314 Rat: rn6
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315
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316 Nematode: c_elegans
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317
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318 A right command line should look like:
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319
1
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320 sigprofiler -ig GRCh37
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321
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322 2. Mutational signatures calculation:
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323
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324 After successful installation of a reference genome, SigProfiler
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325 can be applied to files containing somatic mutations in multiple
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326 formats, for transforming these mutational catalogues into mutational
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327 matrices. Specifically, the tool can read data formats such as
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328 Variant Calling Format (VCF) and Mutation Annotation Format
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329 (MAF) and the following parameters should be provided for
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330 generating the diverse matrices and plots:
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331
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332 --name | -n = Project name
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333 --genome | -g = Reference Genome
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334 -files | -f = Absolute path where the input mutation files are located
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335
1
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336 A right command line should look like:
0
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337
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338 sigprofiler -n MYPROJECT -g GRCh37 -f /path_to_folder_with_VCF_files/ -p
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339
1
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340 **Options**
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341 --version show program's version number and exit
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342
1
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343 -h, --help show this help message and exit
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344
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345 --install_genome Install de novo any of the following reference
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346 genomes: 'GRCh37', 'GRCh38', 'mm9' or 'mm10'.
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347
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348 --name=APPENDIX Provide a project name
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349
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350 --genome=NAME Provide a reference genome (ex: GRCh37, GRCh38,
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351 mm9 or mm10).
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352
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353 --files=Abs_path Path where the input vcf files are located
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354
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355 --exome Use only the exome or not
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356
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357 --bed=FILE BED file containing the set of regions to be used
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358 in generating the matrices
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359
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360 --chrom Create the matrices on a per chromosome basis
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9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
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361
1
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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362 --plot Generate the plots for each context
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9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
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363
1
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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364 --tsb Performs a transcriptional strand bias test for the
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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365 24, 384, and 6144 contexts
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9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
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366
1
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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367 --gs Performs a gene strand bias test
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9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
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368
1
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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369 For further info see: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator
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9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
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370
1
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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371 ]]></help>
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372
1
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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373 <citations>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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374 <citation type="doi">10.1186/s12864-019-6041-2</citation>
02861b32a62f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit bba3eb3950b8772758cc6f19747172be7413ddd9"
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375 </citations>
0
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
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376
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
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377 </tool>