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annotate sigmut.xml @ 0:9f48c5d97be8 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
author artbio
date Mon, 16 Mar 2020 06:15:02 -0400
parents
children 02861b32a62f
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0
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
1 <tool id="SigProfiler" name="SigProfiler" version="@VERSION@">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
2 <description>SigProfiler performs the mutational signature characterization from VCF files.</description>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
3
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
4 <macros>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
5 <import>sigmut_macros.xml</import>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
6 </macros>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
7 <expand macro="requirements"/>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
8 <expand macro="stdio"/>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
10 @VERSION@
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
11 @pipefail@
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
12 #import os
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
13 #import random
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
14 #import datetime
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
15 #set job_dir=os.getcwd()
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
16 #set run_dir = job_dir + (' ' + str(random.randint(1,100000))).strip() + '/'
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
17 #set job_num = "Job_" + (' ' + str(random.randint(1,500))).strip()
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
18
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
19 mkdir $run_dir &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
20
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
21 #if str( $set_analysis.choices ) == "install_genome":
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
22 ln -s -f '$__tool_directory__/install.log' '${logref}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
23 #else if str( $set_analysis.choices ) == "get_sigmut":
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
24 #set err_file = $run_dir + "logs/SigProfilerMatrixGenerator_" + $job_num + "_" + str($set_analysis.refgendat) + str(datetime.date.today()) + ".err"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
25 #set log_file = $run_dir + "logs/SigProfilerMatrixGenerator_" + $job_num + "_" + str($set_analysis.refgendat) + str(datetime.date.today()) + ".out"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
26
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
27 #set plot1 = $run_dir + "output/plots/SBS_6_plots_" + $job_num + ".pdf"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
28 #set plot2 = $run_dir + "output/plots/SBS_24_plots_" + $job_num + ".pdf"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
29 #set plot3 = $run_dir + "output/plots/SBS_78_plots_" + $job_num + ".pdf"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
30 #set plot4 = $run_dir + "output/plots/SBS_96_plots_" + $job_num + ".pdf"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
31 #set plot5 = $run_dir + "output/plots/SBS_384_plots_" + $job_num + ".pdf"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
32 #set plot6 = $run_dir + "output/plots/SBS_1536_plots_" + $job_num + ".pdf"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
33 #set plot7 = $run_dir + "output/plots/DBS_78_plots_" + $job_num + ".pdf"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
34 #set plot8 = $run_dir + "output/plots/DBS_186_plots_" + $job_num + ".pdf"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
35
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
36 #set plot9 = $run_dir + "output/plots/ID_simple_plots_" + $job_num + ".pdf"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
37 #set plot10 = $run_dir + "output/plots/ID_TSB_plots_" + $job_num + ".pdf"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
38 #set plot11 = $run_dir + "output/plots/ID_83_plots_" + $job_num + ".pdf"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
39 #set plot12 = $run_dir + "output/plots/ID_94_plots_" + $job_num + ".pdf"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
40 #set plot13 = $run_dir + "output/plots/ID_96_plots_" + $job_num + ".pdf"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
41
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
42 #set exo1 = $run_dir + "output/DBS/" + $job_num + ".DBS78" + ".exome"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
43 #set exo2 = $run_dir + "output/DBS/" + $job_num + ".DBS186" + ".exome"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
44 #set exo3 = $run_dir + "output/DBS/" + $job_num + ".DBS1248" + ".exome"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
45 #set exo4 = $run_dir + "output/DBS/" + $job_num + ".DBS2976" + ".exome"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
46
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
47 #set exo5 = $run_dir + "output/SBS/" + $job_num + ".SBS6" + ".exome"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
48 #set exo6 = $run_dir + "output/SBS/" + $job_num + ".SBS24" + ".exome"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
49 #set exo7 = $run_dir + "output/SBS/" + $job_num + ".SBS96" + ".exome"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
50 #set exo8 = $run_dir + "output/SBS/" + $job_num + ".SBS384" + ".exome"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
51 #set exo9 = $run_dir + "output/SBS/" + $job_num + ".SBS1536" + ".exome"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
52 #set exo10 = $run_dir + "output/SBS/" + $job_num + ".SBS6144" + ".exome"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
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diff changeset
53
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
54 #set exo11 = $run_dir + "output/vcf_files/DBS/" + $job_num + "_" + "DBS_exome.vcf"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
55 #set exo12 = $run_dir + "output/vcf_files/SNV/" + $job_num + "_" + "SNV_exome.vcf"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
56
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
57 #set tsb1 = $run_dir + "output/TSB/strandBiasTest_24.txt"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
58 #set tsb2 = $run_dir + "output/TSB/strandBiasTest_384.txt"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
59 #set tsb3 = $run_dir + "output/TSB/strandBiasTest_6144.txt"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
60 #set tsb4 = $run_dir + "output/TSB/significantResults_strandBiasTest.txt"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
61
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
62 #set seqinf1 = $run_dir + "output/DBS/" + $job_num + ".DBS78" + ".all"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
63 #set seqinf2 = $run_dir + "output/DBS/" + $job_num + ".DBS186" + ".all"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
64 #set seqinf3 = $run_dir + "output/DBS/" + $job_num + ".DBS1248" + ".all"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
65 #set seqinf4 = $run_dir + "output/DBS/" + $job_num + ".DBS2976" + ".all"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
66
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
67 #set seqinf5 = $run_dir + "output/SBS/" + $job_num + ".SBS6" + ".all"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
68 #set seqinf6 = $run_dir + "output/SBS/" + $job_num + ".SBS24" + ".all"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
69 #set seqinf7 = $run_dir + "output/SBS/" + $job_num + ".SBS96" + ".all"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
70 #set seqinf8 = $run_dir + "output/SBS/" + $job_num + ".SBS384" + ".all"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
71 #set seqinf9 = $run_dir + "output/SBS/" + $job_num + ".SBS1536" + ".all"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
72 #set seqinf10 = $run_dir + "output/SBS/" + $job_num + ".SBS6144" + ".all"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
73
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
74 #set seqinf11 = $run_dir + "output/ID/" + $job_num + ".ID28" + ".all"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
75 #set seqinf12 = $run_dir + "output/ID/" + $job_num + ".ID83" + ".all"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
76 #set seqinf13 = $run_dir + "output/ID/" + $job_num + ".ID94" + ".all"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
77 #set seqinf14 = $run_dir + "output/ID/" + $job_num + ".ID96" + ".all"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
78 #set seqinf15 = $run_dir + "output/ID/" + $job_num + ".ID415" + ".all"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
79 #set seqinf16 = $run_dir + "output/ID/" + $job_num + ".ID8628" + ".all"
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
80
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
81 ln -s -f '$log_file' '${logsmt}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
82
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
83 #if str($set_analysis.plot) == "true":
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
84 ln -s -f '$plot1' '${SBS6}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
85 ln -s -f '$plot2' '${SBS24}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
86 ln -s -f '$plot3' '${SBS78}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
87 ln -s -f '$plot4' '${SBS96}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
88 ln -s -f '$plot5' '${SBS384}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
89 ln -s -f '$plot6' '${SBS1536}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
90 ln -s -f '$plot7' '${DBS78}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
91 ln -s -f '$plot8' '${DBS186}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
92 ln -s -f '$plot9' '${ID_simple}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
93 ln -s -f '$plot10' '${ID_TSB}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
94 ln -s -f '$plot11' '${ID_83}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
95 ln -s -f '$plot12' '${ID_94}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
96 ln -s -f '$plot13' '${ID_96}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
97
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
98 ln -s -f '$seqinf1' '${SeqInf1}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
99 ln -s -f '$seqinf2' '${SeqInf2}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
100 ln -s -f '$seqinf3' '${SeqInf3}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
101 ln -s -f '$seqinf4' '${SeqInf4}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
102 ln -s -f '$seqinf5' '${SeqInf5}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
103 ln -s -f '$seqinf6' '${SeqInf6}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
104 ln -s -f '$seqinf7' '${SeqInf7}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
105 ln -s -f '$seqinf8' '${SeqInf8}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
106 ln -s -f '$seqinf9' '${SeqInf9}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
107 ln -s -f '$seqinf10' '${SeqInf10}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
108
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
109 ln -s -f '$seqinf11' '${SeqInf11}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
110 ln -s -f '$seqinf12' '${SeqInf12}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
111 ln -s -f '$seqinf13' '${SeqInf13}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
112 ln -s -f '$seqinf14' '${SeqInf14}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
113 ln -s -f '$seqinf15' '${SeqInf15}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
114 ln -s -f '$seqinf16' '${SeqInf16}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
115
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
116 #end if
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
117
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
118 #if str($set_analysis.exome) == "true":
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
119 ln -s -f '$exo1' '${Exo1}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
120 ln -s -f '$exo2' '${Exo2}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
121 ln -s -f '$exo3' '${Exo3}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
122 ln -s -f '$exo4' '${Exo4}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
123 ln -s -f '$exo5' '${Exo5}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
124 ln -s -f '$exo6' '${Exo6}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
125 ln -s -f '$exo7' '${Exo7}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
126 ln -s -f '$exo8' '${Exo8}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
127 ln -s -f '$exo9' '${Exo9}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
128 ln -s -f '$exo10' '${Exo10}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
129 ln -s -f '$exo11' '${Exo11}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
130 ln -s -f '$exo12' '${Exo12}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
131 #end if
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
132
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
133 #if str($set_analysis.tsb_stat) == "true":
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
134 ln -s -f '$tsb1' '${TSB24}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
135 ln -s -f '$tsb2' '${TSB384}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
136 ln -s -f '$tsb3' '${TSB6144}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
137 ln -s -f '$tsb4' '${sigRes}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
138 #end if
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
139
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
140
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
141 #if str($set_analysis.seqInfo) == "true":
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
142 ln -s -f '$seqinf1' '${SeqInf1}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
143 ln -s -f '$seqinf2' '${SeqInf2}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
144 ln -s -f '$seqinf3' '${SeqInf3}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
145 ln -s -f '$seqinf4' '${SeqInf4}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
146 ln -s -f '$seqinf5' '${SeqInf5}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
147 ln -s -f '$seqinf6' '${SeqInf6}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
148 ln -s -f '$seqinf7' '${SeqInf7}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
149 ln -s -f '$seqinf8' '${SeqInf8}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
150 ln -s -f '$seqinf9' '${SeqInf9}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
151 ln -s -f '$seqinf10' '${SeqInf10}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
152 ln -s -f '$seqinf11' '${SeqInf11}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
153 ln -s -f '$seqinf12' '${SeqInf12}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
154 ln -s -f '$seqinf13' '${SeqInf13}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
155 ln -s -f '$seqinf14' '${SeqInf14}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
156 ln -s -f '$seqinf15' '${SeqInf15}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
157 ln -s -f '$seqinf16' '${SeqInf16}' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
158 #end if
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
159
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
160
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
161 #if str( $set_analysis.vcfile_input.vcfile ) == "maf":
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
162 #set $infile = $run_dir + 'snps.maf'
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
163 ln -s -f '$set_analysis.vcfile_input.maf_file' '$infile' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
164 #else if str( $set_analysis.vcfile_input.vcfile ) == "icgc":
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
165 #set $infile = $run_dir + 'snps.txt'
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
166 ln -s -f '$set_analysis.vcfile_input.icgc_file' '$infile' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
167 #else if str( $set_analysis.vcfile_input.vcfile ) == "vcf":
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
168 #set $infile = $run_dir + 'snps.vcf'
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
169 ln -s -f '$set_analysis.vcfile_input.vcf_file' '$infile' &&
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
170 #end if
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
171
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
172 #end if
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
173
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
174 sigprofiler
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
175 #if str( $set_analysis.choices ) == "install_genome":
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
176 -ig $set_analysis.refgendwn
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
177 #else if str( $set_analysis.choices ) == "get_sigmut":
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
178 -n $job_num
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
179 -g $set_analysis.refgendat
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
180 -f $run_dir
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
181
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
182 #if str( $set_analysis.exome ) == "true":
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
183 -e
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
184 #end if
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
185 #if str( $set_analysis.chrom_based ) == "true":
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
186 -c
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
187 #end if
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
188 #if str( $set_analysis.plot ) == "true":
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
189 -p
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
190 #end if
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
191 #if str( $set_analysis.tsb_stat ) == "true":
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
192 -t
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
193 #end if
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
194 #if str( $set_analysis.gs ) == "true":
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
195 -s
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
196 #end if
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
197 ##-b $set_analysis.bed
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
198 #end if
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
199 ]]></command>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
200
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
201 <inputs>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
202 <conditional name="set_analysis">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
203 <param name="choices" type="select" label="Which of the following jobs do you want perform?">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
204 <option value="install_genome">Install 'de novo' a reference genome </option>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
205 <option value="get_sigmut">Obtain the mutational signatures from VCF files</option>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
206 </param>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
207 <when value="install_genome">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
208 <param name="refgendwn" type="select" label="Reference genome" help="Get data from any of the following reference genomes:">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
209 <option value="GRCh37">Homo sapiens, GRCh37.p13 [GCA_000001405.14] </option>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
210 <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
parents:
diff changeset
211 <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
212 <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
213 <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
214 <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
215 <option value="dog">Dog</option>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
216 </param>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
217 </when>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
218
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
219 <when value="get_sigmut">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
220 <conditional name="vcfile_input">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
221 <param name="vcfile" type="select" label="VC file" help="Select the format of your input data">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
222 <option value="maf">Mutation Annotation Format</option>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
223 <option value="icgc">Tab-separated file</option>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
224 <option value="vcf">Variant Call Format</option>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
225 </param>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
226 <when value='maf'>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
227 <param name="maf_file" type="data" format="maf" label="select VC file" help="Select the input file in MAF format." />
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
228 </when>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
229 <when value='icgc'>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
230 <param name="icgc_file" type="data" format="txt" label="select VC file" help="Select the input file in ICGC format." />
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
231 </when>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
232 <when value='vcf'>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
233 <param name="vcf_file" type="data" format="vcf" label="select VC file" help="Select the input file in VCF format." />
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
234 </when>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
235 </conditional>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
236
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
237 <param name="refgendat" type="select" label="Reference genome to be analyzed" help="Use the following reference genome:">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
238 <option value="GRCh37">Homo sapiens, GRCh37.p13 [GCA_000001405.14] </option>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
239 <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
parents:
diff changeset
240 <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
241 <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
242 <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
243 <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
244 <option value="dog">Dog</option>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
245 </param>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
246
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
247 <conditional name="bed_input">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
248 <param name="bedfile" type="select" label="BED file" help="Input a BED file">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
249 <option value="yes">Yes</option>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
250 <option value="no" selected="true">No</option>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
251 </param>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
252 <when value='yes'>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
253 <param name="bed_file" format="bed" type="data" label="Use a BED file containing the set of regions" help="Provide a BED file"/>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
254 </when>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
255 <when value='no'>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
256 </when>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
257 </conditional>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
258 <param name="plot" type="boolean" truevalue="true" label="Produce plot results?" checked="False" help="Show plots"/>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
259 <param name="exome" type="boolean" label="Use only the exome?" checked="False" help="Use exome"/>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
260 <param name="chrom_based" type="boolean" label="Create the matrices on a per chromosome basis?" checked="False" help="Show snvs"/>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
261 <param name="tsb_stat" type="boolean" truevalue="true" label="Performs a transcriptional strand bias test?" checked="False" help="Show snvs"/>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
262 <param name="seqInfo" type="boolean" truevalue="true" label="Export sequence information?" checked="False" help="Show sequence information"/>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
263 <param name="gs" type="boolean" label="Performs gene strand bias test?" checked="False" help="Show snvs"/>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
264 </when>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
265 </conditional>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
266 </inputs>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
267
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
268 <outputs>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
269 <data format="txt" name="logref" label="Log file: Install a Reference Genome">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
270 <filter>set_analysis['choices'] == 'install_genome'</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
271 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
272
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
273 <data format="txt" name="logsmt" label="Log file: Calculate Mutational Signatures">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
274 <filter>set_analysis['choices'] == 'get_sigmut'</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
275 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
276
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
277 <data format="pdf" name="SBS6" label="--> Plot SBS 6 Sig. Mut.">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
278 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
279 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
280
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
281 <data format="pdf" name="SBS24" label="--> Plot SBS 24 Sig. Mut.">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
282 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
283 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
284
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
285 <data format="pdf" name="SBS78" label="--> Plot SBS 78 Sig. Mut.">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
286 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
287 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
288
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
289 <data format="pdf" name="SBS96" label="--> Plot SBS 96 Sig. Mut.">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
290 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
291 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
292
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
293 <data format="pdf" name="SBS384" label="--> Plot SBS 384 Sig. Mut.">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
294 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
295 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
296
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
297 <data format="pdf" name="SBS1536" label="--> Plot SBS 1536 Sig. Mut.">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
298 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
299 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
300
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
301 <data format="pdf" name="DBS78" label="--> Plot DBS 78 Sig. Mut.">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
302 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
303 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
304
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
305 <data format="pdf" name="DBS186" label="--> Plot DBS 186 Sig. Mut.">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
306 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
307 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
308
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
309 <data format="pdf" name="ID_simple" label="--> Plot ID simple Sig. Mut.">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
310 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
311 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
312
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
313 <data format="pdf" name="ID_TSB" label="--> Plot ID TSB Sig. Mut.">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
314 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
315 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
316
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
317 <data format="pdf" name="ID_83" label="--> Plot ID 83 Sig. Mut.">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
318 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
319 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
320
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
321 <data format="pdf" name="ID_94" label="--> Plot ID 94 Sig. Mut.">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
322 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
323 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
324
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
325 <data format="pdf" name="ID_96" label="--> Plot ID 96 Sig. Mut.">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
326 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['plot'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
327 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
328
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
329 <data format="txt" name="Exo11" label="--> DBS_exome.vcf">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
330 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
331 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
332
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
333 <data format="txt" name="Exo12" label="--> SNV_exome.vcf">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
334 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
335 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
336
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
337 <data format="txt" name="Exo1" label="--> DBS 78 Sig. Mut. EXOME">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
338 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
339 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
340
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
341 <data format="txt" name="Exo2" label="--> DBS 186 Sig. Mut. EXOME">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
342 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
343 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
344
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
345 <data format="txt" name="Exo3" label="--> DBS 1248 Sig. Mut. EXOME">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
346 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
347 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
348
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
349 <data format="txt" name="Exo4" label="--> DBS 2976 Sig. Mut. EXOME">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
350 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
351 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
352
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
353 <data format="txt" name="Exo5" label="--> SBS 6 Sig. Mut. EXOME">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
354 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
355 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
356
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
357 <data format="txt" name="Exo6" label="--> SBS 24 Sig. Mut. EXOME">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
358 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
359 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
360
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
361 <data format="txt" name="Exo7" label="--> SBS 96 Sig. Mut. EXOME">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
362 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
363 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
364
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
365 <data format="txt" name="Exo8" label="--> SBS 384 Sig. Mut. EXOME">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
366 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
367 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
368
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
369 <data format="txt" name="Exo9" label="--> SBS 1536 Sig. Mut. EXOME">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
370 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
371 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
372
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
373 <data format="txt" name="Exo10" label="--> SBS 6144 Sig. Mut. EXOME">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
374 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['exome'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
375 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
376
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
377 <data format="txt" name="sigRes" label="--> TSB: Significant Results">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
378 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['tsb_stat'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
379 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
380
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
381 <data format="txt" name="TSB24" label="--> TSB: 24 Sig. Mut.">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
382 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['tsb_stat'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
383 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
384
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
385 <data format="txt" name="TSB384" label="--> TSB: 96 Sig. Mut.">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
386 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['tsb_stat'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
387 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
388
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
389 <data format="txt" name="TSB6144" label="--> TSB: 1536 Sig. Mut.">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
390 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['tsb_stat'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
391 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
392
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
393
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
394 <data format="txt" name="SeqInf1" label="--> DBS 78 Sig. Mut. ALL">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
395 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
396 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
397
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
398 <data format="txt" name="SeqInf2" label="--> DBS 186 Sig. Mut. ALL">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
399 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
400 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
401
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
402 <data format="txt" name="SeqInf3" label="--> DBS 1248 Sig. Mut. ALL">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
403 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
404 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
405
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
406 <data format="txt" name="SeqInf4" label="--> DBS 2976 Sig. Mut. ALL">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
407 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
408 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
409
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
410 <data format="txt" name="SeqInf5" label="--> SBS 6 Sig. Mut. ALL">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
411 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
412 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
413
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
414 <data format="txt" name="SeqInf6" label="--> SBS 24 Sig. Mut. ALL">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
415 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
416 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
417
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
418 <data format="txt" name="SeqInf7" label="--> SBS 96 Sig. Mut. ALL">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
419 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
420 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
421
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
422 <data format="txt" name="SeqInf8" label="--> SBS 384 Sig. Mut. ALL">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
423 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
424 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
425
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
426 <data format="txt" name="SeqInf9" label="--> SBS 1536 Sig. Mut. ALL">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
427 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
428 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
429
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
430 <data format="txt" name="SeqInf10" label="--> SBS 6144 Sig. Mut. ALL">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
431 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
432 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
433
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
434
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
435 <data format="txt" name="SeqInf11" label="--> ID 28 Sig. Mut. ALL">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
436 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
437 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
438
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
439 <data format="txt" name="SeqInf12" label="--> ID 83 Sig. Mut. ALL">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
440 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
441 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
442
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
443 <data format="txt" name="SeqInf13" label="--> ID 94 Sig. Mut. ALL">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
444 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
445 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
446
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
447 <data format="txt" name="SeqInf14" label="--> ID 96 Sig. Mut. ALL">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
448 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
449 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
450
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
451 <data format="txt" name="SeqInf15" label="--> ID 415 Sig. Mut. ALL">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
452 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
453 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
454
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
455 <data format="txt" name="SeqInf16" label="--> ID 8628 Sig. Mut. ALL">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
456 <filter>set_analysis['choices'] == 'get_sigmut' and set_analysis['seqInfo'] is True</filter>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
457 </data>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
458
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
459 </outputs>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
460
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
461 <tests>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
462 <test>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
463 <conditional name="set_analysis">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
464 <param name="choices" value="install_genome"/>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
465 <param name="refgendwn" ftype="fasta" value="c_elegans"/>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
466 </conditional>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
467 <output name="logref" file="c_elegans.log" lines_diff="5"/>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
468 </test>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
469
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
470
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
471 <test>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
472 <conditional name="set_analysis">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
473 <param name="choices" value="get_sigmut"/>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
474 <param name="refgendat" ftype="fasta" value="c_elegans"/>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
475 <conditional name="vcfile_input">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
476 <param name="vcfile" value="icgc"/>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
477 <param name="icgc_file" ftype="txt" value="test_matrix.txt"/>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
478 </conditional>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
479 <conditional name="bed_input">
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
480 <param name="bedfile" value="no"/>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
481 </conditional>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
482 <param name="plot" value="True"/>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
483 </conditional>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
484
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
485 <output name="ID_simple" file="ID_simple.pdf" lines_diff="5"/>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
486 <output name="ID_TSB" file="ID_TSB.pdf" lines_diff="5"/>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
487 <output name="ID_83" file="ID_83.pdf" lines_diff="5"/>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
488
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
489 </test>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
490
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
491 </tests>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
492
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
493 <help><![CDATA[
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
494
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
495 **SigProfiler**
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
496
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
497 This script configures the SigProfiler analysis pipeline.
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
498 You must specify a VCF file for at least one sample.
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
499
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
500
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
501 **Options**
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
502 --version show program's version number and exit
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
503
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
504 -h, --help show this help message and exit
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
505
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
506 --install_genome Install de novo any of the following reference
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
507 genomes: 'GRCh37', 'GRCh38', 'mm9' or 'mm10'.
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
508
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
509 --name=APPENDIX Provide a project name
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
510
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
511 --genome=NAME Provide a reference genome (ex: GRCh37, GRCh38,
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
512 mm9 or mm10).
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
513
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
514 --files=Abs_path Path where the input vcf files are located
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
515
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
516 --exome Use only the exome or not
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
517
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
518 --bed=FILE BED file containing the set of regions to be used
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
519 in generating the matrices
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
520
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
521 --chrom Create the matrices on a per chromosome basis
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
522
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
523 --plot Generate the plots for each context
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
524
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
525 --tsb Performs a transcriptional strand bias test for the
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
526 24, 384, and 6144 contexts
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
527
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
528 --gs Performs a gene strand bias test
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
529
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
530 For further info see: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
531
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
532 ]]></help>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
533
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
534 <citations>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
535 <citation type="doi">10.1186/s12864-019-6041-2</citation>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
536 </citations>
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
537
9f48c5d97be8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637"
artbio
parents:
diff changeset
538 </tool>