| Next changeset 1:02861b32a62f (2020-06-14) |
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Commit message:
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sigmut commit 67331c79ccaf0f2a3089e4ca0c62520397f90637" |
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added:
install.log sigmut.xml sigmut_macros.xml test-data/ID_83.pdf test-data/ID_TSB.pdf test-data/ID_simple.pdf test-data/c_elegans.log test-data/test_matrix.txt |
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| diff -r 000000000000 -r 9f48c5d97be8 install.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/install.log Mon Mar 16 06:15:02 2020 -0400 |
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| @@ -0,0 +1,6 @@ +wget: missing URL +Usage: wget [OPTION]... [URL]... + +Try `wget --help' for more options. + +Redirecting output to ‘wget-log’. |
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| diff -r 000000000000 -r 9f48c5d97be8 sigmut.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sigmut.xml Mon Mar 16 06:15:02 2020 -0400 |
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| b'@@ -0,0 +1,538 @@\n+\xef\xbb\xbf<tool id="SigProfiler" name="SigProfiler" version="@VERSION@">\n+\t<description>SigProfiler performs the mutational signature characterization from VCF files.</description>\n+\n+\t<macros>\n+\t\t<import>sigmut_macros.xml</import>\n+\t</macros>\n+\t<expand macro="requirements"/>\n+\t<expand macro="stdio"/>\n+\t<command detect_errors="exit_code"><![CDATA[\n+\t\t@VERSION@\n+\t\t@pipefail@\n+\t\t#import os\n+\t\t#import random\n+\t\t#import datetime\n+ #set job_dir=os.getcwd()\n+\t\t#set run_dir = job_dir + (\' \' + str(random.randint(1,100000))).strip() + \'/\'\n+\t\t#set job_num = "Job_" + (\' \' + str(random.randint(1,500))).strip()\n+\t\t\n+\t\tmkdir $run_dir &&\n+\n+\t\t#if str( $set_analysis.choices ) == "install_genome":\n+\t\tln -s -f \'$__tool_directory__/install.log\' \'${logref}\' &&\n+\t\t#else if str( $set_analysis.choices ) == "get_sigmut":\n+\t\t#set err_file = $run_dir + "logs/SigProfilerMatrixGenerator_" + $job_num + "_" + str($set_analysis.refgendat) + str(datetime.date.today()) + ".err"\n+\t\t#set log_file = $run_dir + "logs/SigProfilerMatrixGenerator_" + $job_num + "_" + str($set_analysis.refgendat) + str(datetime.date.today()) + ".out"\n+\t\t\n+\t\t#set plot1 = $run_dir + "output/plots/SBS_6_plots_" + $job_num + ".pdf" \n+\t\t#set plot2 = $run_dir + "output/plots/SBS_24_plots_" + $job_num + ".pdf"\n+\t\t#set plot3 = $run_dir + "output/plots/SBS_78_plots_" + $job_num + ".pdf"\n+\t\t#set plot4 = $run_dir + "output/plots/SBS_96_plots_" + $job_num + ".pdf"\n+\t\t#set plot5 = $run_dir + "output/plots/SBS_384_plots_" + $job_num + ".pdf"\n+\t\t#set plot6 = $run_dir + "output/plots/SBS_1536_plots_" + $job_num + ".pdf"\n+\t\t#set plot7 = $run_dir + "output/plots/DBS_78_plots_" + $job_num + ".pdf"\n+\t\t#set plot8 = $run_dir + "output/plots/DBS_186_plots_" + $job_num + ".pdf"\n+\n+\t\t#set plot9 = $run_dir + "output/plots/ID_simple_plots_" + $job_num + ".pdf"\n+\t\t#set plot10 = $run_dir + "output/plots/ID_TSB_plots_" + $job_num + ".pdf"\n+\t\t#set plot11 = $run_dir + "output/plots/ID_83_plots_" + $job_num + ".pdf"\n+\t\t#set plot12 = $run_dir + "output/plots/ID_94_plots_" + $job_num + ".pdf"\n+\t\t#set plot13 = $run_dir + "output/plots/ID_96_plots_" + $job_num + ".pdf"\n+\t\t\n+\t\t#set exo1 = $run_dir + "output/DBS/" + $job_num + ".DBS78" + ".exome" \n+\t\t#set exo2 = $run_dir + "output/DBS/" + $job_num + ".DBS186" + ".exome"\n+\t\t#set exo3 = $run_dir + "output/DBS/" + $job_num + ".DBS1248" + ".exome"\n+\t\t#set exo4 = $run_dir + "output/DBS/" + $job_num + ".DBS2976" + ".exome"\n+\n+\t\t#set exo5 = $run_dir + "output/SBS/" + $job_num + ".SBS6" + ".exome"\n+\t\t#set exo6 = $run_dir + "output/SBS/" + $job_num + ".SBS24" + ".exome"\n+\t\t#set exo7 = $run_dir + "output/SBS/" + $job_num + ".SBS96" + ".exome"\n+\t\t#set exo8 = $run_dir + "output/SBS/" + $job_num + ".SBS384" + ".exome"\n+\t\t#set exo9 = $run_dir + "output/SBS/" + $job_num + ".SBS1536" + ".exome"\n+\t\t#set exo10 = $run_dir + "output/SBS/" + $job_num + ".SBS6144" + ".exome"\n+\n+\t\t#set exo11 = $run_dir + "output/vcf_files/DBS/" + $job_num + "_" + "DBS_exome.vcf"\n+\t\t#set exo12 = $run_dir + "output/vcf_files/SNV/" + $job_num + "_" + "SNV_exome.vcf"\n+\t\t\n+\t\t#set tsb1 = $run_dir + "output/TSB/strandBiasTest_24.txt"\n+\t\t#set tsb2 = $run_dir + "output/TSB/strandBiasTest_384.txt"\n+\t\t#set tsb3 = $run_dir + "output/TSB/strandBiasTest_6144.txt"\n+\t\t#set tsb4 = $run_dir + "output/TSB/significantResults_strandBiasTest.txt"\n+\n+\t\t#set seqinf1 = $run_dir + "output/DBS/" + $job_num + ".DBS78" + ".all" \n+\t\t#set seqinf2 = $run_dir + "output/DBS/" + $job_num + ".DBS186" + ".all"\n+\t\t#set seqinf3 = $run_dir + "output/DBS/" + $job_num + ".DBS1248" + ".all"\n+\t\t#set seqinf4 = $run_dir + "output/DBS/" + $job_num + ".DBS2976" + ".all"\n+\n+\t\t#set seqinf5 = $run_dir + "output/SBS/" + $job_num + ".SBS6" + ".all"\n+\t\t#set seqinf6 = $run_dir + "output/SBS/" + $job_num + ".SBS24" + ".all"\n+\t\t#set seqinf7 = $run_dir + "output/SBS/" + $job_num + ".SBS96" + ".all"\n+\t\t#set seqinf8 = $run_dir + "output/SBS/" + $job_num + ".SBS384" + ".all"\n+\t\t#set seqinf9 = $run_dir + "output/SBS/" + $job_num + ".SBS1536'..b'SeqInf7" label="--> SBS 96 Sig. Mut. ALL">\n+\t\t\t<filter>set_analysis[\'choices\'] == \'get_sigmut\' and set_analysis[\'seqInfo\'] is True</filter>\n+\t\t</data>\n+\n+\t\t<data format="txt" name="SeqInf8" label="--> SBS 384 Sig. Mut. ALL">\n+\t\t\t<filter>set_analysis[\'choices\'] == \'get_sigmut\' and set_analysis[\'seqInfo\'] is True</filter>\n+\t\t</data>\n+\n+\t\t<data format="txt" name="SeqInf9" label="--> SBS 1536 Sig. Mut. ALL">\n+\t\t\t<filter>set_analysis[\'choices\'] == \'get_sigmut\' and set_analysis[\'seqInfo\'] is True</filter>\n+\t\t</data>\n+\n+\t\t<data format="txt" name="SeqInf10" label="--> SBS 6144 Sig. Mut. ALL">\n+\t\t\t<filter>set_analysis[\'choices\'] == \'get_sigmut\' and set_analysis[\'seqInfo\'] is True</filter>\n+\t\t</data>\n+\n+\n+\t\t<data format="txt" name="SeqInf11" label="--> ID 28 Sig. Mut. ALL">\n+\t\t\t<filter>set_analysis[\'choices\'] == \'get_sigmut\' and set_analysis[\'seqInfo\'] is True</filter>\n+\t\t</data>\n+\n+\t\t<data format="txt" name="SeqInf12" label="--> ID 83 Sig. Mut. ALL">\n+\t\t\t<filter>set_analysis[\'choices\'] == \'get_sigmut\' and set_analysis[\'seqInfo\'] is True</filter>\n+\t\t</data>\n+\n+\t\t<data format="txt" name="SeqInf13" label="--> ID 94 Sig. Mut. ALL">\n+\t\t\t<filter>set_analysis[\'choices\'] == \'get_sigmut\' and set_analysis[\'seqInfo\'] is True</filter>\n+\t\t</data>\n+\n+\t\t<data format="txt" name="SeqInf14" label="--> ID 96 Sig. Mut. ALL">\n+\t\t\t<filter>set_analysis[\'choices\'] == \'get_sigmut\' and set_analysis[\'seqInfo\'] is True</filter>\n+\t\t</data>\n+\n+\t\t<data format="txt" name="SeqInf15" label="--> ID 415 Sig. Mut. ALL">\n+\t\t\t<filter>set_analysis[\'choices\'] == \'get_sigmut\' and set_analysis[\'seqInfo\'] is True</filter>\n+\t\t</data>\n+\n+\t\t<data format="txt" name="SeqInf16" label="--> ID 8628 Sig. Mut. ALL">\n+\t\t\t<filter>set_analysis[\'choices\'] == \'get_sigmut\' and set_analysis[\'seqInfo\'] is True</filter>\n+\t\t</data>\n+\n+\t</outputs>\n+\n+\t<tests>\n+\t\t<test>\n+\t\t\t<conditional name="set_analysis">\n+\t\t\t\t<param name="choices" value="install_genome"/>\n+\t\t\t\t<param name="refgendwn" ftype="fasta" value="c_elegans"/>\n+\t\t\t</conditional>\n+\t\t\t<output name="logref" file="c_elegans.log" lines_diff="5"/>\n+\t\t</test>\n+\n+\n+\t\t<test>\n+\t\t\t<conditional name="set_analysis">\n+\t\t\t\t<param name="choices" value="get_sigmut"/>\n+\t\t\t\t<param name="refgendat" ftype="fasta" value="c_elegans"/>\n+\t\t\t\t<conditional name="vcfile_input">\n+\t\t\t\t\t<param name="vcfile" value="icgc"/>\n+\t\t\t\t\t<param name="icgc_file" ftype="txt" value="test_matrix.txt"/>\n+\t\t\t\t</conditional>\n+\t\t\t\t<conditional name="bed_input">\n+\t\t\t\t\t<param name="bedfile" value="no"/>\t\n+\t\t\t\t</conditional>\n+\t\t\t\t<param name="plot" value="True"/>\n+\t\t\t</conditional>\n+\n+\t\t<output name="ID_simple" file="ID_simple.pdf" lines_diff="5"/>\n+\t\t<output name="ID_TSB" file="ID_TSB.pdf" lines_diff="5"/>\n+\t\t<output name="ID_83" file="ID_83.pdf" lines_diff="5"/>\n+\n+\t\t</test>\n+\n+\t</tests>\n+\n+\t<help><![CDATA[\n+\n+\t\t**SigProfiler**\n+\n+\t\tThis script configures the SigProfiler analysis pipeline.\n+\t\tYou must specify a VCF file for at least one sample.\n+\n+\n+\t\t**Options**\n+\t\t--version \tshow program\'s version number and exit\n+\n+\t\t-h, --help \tshow this help message and exit\n+\n+\t\t--install_genome\tInstall de novo any of the following reference\n+\t\t\t\t\tgenomes: \'GRCh37\', \'GRCh38\', \'mm9\' or \'mm10\'.\n+\n+\t\t--name=APPENDIX\t\tProvide a project name\n+\n+\t\t--genome=NAME\t\tProvide a reference genome (ex: GRCh37, GRCh38,\n+\t\t\t\t\tmm9 or mm10).\n+\n+\t\t--files=Abs_path\tPath where the input vcf files are located\n+\n+\t\t--exome\t\t\tUse only the exome or not\n+\n+\t\t--bed=FILE\t\tBED file containing the set of regions to be used\n+\t\t\t\t\tin generating the matrices\n+\n+\t\t--chrom\t\t\tCreate the matrices on a per chromosome basis\n+\n+\t\t--plot\t\t\tGenerate the plots for each context\n+\n+\t\t--tsb\t\t\tPerforms a transcriptional strand bias test for the\n+\t\t\t\t\t24, 384, and 6144 contexts\n+\n+\t\t--gs\t\t\tPerforms a gene strand bias test\n+\n+\t\tFor further info see: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator\n+\n+\t\t]]></help>\n+\n+\t<citations>\n+\t\t<citation type="doi">10.1186/s12864-019-6041-2</citation>\n+\t</citations>\n+\n+</tool>\n' |
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| diff -r 000000000000 -r 9f48c5d97be8 sigmut_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sigmut_macros.xml Mon Mar 16 06:15:02 2020 -0400 |
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| @@ -0,0 +1,23 @@ +<macros> + + <token name="@VERSION@">0.9.1</token> + + <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.0">sigmut</requirement> + </requirements> + </xml> + + <xml name="stdio"> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <regex match="Error:" /> + <regex match="Exception:" /> + <regex match="\[bns_restore_core\] Parse error reading" /> + </stdio> + </xml> + +</macros> |
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| diff -r 000000000000 -r 9f48c5d97be8 test-data/ID_83.pdf |
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| Binary file test-data/ID_83.pdf has changed |
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| diff -r 000000000000 -r 9f48c5d97be8 test-data/ID_TSB.pdf |
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| Binary file test-data/ID_TSB.pdf has changed |
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| diff -r 000000000000 -r 9f48c5d97be8 test-data/ID_simple.pdf |
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| Binary file test-data/ID_simple.pdf has changed |
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| diff -r 000000000000 -r 9f48c5d97be8 test-data/c_elegans.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/c_elegans.log Mon Mar 16 06:15:02 2020 -0400 |
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| @@ -0,0 +1,6 @@ +wget: missing URL +Usage: wget [OPTION]... [URL]... + +Try `wget --help' for more options. + +Redirecting output to ‘wget-log’. |
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| diff -r 000000000000 -r 9f48c5d97be8 test-data/test_matrix.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_matrix.txt Mon Mar 16 06:15:02 2020 -0400 |
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| b'@@ -0,0 +1,440469 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