Mercurial > repos > iuc > control_freec
changeset 1:1204e79d3a99 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
| author | iuc |
|---|---|
| date | Tue, 31 Aug 2021 08:10:37 +0000 |
| parents | 5330cf818142 |
| children | 74cb429038c1 |
| files | control_freec.xml macros.xml ratio2circos.py |
| diffstat | 3 files changed, 34 insertions(+), 25 deletions(-) [+] |
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--- a/control_freec.xml Thu Aug 13 13:49:44 2020 +0000 +++ b/control_freec.xml Tue Aug 31 08:10:37 2021 +0000 @@ -1,5 +1,8 @@ <tool id="control_freec" name="Control-FREEC" version="@WRAPPER_VERSION@"> <description>detects copy-number changes and allelic imbalances</description> + <xrefs> + <xref type="bio.tools">freec</xref> + </xrefs> <macros> <import>macros.xml</import> </macros> @@ -13,11 +16,15 @@ samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for control-freec' >&2 && #else ln -s '$reference_source.ref.fields.path' ./genome.fa && - ln -s '${reference_source.ref.fields.path}.fai' ./genome.fa.fai && + cp '${reference_source.ref.fields.path}.fai' ./genome.fa.fai && #end if #if int($WGS_WES.advanced_settings.window_section.window) == 0 ln -s '$WGS_WES.input_capture_file' ./capture.bed && + + cat ./capture.bed | cut -f 1 | sort | uniq > ./capture.bed_tmp && + cp ./genome.fa.fai ./genome.fa.fai_tmp && + awk 'NR==FNR{A[$1];next}($1 in A)' ./capture.bed_tmp ./genome.fa.fai_tmp > ./genome.fa.fai && #end if mkdir ./chromosomes && @@ -42,10 +49,7 @@ #end if #if $output_section.circos_data - && python '$__tool_directory__/ratio2circos.py' - -i ./output/sample.bam_ratio.BedGraph - -p '$WGS_WES.advanced_settings.ploidy' - -o sample.bam_ratio_log2_circos.txt + && python '$__tool_directory__/ratio2circos.py' '$WGS_WES.advanced_settings.ploidy' #end if ]]></command> <configfiles> @@ -159,7 +163,10 @@ <data name="out_gc_profile" format="tabular" label="${tool.name} on ${on_string}: GC-content profile" from_work_dir="output/GC_profile.targetedRegions.cnp"> <filter>int(WGS_WES['advanced_settings']['window_section']['window']) == 0</filter> </data> - <data name="out_ratio_log2_circos" format="tabular" label="${tool.name} on ${on_string}: Circos 2D-track data" from_work_dir="output/sample.bam_ratio_log2_circos.txt"> + <data name="out_ratio_log2_circos" format="tabular" label="${tool.name} on ${on_string}: Circos Log2 Ratio (2D Data Track)" from_work_dir="output/sample.bam_ratio_log2_circos.txt"> + <filter>output_section['circos_data']</filter> + </data> + <data name="out_chr_sorted_circos" format="tabular" label="${tool.name} on ${on_string}: Circos Karyotype" from_work_dir="output/karyotype_circos.txt"> <filter>output_section['circos_data']</filter> </data> </outputs>
--- a/macros.xml Thu Aug 13 13:49:44 2020 +0000 +++ b/macros.xml Tue Aug 31 08:10:37 2021 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy0</token> + <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy1</token> <token name="@TOOL_VERSION@">11.6</token> <xml name="reference_interface"> <conditional name="reference_source"> @@ -40,6 +40,8 @@ <param name="window" type="integer" value="50000" label="Explicit window size" help="Higher priority than coefficientOfVariation. Ex: for whole genome sequencing: "50000"; for whole exome sequencing: "0"" /> <param name="step" type="integer" value="10000" label="Step" help="Used only when "window" is specified. Do not use for exome sequencing (instead set "0"). Ex: 10000" /> </section> + <param name="printNA" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Print NA to avoid "-1"" help="Set "No" to avoid printing "-1" to the _ratio.txt files. Useful for exome-seq or targeted sequencing data." /> + <param name="noisyData" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Noisy Data" help="Set "Yes" for target resequencing data (e.g., exome-seq) to avoid false positive predictions due to non-uniform capture" /> </xml> <xml name="WES"> <param name="degree" type="select" label="Degree of polynomial" help=""> @@ -61,6 +63,8 @@ <param name="window" type="integer" value="0" label="Explicit window size" help="Higher priority than coefficientOfVariation. Ex: for whole genome sequencing: "50000"; for whole exome sequencing: "0"" /> <param name="step" type="integer" value="0" label="Step" help="Used only when "window" is specified. Do not use for exome sequencing (instead set "0"). Ex: 10000" /> </section> + <param name="printNA" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Print NA to avoid "-1"" help="Set "No" to avoid printing "-1" to the _ratio.txt files. Useful for exome-seq or targeted sequencing data." /> + <param name="noisyData" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Noisy Data" help="Set "Yes" for target resequencing data (e.g., exome-seq) to avoid false positive predictions due to non-uniform capture" /> </xml> <xml name="other"> <param name="degree" type="select" label="Degree of polynomial" help=""> @@ -82,6 +86,8 @@ <param name="window" type="integer" value="50000" label="Explicit window size" help="Higher priority than coefficientOfVariation. Ex: for whole genome sequencing: "50000"; for whole exome sequencing: "0"" /> <param name="step" type="integer" value="10000" label="Step" help="Used only when "window" is specified. Do not use for exome sequencing (instead set "0"). Ex: 10000" /> </section> + <param name="printNA" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Print NA to avoid "-1"" help="Set "No" to avoid printing "-1" to the _ratio.txt files. Useful for exome-seq or targeted sequencing data." /> + <param name="noisyData" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Noisy Data" help="Set "Yes" for target resequencing data (e.g., exome-seq) to avoid false positive predictions due to non-uniform capture" /> </xml> <xml name="shared"> <!-- general parameters --> @@ -105,9 +111,7 @@ <param name="minMappabilityPerWindow" type="float" label="Minimal mappability per window" value="0.85" min="0" max="1" help="Only windows with fraction of mappable positions higher than or equal to this threshold will be considered (if "gemMappabilityFile" is not provided, one uses the percentage of non-N letters per window)" /> <param name="minExpectedGC" type="float" label="Minimal expected value of the GC-content" value="0.35" min="0" max="1" help="Minimal expected value of the GC-content for the prior evaluation of "Read Count ~ GC-content" dependency. Change only if you run Control-FREEC on a bacterial genome." /> <param name="maxExpectedGC" type="float" label="Maximal expected value of the GC-content" value="0.55" min="0" max="1" help="Maximal expected value of the GC-content for the prior evaluation of "Read Count ~ GC-content" dependency. Change only if you run Control-FREEC on a bacterial genome." /> - <param name="noisyData" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Noisy Data" help="Set "Yes" for target resequencing data (e.g., exome-seq) to avoid false positive predictions due to non-uniform capture" /> <param name="ploidy" type="text" value="2" label="Genome ploidy" help="In case of doubt, you can set different values and Control-FREEC will select the one that explains most observed CNAs. Ex: 2 or 2,3,4" /> - <param name="printNA" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Print NA to avoid "-1"" help="Set "No" to avoid printing "-1" to the _ratio.txt files. Useful for exome-seq or targeted sequencing data." /> <param name="sex" type="select" label="Sample sex" help=""XX" will exclude chr Y from the analysis. "XY" will not annotate one copy of chr X and Y as a loss."> <option value="XY" selected="True">XY</option> <option value="XX">XX</option>
--- a/ratio2circos.py Thu Aug 13 13:49:44 2020 +0000 +++ b/ratio2circos.py Tue Aug 31 08:10:37 2021 +0000 @@ -1,20 +1,18 @@ -import argparse import math -import os +import sys -parser = argparse.ArgumentParser() -parser.add_argument('-i', '--input', required=True, default='./output/sample.bam_ratio.BedGraph', type=str) -parser.add_argument('-o', '--output', required=True, default='./output/sample.bam_ratio_log2_circos.txt', type=str) -parser.add_argument('-p', '--ploidy', required=True, default=2, type=int) -args = parser.parse_args() +ploidy = int(sys.argv[1]) -path = os.path.dirname(args.input) -output = os.path.join(path, args.output) +with open("./output/sample.bam_ratio.BedGraph") as bed: + with open("./output/sample.bam_ratio_log2_circos.txt", "w+") as olog2r: + for line in bed.readlines(): + ls = line.split() + if ls[0] != "track" and float(ls[3]) > 0: + log2_ratio = math.log2(float(ls[3]) / ploidy) + olog2r.write("{}\t{}\t{}\t{}\n".format(ls[0], ls[1], ls[2], log2_ratio)) -with open(args.input) as file: - for line in file.readlines(): - ls = line.split() - if ls[0] != "track" and float(ls[3]) > 0: - log2_ratio = math.log2(float(ls[3]) / args.ploidy) - with open(output, "a") as out: - out.write("{}\t{}\t{}\t{}\n".format(ls[0], ls[1], ls[2], log2_ratio)) +with open("./genome.fa.fai") as fai: + with open("./output/karyotype_circos.txt", "w+") as ochr: + for line in fai.readlines(): + ls = line.split() + ochr.write("chr - {}\t{}\t0\t{}\t{}\n".format(ls[0], ls[0].strip("chr").lower(), ls[1], ls[0]))