Mercurial > repos > artbio > manta
changeset 6:cb5691381acb draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 01bc6749826f5ef4a22540a9aa6a5ffd93786d4c
| author | artbio |
|---|---|
| date | Thu, 08 Jun 2023 17:36:38 +0000 |
| parents | f55d45b0c6d1 |
| children | 555971edd46e |
| files | manta.xml manta_macros.xml |
| diffstat | 2 files changed, 40 insertions(+), 113 deletions(-) [+] |
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--- a/manta.xml Tue Jun 09 06:23:39 2020 -0400 +++ b/manta.xml Thu Jun 08 17:36:38 2023 +0000 @@ -1,7 +1,5 @@ -<tool id="manta" name="Manta" version="@WRAPPER_VERSION@"> - +<tool id="manta" name="Manta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> <description>Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads.</description> - <macros> <import>manta_macros.xml</import> </macros> @@ -9,7 +7,6 @@ <expand macro="stdio"/> <command detect_errors="exit_code"><![CDATA[ - @VERSION@ @pipefail@ @set_reference_fasta_filename@ #set run_dir = './MantaWorkflow' @@ -29,7 +26,7 @@ #end if #if str( $set_configuration.set_configuration_switch ) == "Customized": rm ./configManta.py.ini && - python $__tool_directory__/customConfigManta.py + python '$__tool_directory__/customConfigManta.py' --minCandidateVariantSize '$set_configuration.minCandidateVariantSize' --rnaMinCandidateVariantSize '$set_configuration.rnaMinCandidateVariantSize' --minEdgeObservations '$set_configuration.minEdgeObservations' @@ -46,22 +43,22 @@ --useOverlapPairEvidence '$set_configuration.useOverlapPairEvidence' && #end if - configManta.py --referenceFasta='${reference_fasta_filename}' - --config='./configManta.py.ini' - #if str( $bam_input.bam_input_selector ) == "not_tumor_bam": - --bam='normal.bam' - #else if str( $bam_input.bam_input_selector ) == "tumor_bam": - --bam='normal.bam' - --tumorBam='tumor.bam' - #end if - --runDir='${run_dir}' - --scanSizeMb=${advanced.scanSizeMb} - --callMemMb=${advanced.callMemMb} && + configManta.py + --referenceFasta='${reference_fasta_filename}' + --config='./configManta.py.ini' + #if str( $bam_input.bam_input_selector ) == "not_tumor_bam": + --bam='normal.bam' + #else if str( $bam_input.bam_input_selector ) == "tumor_bam": + --bam='normal.bam' + --tumorBam='tumor.bam' + #end if + --runDir='${run_dir}' + --scanSizeMb=${advanced.scanSizeMb} + --callMemMb=${advanced.callMemMb} && python2 '${run_dir}/runWorkflow.py' -m local -j \${GALAXY_SLOTS:-4} ]]></command> - <inputs> <expand macro="reference_source_conditional" /> <conditional name="bam_input"> @@ -143,30 +140,30 @@ </outputs> <tests> <test> - <param name="reference_source_selector" value="cached"/> - <param name="index" value="hg19"/> - <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/> - <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/> - <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/> - <param name="set_configuration_switch" value="Default_config_file"/> - <param name="callMemMb" value="1000"/> - <param name="candidateSmallIndels_check" value="True"/> - <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/> - <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/> + <param name="reference_source_selector" value="cached"/> + <param name="index" value="hg19"/> + <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/> + <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/> + <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/> + <param name="set_configuration_switch" value="Default_config_file"/> + <param name="callMemMb" value="1000"/> + <param name="candidateSmallIndels_check" value="True"/> + <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/> + <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/> </test> - <test> - <param name="reference_source_selector" value="cached"/> - <param name="index" value="hg19"/> - <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/> - <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/> - <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/> - <param name="set_configuration_switch" value="Customized"/> - <param name="callMemMb" value="1000"/> - <param name="candidateSmallIndels_check" value="True"/> - <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/> - <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/> + <test> + <param name="reference_source_selector" value="cached"/> + <param name="index" value="hg19"/> + <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/> + <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/> + <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/> + <param name="set_configuration_switch" value="Customized"/> + <param name="callMemMb" value="1000"/> + <param name="candidateSmallIndels_check" value="True"/> + <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/> + <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/> </test> - <test> + <test> <param name="reference_source_selector" value="cached"/> <param name="index" value="hg19"/> <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/> @@ -252,78 +249,8 @@ can execute the workflow on a single node or through sge and resume any interrupted execution. -**Options** - --version show program's version number and exit - -h, --help show this help message and exit - --config=FILE provide a configuration file to override defaults in - global config file (/home/lpanunzi/Desktop/Hackaton_GC - C2019/manta_sv/manta/bin/configManta.py.ini) - --allHelp show all extended/hidden options -**Workflow options** - --bam=FILE, --normalBam=FILE - Normal sample BAM or CRAM file. May be specified more - than once, multiple inputs will be treated as each BAM - file representing a different sample. [optional] (no - default) - --tumorBam=FILE, --tumourBam=FILE - Tumor sample BAM or CRAM file. Only up to one tumor - bam file accepted. [optional] (no default) - --exome Set options for WES input: turn off depth filters - --rna Set options for RNA-Seq input. Must specify exactly - one bam input file - --unstrandedRNA Set if RNA-Seq input is unstranded: Allows splice- - junctions on either strand - --referenceFasta=FILE - samtools-indexed reference fasta file [required] - --runDir=DIR Name of directory to be created where all workflow - scripts and output will be written. Each analysis - requires a separate directory. (default: - MantaWorkflow) - --callRegions=FILE Optionally provide a bgzip-compressed/tabix-indexed - BED file containing the set of regions to call. No VCF - output will be provided outside of these regions. The - full genome will still be used to estimate statistics - from the input (such as expected fragment size - distribution). Only one BED file may be specified. - (default: call the entire genome) -**Extended options** - These options are either unlikely to be reset after initial site - configuration or only of interest for workflow development/debugging. - They will not be printed here if a default exists unless --allHelp is - specified - - --existingAlignStatsFile=FILE - Pre-calculated alignment statistics file. Skips - alignment stats calculation. - --useExistingChromDepths - Use pre-calculated chromosome depths. - --candidateBins=candidateBins - Provide the total number of tasks which candidate - generation will be sub-divided into. (default: 256) - --retainTempFiles Keep all temporary files (for workflow debugging) - --generateEvidenceBam - Generate a bam of supporting reads for all SVs - --outputContig Output assembled contig sequences in VCF file - --scanSizeMb=INT Maximum sequence region size (in megabases) scanned by - each task during SV Locus graph generation. (default: - 12) - --region=REGION Limit the analysis to a region of the genome for - debugging purposes. If this argument is provided - multiple times all specified regions will be analyzed - together. All regions must be non-overlapping to get a - meaningful result. Examples: '--region chr20' (whole - chromosome), '--region chr2:100-2000 --region - chr3:2500-3000' (two regions)'. If this option is - specified (one or more times) together with the - --callRegions BED file, then all region arguments will - be intersected with the callRegions BED track. - --callMemMb=INT Set default task memory requirement (in megabytes) for - common tasks. This may benefit an analysis of unusual - depth, chimera rate, etc.. 'Common' tasks refers to - most compute intensive scatter-phase tasks of graph - creation and candidate generation. - For further info see: https://github.com/Illumina/manta +For further info see: https://github.com/Illumina/manta ]]></help> <citations>
--- a/manta_macros.xml Tue Jun 09 06:23:39 2020 -0400 +++ b/manta_macros.xml Thu Jun 08 17:36:38 2023 +0000 @@ -1,7 +1,7 @@ <macros> - <token name="@VERSION@">1.6</token> - <token name="@WRAPPER_VERSION@">@VERSION@+galaxy7</token> + <token name="@TOOL_VERSION@">1.6</token> + <token name="@VERSION_SUFFIX@">8</token> <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token> <token name="@set_reference_fasta_filename@"><![CDATA[ @@ -29,7 +29,7 @@ <xml name="requirements"> <requirements> <requirement type="package" version="1.7">samtools</requirement> - <requirement type="package" version="@VERSION@">manta</requirement> + <requirement type="package" version="@TOOL_VERSION@">manta</requirement> </requirements> </xml>