manta: manta.xml comparison

comparison manta.xml @ 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

comparison

equal deleted inserted replaced

-:f55d45b0c6d1
+:cb5691381acb
-<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>
 <expand macro="requirements"/>
 <expand macro="stdio"/>
 <command detect_errors="exit_code"><![CDATA[
-@VERSION@
 @pipefail@
 @set_reference_fasta_filename@
 #set run_dir = './MantaWorkflow'
 cp $__tool_directory__/configManta.py.ini configManta.py.ini &&
 #if str( $bam_input.bam_input_selector ) == "not_tumor_bam":
 #if str( $set_configuration.set_configuration_switch ) == "Custom_config_file":
 cp '$set_configuration.CustomConfigFile' ./configManta.py.ini &&
 #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 '$set_configuration.minEdgeObservations'
 --graphNodeMaxEdgeCount '$set_configuration.graphNodeMaxEdgeCount'
 --minCandidateSpanningCount '$set_configuration.minCandidateSpanningCount'
 --enableRemoteReadRetrievalForInsertionsInGermlineCallingModes '$set_configuration.enableRemoteReadRetrievalForInsertionsInGermlineCallingModes'
 --enableRemoteReadRetrievalForInsertionsInCancerCallingModes '$set_configuration.enableRemoteReadRetrievalForInsertionsInCancerCallingModes'
 --useOverlapPairEvidence '$set_configuration.useOverlapPairEvidence' &&
 #end if
-configManta.py --referenceFasta='${reference_fasta_filename}'
+configManta.py
---config='./configManta.py.ini'
+--referenceFasta='${reference_fasta_filename}'
-#if str( $bam_input.bam_input_selector ) == "not_tumor_bam":
+--config='./configManta.py.ini'
---bam='normal.bam'
+#if str( $bam_input.bam_input_selector ) == "not_tumor_bam":
-#else if str( $bam_input.bam_input_selector ) == "tumor_bam":
+--bam='normal.bam'
---bam='normal.bam'
+#else if str( $bam_input.bam_input_selector ) == "tumor_bam":
---tumorBam='tumor.bam'
+--bam='normal.bam'
-#end if
+--tumorBam='tumor.bam'
---runDir='${run_dir}'
+#end if
---scanSizeMb=${advanced.scanSizeMb}
+--runDir='${run_dir}'
---callMemMb=${advanced.callMemMb} &&
+--scanSizeMb=${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">
 <param name="bam_input_selector" type="select" label="Single 'normal' or 'normal vs tumor' analysis" help="Select between a single normal BAM file or a pair of normal/tumor BAM files">
 <option value="not_tumor_bam">Normal</option>
 <filter>bam_input['bam_input_selector'] == 'tumor_bam'</filter>
 </data>
 </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"/>
+</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>
+<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="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>
-<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"/>
-</test>
 <test>
 <param name="reference_source_selector" value="history"/>
 <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>
 <param name="bam_input_selector" value="tumor_bam"/>
 <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
 You must specify a BAM or CRAM file for at least one sample.
 Configuration will produce a workflow run script which
 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
+For further info see: https://github.com/Illumina/manta
--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
 ]]></help>
 <citations>
 <citation type="doi">10.1093/bioinformatics/btv710</citation>
 </citations>

Mercurial > repos > artbio > manta

comparison manta.xml @ 6:cb5691381acb draft