| Previous changeset 5:f55d45b0c6d1 (2020-06-09) Next changeset 7:555971edd46e (2024-02-20) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 01bc6749826f5ef4a22540a9aa6a5ffd93786d4c |
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modified:
manta.xml manta_macros.xml |
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| diff -r f55d45b0c6d1 -r cb5691381acb manta.xml --- a/manta.xml Tue Jun 09 06:23:39 2020 -0400 +++ b/manta.xml Thu Jun 08 17:36:38 2023 +0000 |
| [ |
| b'@@ -1,7 +1,5 @@\n-\xef\xbb\xbf<tool id="manta" name="Manta" version="@WRAPPER_VERSION@">\n-\n+<tool id="manta" name="Manta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">\n <description>Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads.</description>\n-\n <macros>\n <import>manta_macros.xml</import>\n </macros>\n@@ -9,7 +7,6 @@\n <expand macro="stdio"/>\n \n <command detect_errors="exit_code"><![CDATA[\n- @VERSION@\n @pipefail@\n @set_reference_fasta_filename@\n #set run_dir = \'./MantaWorkflow\'\n@@ -29,7 +26,7 @@\n #end if\n #if str( $set_configuration.set_configuration_switch ) == "Customized":\n rm ./configManta.py.ini &&\n- python $__tool_directory__/customConfigManta.py\n+ python \'$__tool_directory__/customConfigManta.py\'\n --minCandidateVariantSize \'$set_configuration.minCandidateVariantSize\'\n --rnaMinCandidateVariantSize \'$set_configuration.rnaMinCandidateVariantSize\'\n --minEdgeObservations \'$set_configuration.minEdgeObservations\'\n@@ -46,22 +43,22 @@\n --useOverlapPairEvidence \'$set_configuration.useOverlapPairEvidence\' &&\n #end if\n \n- configManta.py --referenceFasta=\'${reference_fasta_filename}\'\n- --config=\'./configManta.py.ini\'\n- #if str( $bam_input.bam_input_selector ) == "not_tumor_bam":\n- --bam=\'normal.bam\'\n- #else if str( $bam_input.bam_input_selector ) == "tumor_bam":\n- --bam=\'normal.bam\'\n- --tumorBam=\'tumor.bam\'\n- #end if\n- --runDir=\'${run_dir}\'\n- --scanSizeMb=${advanced.scanSizeMb}\n- --callMemMb=${advanced.callMemMb} &&\n+ configManta.py\n+ --referenceFasta=\'${reference_fasta_filename}\'\n+ --config=\'./configManta.py.ini\'\n+ #if str( $bam_input.bam_input_selector ) == "not_tumor_bam":\n+ --bam=\'normal.bam\'\n+ #else if str( $bam_input.bam_input_selector ) == "tumor_bam":\n+ --bam=\'normal.bam\'\n+ --tumorBam=\'tumor.bam\'\n+ #end if\n+ --runDir=\'${run_dir}\'\n+ --scanSizeMb=${advanced.scanSizeMb}\n+ --callMemMb=${advanced.callMemMb} &&\n \n python2 \'${run_dir}/runWorkflow.py\' -m local -j \\${GALAXY_SLOTS:-4}\n \n ]]></command>\n-\n <inputs>\n <expand macro="reference_source_conditional" />\n <conditional name="bam_input">\n@@ -143,30 +140,30 @@\n </outputs>\n <tests>\n <test>\n- <param name="reference_source_selector" value="cached"/>\n- <param name="index" value="hg19"/>\n- <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>\n- <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>\n- <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>\n- <param name="set_configuration_switch" value="Default_config_file"/>\n- <param name="callMemMb" value="1000"/>\n- <param name="candidateSmallIndels_check" value="True"/>\n- <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/>\n- <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>\n+ <param name="reference_source_selector" value="cached"/>\n+ <param name="index" value="hg19"/>\n+ <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>\n+ <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>\n+ <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>\n+ <param name="set_configuration_switch" value="Default_config_file"/>\n+ <param name="callMemMb" value="1000"/>\n+ <param name="candidateSmallIndels_check" value="True"/>\n+ <output name="candidateSm'..b" than once, multiple inputs will be treated as each BAM\n- file representing a different sample. [optional] (no\n- default)\n- --tumorBam=FILE, --tumourBam=FILE\n- Tumor sample BAM or CRAM file. Only up to one tumor\n- bam file accepted. [optional] (no default)\n- --exome Set options for WES input: turn off depth filters\n- --rna Set options for RNA-Seq input. Must specify exactly\n- one bam input file\n- --unstrandedRNA Set if RNA-Seq input is unstranded: Allows splice-\n- junctions on either strand\n- --referenceFasta=FILE\n- samtools-indexed reference fasta file [required]\n- --runDir=DIR Name of directory to be created where all workflow\n- scripts and output will be written. Each analysis\n- requires a separate directory. (default:\n- MantaWorkflow)\n- --callRegions=FILE Optionally provide a bgzip-compressed/tabix-indexed\n- BED file containing the set of regions to call. No VCF\n- output will be provided outside of these regions. The\n- full genome will still be used to estimate statistics\n- from the input (such as expected fragment size\n- distribution). Only one BED file may be specified.\n- (default: call the entire genome)\n-**Extended options**\n- These options are either unlikely to be reset after initial site\n- configuration or only of interest for workflow development/debugging.\n- They will not be printed here if a default exists unless --allHelp is\n- specified\n- \n- --existingAlignStatsFile=FILE\n- Pre-calculated alignment statistics file. Skips\n- alignment stats calculation.\n- --useExistingChromDepths\n- Use pre-calculated chromosome depths.\n- --candidateBins=candidateBins\n- Provide the total number of tasks which candidate\n- generation will be sub-divided into. (default: 256)\n- --retainTempFiles Keep all temporary files (for workflow debugging)\n- --generateEvidenceBam\n- Generate a bam of supporting reads for all SVs\n- --outputContig Output assembled contig sequences in VCF file\n- --scanSizeMb=INT Maximum sequence region size (in megabases) scanned by\n- each task during SV Locus graph generation. (default:\n- 12)\n- --region=REGION Limit the analysis to a region of the genome for\n- debugging purposes. If this argument is provided\n- multiple times all specified regions will be analyzed\n- together. All regions must be non-overlapping to get a\n- meaningful result. Examples: '--region chr20' (whole\n- chromosome), '--region chr2:100-2000 --region\n- chr3:2500-3000' (two regions)'. If this option is\n- specified (one or more times) together with the\n- --callRegions BED file, then all region arguments will\n- be intersected with the callRegions BED track.\n- --callMemMb=INT Set default task memory requirement (in megabytes) for\n- common tasks. This may benefit an analysis of unusual\n- depth, chimera rate, etc.. 'Common' tasks refers to\n- most compute intensive scatter-phase tasks of graph\n- creation and candidate generation.\n \n- For further info see: https://github.com/Illumina/manta\n+For further info see: https://github.com/Illumina/manta\n \n ]]></help>\n <citations>\n" |
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| diff -r f55d45b0c6d1 -r cb5691381acb manta_macros.xml --- 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> |