| Previous 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 097dc42275535b1ace343a7842d0dcfbb6ef6f38 |
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modified:
manta.xml manta_macros.xml |
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| diff -r 555971edd46e -r bebb4f9eba4f manta.xml --- a/manta.xml Tue Feb 20 08:31:27 2024 +0000 +++ b/manta.xml Fri Jan 16 17:19:22 2026 +0000 |
| [ |
| b'@@ -96,7 +96,7 @@\n <when value="Default_config_file">\n </when>\n <when value="Custom_config_file">\n- <param format="ini" name="CustomConfigFile" type="data" label="config file"/>\n+ <param format="txt" name="CustomConfigFile" type="data" label="config file"/>\n </when>\n <when value="Customized">\n <param name="minCandidateVariantSize" type="integer" value="8" label="minCandidateVariantSize" help="Run discovery and candidate reporting for all SVs/indels at or above this size."/>\n@@ -138,73 +138,99 @@\n <filter>bam_input[\'bam_input_selector\'] == \'tumor_bam\'</filter>\n </data>\n </outputs>\n+\n <tests>\n <test expect_num_outputs="3">\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="reference_source|reference_source_selector" value="cached"/>\n+ <param name="reference_source|index" value="hg19"/>\n+\n+ <param name="bam_input|bam_input_selector" value="tumor_bam" dbkey="hg19"/>\n+ <param name="bam_input|normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>\n+ <param name="bam_input|tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>\n+\n+ <param name="set_configuration|set_configuration_switch" value="Default_config_file"/>\n+ \n+ <param name="advanced|callMemMb" value="1000"/>\n+ \n <param name="candidateSmallIndels_check" value="True"/>\n <output name="conf_file" file="conf_file_1.ini" ftype="txt"/>\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 </test>\n+\n <test expect_num_outputs="3">\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="Customized"/>\n- <param name="callMemMb" value="1000"/>\n+ <param name="reference_source|reference_source_selector" value="cached"/>\n+ <param name="reference_source|index" value="hg19"/>\n+\n+ <param name="bam_input|bam_input_selector" value="tumor_bam" dbkey="hg19"/>\n+ <param name="bam_input|normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>\n+ <param name="bam_input|tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>\n+\n+ <param name="set_configuration|set_configuration_switch" value="Customized"/>\n+ \n+ <param name="advanced|callMemMb" value="1000"/>\n+ \n <param name="candidateSmallIndels_check" value="True"/>\n <output name="conf_file" file="conf_file_2.ini" ftype="txt"/>\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 </test>\n+\n <test expect_num_outputs="3">\n- <param name="reference_source_selector" value="cached"/>\n- <param name="index" value="hg19"/>\n- <param name="bam_input_selector" '..b'num_outputs="3">\n- <param name="reference_source_selector" value="history"/>\n- <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>\n- <param name="bam_input_selector" value="tumor_bam"/>\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="candidateSV_check" value="True"/>\n- <output name="conf_file" file="conf_file_4.ini" ftype="txt"/>\n- <output name="candidateSV" file="candidateSV.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|reference_source_selector" value="history"/>\n+ <param name="reference_source|ref_file" ftype="fasta" value="hg19_region.fa"/>\n+\n+ <param name="bam_input|bam_input_selector" value="tumor_bam"/>\n+ <param name="bam_input|normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>\n+ <param name="bam_input|tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>\n+\n+ <param name="set_configuration|set_configuration_switch" value="Default_config_file"/>\n+ \n+ <param name="advanced|callMemMb" value="1000"/>\n+ \n+ <param name="candidateSV_check" value="True"/>\n+ <output name="conf_file" file="conf_file_4.ini" ftype="txt"/>\n+ <output name="candidateSV" file="candidateSV.vcf.gz" decompress="true" lines_diff="6"/>\n+ <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>\n </test>\n+\n <test expect_num_outputs="3">\n- <param name="reference_source_selector" value="history"/>\n- <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>\n- <param name="bam_input_selector" value="tumor_bam"/>\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="conf_file" file="conf_file_5.ini" ftype="txt"/>\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|reference_source_selector" value="history"/>\n+ <param name="reference_source|ref_file" ftype="fasta" value="hg19_region.fa"/>\n+\n+ <param name="bam_input|bam_input_selector" value="tumor_bam"/>\n+ <param name="bam_input|normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>\n+ <param name="bam_input|tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>\n+\n+ <param name="set_configuration|set_configuration_switch" value="Default_config_file"/>\n+ \n+ <param name="advanced|callMemMb" value="1000"/>\n+ \n+ <param name="candidateSmallIndels_check" value="True"/>\n+ <output name="conf_file" file="conf_file_5.ini" ftype="txt"/>\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 </test>\n </tests>\n+\n <help><![CDATA[\n **Outputs**\n The primary Manta outputs are a set of VCF 4.1 files. Currently there are 3 VCF files\n' |
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| diff -r 555971edd46e -r bebb4f9eba4f manta_macros.xml --- a/manta_macros.xml Tue Feb 20 08:31:27 2024 +0000 +++ b/manta_macros.xml Fri Jan 16 17:19:22 2026 +0000 |
| [ |
| @@ -1,7 +1,7 @@ <macros> <token name="@TOOL_VERSION@">1.6</token> - <token name="@VERSION_SUFFIX@">9</token> + <token name="@VERSION_SUFFIX@">10</token> <token name="@PROFILE@">20.05</token> <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token> @@ -30,7 +30,7 @@ <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">manta</requirement> - <requirement type="package" version="1.7">samtools</requirement> + <requirement type="package" version="1.9">samtools</requirement> </requirements> </xml> @@ -65,33 +65,4 @@ </when> </conditional> </macro> - - <macro name="manta_configuration"> - <conditional name="configuration"> - <param name="configuration_switch" type="select" label="How do you want to configure manta?"> - <option value="Custom_config_file">Upload a different config file</option> - <option value="Customized">Customize the options</option> - </param> - <when value="Custom_config_file"> - <param format="ini" name="CustomConfigFile" type="data" label="config file"/> - </when> - <when value="Customized"> - <param name="minCandidateVariantSize" type="integer" value="8" label="minCandidateVariantSize" help="Run discovery and candidate reporting for all SVs/indels at or above this size."/> - <param name="rnaMinCandidateVariantSize" type="integer" value="1000" label="rnaMinCandidateVariantSize" help="Separate option (to provide different default) used for runs in RNA-mode."/> - <param name="minEdgeObservations" type="integer" value="3" label="minEdgeObservations" help="Remove all edges from the graph unless they're supported by this many 'observations'."/> - <param name="graphNodeMaxEdgeCount" type="integer" value="10" label="graphNodeMaxEdgeCount" help="If both nodes of an edge have an edge count higher than this, then skip evaluation of the edge."/> - <param name="minCandidateSpanningCount" type="integer" value="3" label="minCandidateSpanningCount" help="Run discovery and candidate reporting for all SVs/indels with at least this many spanning support observations."/> - <param name="minScoredVariantSize" type="integer" value="50" label="minScoredVariantSize" help="After candidate identification, only score and report SVs/indels at or above this size."/> - <param name="minDiploidVariantScore" type="integer" value="10" label="minDiploidVariantScore" help="Minimum VCF 'QUAL' score for a variant to be included in the diploid vcf."/> - <param name="minPassDiploidVariantScore" type="integer" value="20" label="minPassDiploidVariantScore" help="VCF 'QUAL' score below which a variant is marked as filtered in the diploid vcf."/> - <param name="minPassDiploidGTScore" type="integer" value="15" label="minPassDiploidGTScore" help="Minimum genotype quality score below which single samples are filtered for a variant in the diploid vcf."/> - <param name="minSomaticScore" type="integer" value="10" label="minSomaticScore" help="Somatic quality scores below this level are not included in the somatic vcf."/> - <param name="minPassSomaticScore" type="integer" value="30" label="minPassSomaticScore" help="Somatic quality scores below this level are filtered in the somatic vcf."/> - <param name="enableRemoteReadRetrievalForInsertionsInGermlineCallingModes" type="integer" value="1" label="enableRemoteReadRetrievalForInsertionsInGermlineCallingModes" help="Remote read retrieval is used ot improve the assembly of putative insertions by retrieving any mate reads in remote locations with poor mapping quality. This feature can be enabled/disabled separately for germline and cancer calling below."/> - <param name="enableRemoteReadRetrievalForInsertionsInCancerCallingModes" type="integer" value="0" label="enableRemoteReadRetrievalForInsertionsInCancerCallingModes" help="Here 'CancerCallingModes' includes tumor-normal subtraction and tumor-only calling. 'GermlineCallingModes' includes all other calling modes."/> - <param name="useOverlapPairEvidence" type="integer" value="0" label="useOverlapPairEvidence" help="Set if an overlapping read pair will be considered as evidence. Set this value <= 0 to skip overlapping read pairs."/> - </when> - </conditional> - </macro> - </macros> |