Mercurial > repos > artbio > manta
diff manta.xml @ 7:555971edd46e draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
| author | artbio |
|---|---|
| date | Tue, 20 Feb 2024 08:31:27 +0000 |
| parents | cb5691381acb |
| children |
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--- a/manta.xml Thu Jun 08 17:36:38 2023 +0000 +++ b/manta.xml Tue Feb 20 08:31:27 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="manta" name="Manta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> +<tool id="manta" name="Manta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads.</description> <macros> <import>manta_macros.xml</import> @@ -10,6 +10,9 @@ @pipefail@ @set_reference_fasta_filename@ #set run_dir = './MantaWorkflow' + configManta=\$(which configManta.py) && + PATH=\${configManta/"configManta.py"/}:\$PATH && + printenv && cp $__tool_directory__/configManta.py.ini configManta.py.ini && #if str( $bam_input.bam_input_selector ) == "not_tumor_bam": ln -s '$bam_input.normal_bam_file' normal.bam && @@ -26,7 +29,7 @@ #end if #if str( $set_configuration.set_configuration_switch ) == "Customized": rm ./configManta.py.ini && - python '$__tool_directory__/customConfigManta.py' + python2 '$__tool_directory__/customConfigManta.py' --minCandidateVariantSize '$set_configuration.minCandidateVariantSize' --rnaMinCandidateVariantSize '$set_configuration.rnaMinCandidateVariantSize' --minEdgeObservations '$set_configuration.minEdgeObservations' @@ -112,7 +115,6 @@ <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> - <param name="config_file_check" type="boolean" label="output conf file" checked="False" help="Show configuration file on history"/> <param name="candidateSV_check" type="boolean" label="Unfiltered structural variants" checked="False" help="All unscored structural variant candidates"/> <param name="candidateSmallIndels_check" type="boolean" label="Unfiltered small indel candidates" checked="False" @@ -122,9 +124,7 @@ reflect any information from the tumor sample" /> </inputs> <outputs> - <data format="tabular" name="conf_file" label="conf_file.ini" from_work_dir="./configManta.py.ini"> - <filter>config_file_check == True</filter> - </data> + <data format="txt" name="conf_file" label="conf_file.ini" from_work_dir="./configManta.py.ini"/> <data format="vcf_bgzip" name="candidateSV" label="Manta unfiltered variants" from_work_dir="MantaWorkflow/results/variants/candidateSV.vcf.gz"> <filter>candidateSV_check == True</filter> </data> @@ -139,7 +139,7 @@ </data> </outputs> <tests> - <test> + <test expect_num_outputs="3"> <param name="reference_source_selector" value="cached"/> <param name="index" value="hg19"/> <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/> @@ -148,10 +148,11 @@ <param name="set_configuration_switch" value="Default_config_file"/> <param name="callMemMb" value="1000"/> <param name="candidateSmallIndels_check" value="True"/> + <output name="conf_file" file="conf_file_1.ini" ftype="txt"/> <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 expect_num_outputs="3"> <param name="reference_source_selector" value="cached"/> <param name="index" value="hg19"/> <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/> @@ -160,10 +161,11 @@ <param name="set_configuration_switch" value="Customized"/> <param name="callMemMb" value="1000"/> <param name="candidateSmallIndels_check" value="True"/> + <output name="conf_file" file="conf_file_2.ini" ftype="txt"/> <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 expect_num_outputs="3"> <param name="reference_source_selector" value="cached"/> <param name="index" value="hg19"/> <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/> @@ -172,10 +174,11 @@ <param name="set_configuration_switch" value="Default_config_file"/> <param name="callMemMb" value="1000"/> <param name="candidateSmallIndels_check" value="True"/> + <output name="conf_file" file="conf_file_3.ini" ftype="txt"/> <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 expect_num_outputs="3"> <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"/> @@ -184,10 +187,11 @@ <param name="set_configuration_switch" value="Default_config_file"/> <param name="callMemMb" value="1000"/> <param name="candidateSV_check" value="True"/> + <output name="conf_file" file="conf_file_4.ini" ftype="txt"/> <output name="candidateSV" file="candidateSV.vcf.gz" decompress="true" lines_diff="6"/> <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/> </test> - <test> + <test expect_num_outputs="3"> <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"/> @@ -196,6 +200,7 @@ <param name="set_configuration_switch" value="Default_config_file"/> <param name="callMemMb" value="1000"/> <param name="candidateSmallIndels_check" value="True"/> + <output name="conf_file" file="conf_file_5.ini" ftype="txt"/> <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>