| Previous changeset 3:d648e40c6da9 (2020-06-07) Next changeset 5:f55d45b0c6d1 (2020-06-09) |
|
Commit message:
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838" |
|
modified:
manta.xml manta_macros.xml test-data/candidateSV.vcf.gz test-data/candidateSmallIndels.vcf.gz |
|
added:
candidateSV.vcf.gz candidateSmallIndels.vcf.gz somaticSV.vcf.gz test-data/somaticSV.vcf.gz |
| b |
| diff -r d648e40c6da9 -r d09254e37c68 candidateSV.vcf.gz |
| b |
| Binary file candidateSV.vcf.gz has changed |
| b |
| diff -r d648e40c6da9 -r d09254e37c68 candidateSmallIndels.vcf.gz |
| b |
| Binary file candidateSmallIndels.vcf.gz has changed |
| b |
| diff -r d648e40c6da9 -r d09254e37c68 manta.xml --- a/manta.xml Sun Jun 07 16:43:54 2020 -0400 +++ b/manta.xml Mon Jun 08 03:11:56 2020 -0400 |
| [ |
| b'@@ -59,10 +59,7 @@\n \n ln -s -f \'${run_dir}/runWorkflow.py\' \'${run_manta_workflow}\' &&\n ln -s -f \'./configManta.py.ini\' \'${set_conf_file}\' &&\n- python2 \'${run_dir}/runWorkflow.py\' -m local -j \\${GALAXY_SLOTS:-4} &&\n- cp \'${run_dir}/results/variants/candidateSV.vcf.gz\' \'${out_vcf1}\' &&\n- cp \'${run_dir}/results/variants/diploidSV.vcf.gz\' \'${out_vcf2}\' &&\n- cp \'${run_dir}/results/variants/candidateSmallIndels.vcf.gz\' \'${out_vcf3}\'\n+ python2 \'${run_dir}/runWorkflow.py\' -m local -j \\${GALAXY_SLOTS:-4}\n \n ]]></command>\n \n@@ -85,7 +82,7 @@\n </when>\n </conditional>\n \n- <param name="additional_param" type="select" multiple="true" display="checkboxes" label="Additional outputs" help="Additional parameters.">\n+ <param name="additional_param" type="select" multiple="true" display="checkboxes" label="Additional parameters" >\n <option value="exome">Set options for WES input: turn off depth filters</option>\n <option value="rna">Set options for RNA-Seq input. Must specify exactly one bam input file</option>\n <option value="unstrandedRNA">Set if RNA-Seq input is unstranded: Allows splice-junctions on either strand</option>\n@@ -95,8 +92,7 @@\n \n <param name="callMemMb" type="integer" value="8000" label="Set default task memory requirements" help="The maximum memory size to assign to tasks" />\n <param name="scanSizeMb" type="integer" value="12" label="Set maximum sequence region size" help="The maximum sequence region size (in megabases) scanned by each task during SV Locus graph generation. (default: 12)" />\n- <param name="retainTempFiles" type="boolean" checked="False" truevalue="-s" falsevalue="" label="Keep all temporary files" help="Click yes so all temporary files (for workflow debugging) will be kept."/>\n- <param name="generateEvidenceBam" type="boolean" checked="False" truevalue="-s" falsevalue="" label="Generate a bam of supporting reads for all SVs" help="Click yes for generating a BAM of supporting reads for all SVs."/>\n+ <!-- <param name="generateEvidenceBam" type="boolean" checked="False" truevalue="-s" falsevalue="" label="Generate a bam of supporting reads for all SVs" help="Click yes for generating a BAM of supporting reads for all SVs."/> -->\n \n </section>\n \n@@ -104,9 +100,9 @@\n \n <conditional name="set_configuration">\n <param name="set_configuration_switch" type="select" label="Do you want to change default configuration settings?">\n- <option value="Default_config_file">Default</option> \n- <option value="Custom_config_file">Upload a different config file</option>\n- <option value="Customized">Customize the options</option>\n+ <option value="Default_config_file">Default Manta Configuration File</option> \n+ <option value="Custom_config_file">Upload your Own Configuration File</option>\n+ <option value="Customized">Customize a Configuration File using this Galaxy Form</option>\n </param>\n <when value="Default_config_file">\n </when>\n@@ -133,14 +129,18 @@\n \n <param name="runworkflow_file_check" type="boolean" label="output manta run_workflow file" checked="False" help="Show run_workflow file on history"/>\n <param name="config_file_check" type="boolean" label="output conf file" checked="False" help="Show configuration file on history"/>\n- <param name="O1_check" type="boolean" label="snvs filtred" checked="False" help="Show filtred snvs"/>\n- <param name="O2_check" type="boolean" label="indels filtred" checked="False" help="Show filtred indels"/>\n- <param name="O3_check" type="boolean" label="all snvs" checked="False" help="Show snvs"/>\n- \n+ <param name="candidateSV_check" type="boolean" label="Unscored candidate SV and indels" checked="False"\n+ help="Show unfiltered s'..b'ple analysis or for the normal sample in a tumor/normal subtraction\n+ analysis. **In the case of a tumor/normal subtraction, the scores in this file do not\n+ reflect any information from the tumor sample.**\n+ \n+ - somaticSV.vcf.gz\n+ SVs and indels scored under a somatic variant model. This file will only be produced\n+ if a tumor sample alignment file is supplied during configuration\n+ \n+ - candidateSV.vcf.gz\n+ Unscored SV and indel candidates. Only a minimal amount of supporting evidence is\n+ required for an SV to be entered as a candidate in this file. An SV or indel must be a\n+ candidate to be considered for scoring, therefore an SV cannot appear in the other VCF\n+ outputs if it is not present in this file. Note that by default this file includes\n+ indels of size 8 and larger. The smallest indels in this set are intended to be passed\n+ on to a small variant caller without scoring by manta itself (by default manta scoring\n+ starts at size 50).\n+ \n+ - candidateSmallIndels.vcf.gz\n+ Subset of the candidateSV.vcf.gz file containing only simple insertion and deletion\n+ variants less than the minimum scored variant size (50 by default). Passing this file\n+ to a small variant caller will provide continuous coverage over all indel sizes when\n+ the small variant caller and manta outputs are evaluated together. Alternate small\n+ indel candidate sets can be parsed out of the candidateSV.vcf.gz file if this\n+ candidate set is not appropriate.\n+ \n+ For tumor-only analysis, Manta will produce an additional VCF:\n \n- <conditional name="bam_input">\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- </conditional>\n+ - tumorSV.vcf.gz\n+ Subset of the candidateSV.vcf.gz file after removing redundant candidates and small\n+ indels less than the minimum scored variant size (50 by default). The SVs are not\n+ scored, but include additional details: (1) paired and split read supporting evidence\n+ counts for each allele (2) a subset of the filters from the scored tumor-normal model\n+ are applied to the single tumor case to improve precision.\n \n- <conditional name="set_configuration">\n- <param name="set_configuration_switch" value="Default_config_file"/>\n- </conditional>\n- <param name="callMemMb" value="1000"/>\n- <param name="O3_check" value="True"/>\n- <output name="out_vcf3" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/>\n- </test>\n- </tests>\n- \n- <help><![CDATA[\n-**Manta**\n-This script configures the Manta SV analysis pipeline.\n-You must specify a BAM or CRAM file for at least one sample.\n-Configuration will produce a workflow run script which\n-can execute the workflow on a single node or through\n-sge and resume any interrupted execution.\n+**Manta helps**\n+ This script configures the Manta SV analysis pipeline.\n+ You must specify a BAM or CRAM file for at least one sample.\n+ Configuration will produce a workflow run script which\n+ can execute the workflow on a single node or through\n+ sge and resume any interrupted execution.\n \n **Options**\n --version show program\'s version number and exit\n@@ -266,6 +299,7 @@\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' |
| b |
| diff -r d648e40c6da9 -r d09254e37c68 manta_macros.xml --- a/manta_macros.xml Sun Jun 07 16:43:54 2020 -0400 +++ b/manta_macros.xml Mon Jun 08 03:11:56 2020 -0400 |
| [ |
| @@ -1,7 +1,7 @@ <macros> <token name="@VERSION@">1.6</token> - <token name="@WRAPPER_VERSION@">@VERSION@+galaxy5</token> + <token name="@WRAPPER_VERSION@">@VERSION@+galaxy6</token> <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token> <token name="@set_reference_fasta_filename@"><![CDATA[ |
| b |
| diff -r d648e40c6da9 -r d09254e37c68 somaticSV.vcf.gz |
| b |
| Binary file somaticSV.vcf.gz has changed |
| b |
| diff -r d648e40c6da9 -r d09254e37c68 test-data/candidateSV.vcf.gz |
| b |
| Binary file test-data/candidateSV.vcf.gz has changed |
| b |
| diff -r d648e40c6da9 -r d09254e37c68 test-data/candidateSmallIndels.vcf.gz |
| b |
| Binary file test-data/candidateSmallIndels.vcf.gz has changed |
| b |
| diff -r d648e40c6da9 -r d09254e37c68 test-data/somaticSV.vcf.gz |
| b |
| Binary file test-data/somaticSV.vcf.gz has changed |