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comparison manta_macros.xml @ 0:42ba283a0fe2 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit e6c5d87dcd848fc4910af968e73adc481c811d15"
author artbio
date Wed, 13 May 2020 15:15:07 -0400
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children c35d9902100e
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-1:000000000000 0:42ba283a0fe2
1 <macros>
2
3 <token name="@VERSION@">1.6</token>
4 <token name="@WRAPPER_VERSION@">@VERSION@+galaxy2</token>
5 <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token>
6
7 <token name="@set_reference_fasta_filename@"><![CDATA[
8 #set $reference_fasta_filename = "localref.fa"
9
10 #if str( $reference_source.reference_source_selector ) == "history":
11 ln -s -f '${reference_source.ref_file}' '${reference_fasta_filename}' &&
12 samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for Manta" >&2 &&
13 #else:
14 #set $reference_fasta_filename = str( $reference_source.index.fields.path )
15 #end if
16 ]]></token>
17
18 <token name="@set_configuration_file@"><![CDATA[
19 #if str( $configuration.configuration_switch ) == "Custom_config_file":
20 #set $config_file = '$configuration.CustomConfigFile'
21 #else if str( $configuration.configuration_switch )== "Customized":
22 #set $config_file = '$configuration.Customized'
23 #else:
24 #set $config_file = $__tool_directory__ + '/configManta.py.ini'
25 #end if
26 ]]></token>
27
28
29 <xml name="requirements">
30 <requirements>
31 <requirement type="package" version="1.7">samtools</requirement>
32 <requirement type="package" version="@VERSION@">manta</requirement>
33 </requirements>
34 </xml>
35
36 <xml name="stdio">
37 <stdio>
38 <exit_code range="1:" />
39 <exit_code range=":-1" />
40 <regex match="Error:" />
41 <regex match="Exception:" />
42 <regex match="\[bns_restore_core\] Parse error reading" />
43 </stdio>
44 </xml>
45
46 <macro name="reference_source_conditional">
47 <conditional name="reference_source">
48 <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
49 <option value="cached">Use a built-in genome index</option>
50 <option value="history">Use a genome from history and build index</option>
51 </param>
52 <when value="cached">
53 <param name="index" type="select" label="Using reference genome" help="Select genome from the list">
54 <options from_data_table="all_fasta">
55 <filter type="sort_by" column="2" />
56 <validator type="no_options" message="No indexes are available" />
57 </options>
58 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
59 </param>
60 </when>
61 <when value="history">
62 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence"
63 help="You can upload a FASTA sequence to the history and use it as reference" />
64 </when>
65 </conditional>
66 </macro>
67
68 <macro name="manta_configuration">
69 <conditional name="configuration">
70 <param name="configuration_switch" type="select" label="How do you want to configure manta?">
71 <option value="Custom_config_file">Upload a different config file</option>
72 <option value="Customized">Customize the options</option>
73 </param>
74 <when value="Custom_config_file">
75 <param format="ini" name="CustomConfigFile" type="data" label="config file"/>
76 </when>
77 <when value="Customized">
78 <param name="minCandidateVariantSize" type="integer" value="8" label="minCandidateVariantSize" help="Run discovery and candidate reporting for all SVs/indels at or above this size."/>
79 <param name="rnaMinCandidateVariantSize" type="integer" value="1000" label="rnaMinCandidateVariantSize" help="Separate option (to provide different default) used for runs in RNA-mode."/>
80 <param name="minEdgeObservations" type="integer" value="3" label="minEdgeObservations" help="Remove all edges from the graph unless they're supported by this many 'observations'."/>
81 <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."/>
82 <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."/>
83 <param name="minScoredVariantSize" type="integer" value="50" label="minScoredVariantSize" help="After candidate identification, only score and report SVs/indels at or above this size."/>
84 <param name="minDiploidVariantScore" type="integer" value="10" label="minDiploidVariantScore" help="Minimum VCF 'QUAL' score for a variant to be included in the diploid vcf."/>
85 <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."/>
86 <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."/>
87 <param name="minSomaticScore" type="integer" value="10" label="minSomaticScore" help="Somatic quality scores below this level are not included in the somatic vcf."/>
88 <param name="minPassSomaticScore" type="integer" value="30" label="minPassSomaticScore" help="Somatic quality scores below this level are filtered in the somatic vcf."/>
89 <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."/>
90 <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."/>
91 <param name="useOverlapPairEvidence" type="integer" value="0" label="useOverlapPairEvidence" help="Set if an overlapping read pair will be considered as evidence. Set this value &lt;= 0 to skip overlapping read pairs."/>
92 </when>
93 </conditional>
94 </macro>
95
96 </macros>