Mercurial > repos > iuc > gemini_actionable_mutations
view gemini_macros.xml @ 2:a0379503290f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
author | iuc |
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date | Thu, 09 Nov 2017 13:19:15 -0500 |
parents | 9f0f5e984ae3 |
children | 3630a6e624d4 |
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<macros> <xml name="requirements"> <requirements> <requirement type="package" version="0.18.1">gemini</requirement> <requirement type="package" version="0.2.6">tabix</requirement> <!-- for conda useage --> <!--requirement type="package" version="1.3.1">htslib</requirement--> <yield /> </requirements> </xml> <xml name="version_command"> <version_command>gemini --version</version_command> </xml> <xml name="stdio"> <stdio> <exit_code range="1:" /> <exit_code range=":-1" /> <regex match="Error:" /> <regex match="Exception:" /> </stdio> </xml> <xml name="annotation_dir"> <param name="annotation_databases" type="select" optional="True" label="Choose a gemini annotation database"> <options from_data_table="gemini_databases"> <filter type="sort_by" column="0" /> </options> </param> </xml> <xml name="add_header_column"> <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" label="Add a header of column names to the output" help="(--header)"/> </xml> <xml name="radius"> <param name="radius" type="integer" value="3" label="Set filter for Breadth-first search (BFS) in the Protein-Protein Interaction network" help="(-r)" > <validator type="in_range" min="0"/> </param> </xml> <xml name="variant_mode"> <param name="variant_mode" type="boolean" truevalue="--var" falsevalue="" checked="False" label="Returns variant info (e.g. impact, biotype) for interacting genes" help="(--var)"/> </xml> <xml name="column_filter"> <conditional name="report"> <param name="report_selector" type="select" label="Columns to include in the report" help="By default, this tool reports all columns in the variants table. One may choose to report only a subset of the columns."> <option value="all" selected="True">all</option> <option value="column_filter">User given columns</option> </param> <when value="all"/> <when value="column_filter"> <param name="columns" type="select" display="checkboxes" multiple="True" label="Choose columns to include in the report" help="(--columns)"> <option value="gene">gene</option> <option value="chrom">chrom</option> <option value="start">start</option> <option value="end">end</option> <option value="ref">ref</option> <option value="alt">alt</option> <option value="impact">impact</option> <option value="impact_severity">impact_severity</option> <option value="max_aaf_all">alternative allele frequency</option> </param> <param name="extra_cols" type="text" label="Additional columns." help="Separate by whitespace"/> </when> </conditional> </xml> <xml name="filter"> <conditional name="filter"> <param name="filter_selector" type="select" label="Apply additional constraints" help="By default, this tool will report all variants regardless of their putative functional impact. In order to apply additional constraints on the variants returned, you can this optional filter."> <option value="no">No additional constraints</option> <option value="yes">Apply additional constraints</option> </param> <when value="no"/> <when value="yes"> <param name="filter" type="text" label="Contraints in SQL syntax" help="Conditions applied here will become WHERE clauses in the query issued to the GEMINI database. E.g. alt='G' or impact_severity = 'HIGH'. (--filter)"> <expand macro="sanitize_query" /> </param> </when> </conditional> </xml> <xml name="sanitize_query"> <sanitizer invalid_char=""> <valid initial="string.printable"/> </sanitizer> </xml> <token name="@CMDLN_SQL_FILTER_FILTER_OPTION@"> #if str($filter.filter_selector) == 'yes' and $filter.filter: #import pipes --filter ${ pipes.quote( str( $filter.filter ) ) or "''" } #end if </token> <token name="@COLUMN_SELECT@"> #if $report.report_selector != 'all': --columns "${report.columns} #if str($report.extra_cols).strip() #echo ','+','.join(str($report.extra_cols).split()) #end if " #end if </token> <xml name="family"> <param name="families" type="text" value="" label="Comma seperated list of families to restrict the analysis to." help="e.g. Family1,Family3 (--families)"/> </xml> <xml name="lenient"> <param name="lenient" type="boolean" truevalue="--lenient" falsevalue="" checked="False" label="Loosen the restrictions on family structure"/> </xml> <xml name="unaffected"> <param name="allow_unaffected" type="boolean" truevalue="--allow-unaffected" falsevalue="" checked="False" label="Report candidates that also impact samples labeled as unaffected." help="(--allow-unaffected)"/> </xml> <xml name="min_kindreds"> <param name="min_kindreds" type="integer" value="1" label="The min. number of kindreds that must have a candidate variant in a gene" help="default: 1 (--min-kindreds)" /> </xml> <xml name="min_sequence_depth"> <param name="d" type="integer" value="0" min="0" label="The minimum aligned sequence depth (genotype DP) required for each sample" help="default: 0 (-d)" /> </xml> <xml name="min_gq"> <param name="min_gq" type="integer" value="0" label="the minimum genotype quality required for each sample in a family" help="default: 0 (--min-gq)"> <validator type="in_range" min="0"/> </param> </xml> <xml name="gt_pl_max"> <param name="gt_pl_max" type="integer" value="-1" min="-1" label="The maximum phred-scaled genotype likelihod (PL) allowed for each sample in a family" help="default: -1 (not set) (--gt-pl-max)" /> </xml> <token name="@VERSION@">0.18.1</token> <xml name="citations"> <citations> <citation type="doi">10.1371/journal.pcbi.1003153</citation> <yield /> </citations> </xml> <xml name="infile"> <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." > <options options_filter_attribute="metadata.gemini_version" > <filter type="add_value" value="@VERSION@" /> </options> <validator type="expression" message="This version of Gemini will only work with Gemini files that are for version @VERSION@.">value is not None and value.metadata.gemini_version == "@VERSION@"</validator> </param> </xml> </macros>