Mercurial > repos > iuc > gemini_actionable_mutations

annotate gemini_macros.xml @ 2:a0379503290f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
author iuc
date Thu, 09 Nov 2017 13:19:15 -0500
parents 9f0f5e984ae3
children 3630a6e624d4
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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
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4 <requirement type="package" version="0.18.1">gemini</requirement>
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5 <requirement type="package" version="0.2.6">tabix</requirement>
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6 <!-- for conda useage -->
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7 <!--requirement type="package" version="1.3.1">htslib</requirement-->
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8 <yield />
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9 </requirements>
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10 </xml>
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11
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12 <xml name="version_command">
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13 <version_command>gemini --version</version_command>
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14 </xml>
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16 <xml name="stdio">
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17 <stdio>
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18 <exit_code range="1:" />
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19 <exit_code range=":-1" />
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20 <regex match="Error:" />
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21 <regex match="Exception:" />
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22 </stdio>
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23 </xml>
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24
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25 <xml name="annotation_dir">
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26 <param name="annotation_databases" type="select" optional="True" label="Choose a gemini annotation database">
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27 <options from_data_table="gemini_databases">
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28 <filter type="sort_by" column="0" />
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29 </options>
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30 </param>
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31 </xml>
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32
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33 <xml name="add_header_column">
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34 <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False"
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35 label="Add a header of column names to the output" help="(--header)"/>
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36 </xml>
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37
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38 <xml name="radius">
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39 <param name="radius" type="integer" value="3" label="Set filter for Breadth-first search (BFS) in the Protein-Protein Interaction network" help="(-r)" >
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40 <validator type="in_range" min="0"/>
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41 </param>
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42 </xml>
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43 <xml name="variant_mode">
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44 <param name="variant_mode" type="boolean" truevalue="--var" falsevalue="" checked="False"
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45 label="Returns variant info (e.g. impact, biotype) for interacting genes" help="(--var)"/>
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46 </xml>
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47
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48 <xml name="column_filter">
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49 <conditional name="report">
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50 <param name="report_selector" type="select" label="Columns to include in the report"
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51 help="By default, this tool reports all columns in the variants table. One may choose to report only a subset of the columns.">
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52 <option value="all" selected="True">all</option>
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53 <option value="column_filter">User given columns</option>
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54 </param>
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55 <when value="all"/>
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56 <when value="column_filter">
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57 <param name="columns" type="select" display="checkboxes" multiple="True" label="Choose columns to include in the report" help="(--columns)">
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58 <option value="gene">gene</option>
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59 <option value="chrom">chrom</option>
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60 <option value="start">start</option>
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61 <option value="end">end</option>
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62 <option value="ref">ref</option>
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63 <option value="alt">alt</option>
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64 <option value="impact">impact</option>
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65 <option value="impact_severity">impact_severity</option>
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66 <option value="max_aaf_all">alternative allele frequency</option>
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67 </param>
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68 <param name="extra_cols" type="text" label="Additional columns." help="Separate by whitespace"/>
0
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69 </when>
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70 </conditional>
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71 </xml>
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72
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73 <xml name="filter">
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74 <conditional name="filter">
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75 <param name="filter_selector" type="select" label="Apply additional constraints"
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76 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.">
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77 <option value="no">No additional constraints</option>
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78 <option value="yes">Apply additional constraints</option>
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79 </param>
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80 <when value="no"/>
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81 <when value="yes">
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82 <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)">
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83 <expand macro="sanitize_query" />
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84 </param>
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85 </when>
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86 </conditional>
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87 </xml>
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88
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89 <xml name="sanitize_query">
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90 <sanitizer invalid_char="">
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91 <valid initial="string.printable"/>
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92 </sanitizer>
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93 </xml>
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94
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95 <token name="@CMDLN_SQL_FILTER_FILTER_OPTION@">
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96 #if str($filter.filter_selector) == 'yes' and $filter.filter:
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97 #import pipes
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98 --filter ${ pipes.quote( str( $filter.filter ) ) or "''" }
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99 #end if
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100 </token>
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101
2
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102 <token name="@COLUMN_SELECT@">
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103 #if $report.report_selector != 'all':
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104 --columns "${report.columns}
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105 #if str($report.extra_cols).strip()
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106 #echo ','+','.join(str($report.extra_cols).split())
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107 #end if
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108 "
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109 #end if
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110 </token>
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111
0
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112 <xml name="family">
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113 <param name="families" type="text" value="" label="Comma seperated list of families to restrict the analysis to." help="e.g. Family1,Family3 (--families)"/>
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114 </xml>
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115
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116 <xml name="lenient">
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117 <param name="lenient" type="boolean" truevalue="--lenient" falsevalue="" checked="False" label="Loosen the restrictions on family structure"/>
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118 </xml>
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119
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120 <xml name="unaffected">
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121 <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)"/>
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122 </xml>
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123
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124 <xml name="min_kindreds">
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125 <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)" />
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126 </xml>
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127
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128 <xml name="min_sequence_depth">
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129 <param name="d" type="integer" value="0" min="0" label="The minimum aligned sequence depth (genotype DP) required for each sample"
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130 help="default: 0 (-d)" />
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131 </xml>
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132
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133 <xml name="min_gq">
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134 <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)">
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135 <validator type="in_range" min="0"/>
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136 </param>
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137 </xml>
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138
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139 <xml name="gt_pl_max">
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140 <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)" />
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141 </xml>
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142 <token name="@VERSION@">0.18.1</token>
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143
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144 <xml name="citations">
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145 <citations>
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146 <citation type="doi">10.1371/journal.pcbi.1003153</citation>
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147 <yield />
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148 </citations>
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149 </xml>
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150
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151 <xml name="infile">
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152 <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." >
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153 <options options_filter_attribute="metadata.gemini_version" >
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154 <filter type="add_value" value="@VERSION@" />
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155 </options>
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156 <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>
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157 </param>
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158 </xml>
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159
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160 </macros>