Mercurial > repos > iuc > gemini_db_info

annotate gemini_macros.xml @ 4:f3cc64057b4e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
author iuc
date Fri, 14 Dec 2018 12:41:01 -0500
parents 4c5f4e9b1931
children bc8b01d1b496
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1 <macros>
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2 <!-- gemini version to be used -->
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3 <token name="@VERSION@">0.18.1</token>
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4 <!-- minimal annotation files version required by this version of gemini -->
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5 <token name="@DB_VERSION@">181</token>
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6
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7 <xml name="requirements">
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8 <requirements>
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9 <requirement type="package" version="@VERSION@">gemini</requirement>
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10 <requirement type="package" version="0.2.6">tabix</requirement>
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11 <!-- for conda useage -->
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12 <!--requirement type="package" version="1.3.1">htslib</requirement-->
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13 <yield />
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14 </requirements>
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15 </xml>
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17 <xml name="version_command">
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18 <version_command>gemini --version</version_command>
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19 </xml>
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21 <xml name="stdio">
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22 <stdio>
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23 <exit_code range="1:" />
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24 <exit_code range=":-1" />
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25 <regex match="Error:" />
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26 <regex match="Exception:" />
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27 </stdio>
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28 </xml>
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30 <xml name="annotation_dir">
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31 <param name="annotation_databases" type="select" label="Choose a gemini annotation source">
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32 <options from_data_table="gemini_versioned_databases">
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33 <filter type="sort_by" column="0" />
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34 <filter type="static_value" column="2" value="@DB_VERSION@" />
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35 </options>
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36 </param>
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37 </xml>
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38
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39 <xml name="add_header_column">
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40 <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False"
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41 label="Add a header of column names to the output" help="(--header)"/>
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42 </xml>
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43
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44 <xml name="radius">
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45 <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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46 <validator type="in_range" min="0"/>
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47 </param>
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48 </xml>
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49 <xml name="variant_mode">
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50 <param name="variant_mode" type="boolean" truevalue="--var" falsevalue="" checked="False"
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51 label="Returns variant info (e.g. impact, biotype) for interacting genes" help="(--var)"/>
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52 </xml>
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53
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54 <xml name="column_filter">
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55 <conditional name="report">
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56 <param name="report_selector" type="select" label="Columns to include in the report"
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57 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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58 <option value="all" selected="True">all</option>
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59 <option value="column_filter">User given columns</option>
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60 </param>
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61 <when value="all"/>
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62 <when value="column_filter">
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63 <param name="columns" type="select" display="checkboxes" multiple="True" label="Choose columns to include in the report" help="(--columns)">
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64 <option value="gene">gene</option>
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65 <option value="chrom">chrom</option>
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66 <option value="start">start</option>
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67 <option value="end">end</option>
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68 <option value="ref">ref</option>
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69 <option value="alt">alt</option>
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70 <option value="impact">impact</option>
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71 <option value="impact_severity">impact_severity</option>
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72 <option value="max_aaf_all">alternative allele frequency</option>
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73 </param>
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74 <param name="extra_cols" type="text" label="Additional columns." help="Separate by whitespace"/>
0
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75 </when>
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76 </conditional>
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77 </xml>
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78
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79 <xml name="filter">
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80 <conditional name="filter">
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81 <param name="filter_selector" type="select" label="Apply additional constraints"
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82 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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83 <option value="no">No additional constraints</option>
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84 <option value="yes">Apply additional constraints</option>
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85 </param>
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86 <when value="no"/>
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87 <when value="yes">
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88 <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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89 <expand macro="sanitize_query" />
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90 </param>
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91 </when>
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92 </conditional>
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93 </xml>
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94
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95 <xml name="sanitize_query">
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96 <sanitizer invalid_char="">
3
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97 <valid initial="string.printable">
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98 <remove value="&apos;" />
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99 </valid>
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100 <mapping initial="none">
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101 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
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102 </mapping>
0
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103 </sanitizer>
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104 </xml>
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105
4
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106 <token name="@PROVIDE_ANNO_DATA@"><![CDATA[
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107 mkdir gemini &&
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108 ln -s "${annotation_databases.fields.path}/gemini/data" gemini/data &&
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109 export GEMINI_CONFIG="${annotation_databases.fields.path}" &&
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110 ]]></token>
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111
3
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112 <token name="@MULTILN_SQL_EXPR_TO_CMDLN@">
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113 #set $sql_expr = str($multiline_sql_expr).strip()
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114 #if str($sql_expr):
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115 #set $sql_expr = $sql_expr.replace('\r\n', '\n')
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116 #set $sql_expr = $sql_expr.replace('\r', '\n')
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117 #set $sql_expr = $sql_expr.replace('\\\n', ' ')
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118 $cmdln_param '$sql_expr'
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119 #end if
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120 </token>
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121
0
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122 <token name="@CMDLN_SQL_FILTER_FILTER_OPTION@">
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123 #if str($filter.filter_selector) == 'yes' and $filter.filter:
3
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124 --filter '${ str( $filter.filter ) }'
0
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125 #end if
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126 </token>
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127
2
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128 <token name="@COLUMN_SELECT@">
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129 #if $report.report_selector != 'all':
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130 --columns "${report.columns}
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131 #if str($report.extra_cols).strip()
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132 #echo ','+','.join(str($report.extra_cols).split())
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133 #end if
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134 "
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135 #end if
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136 </token>
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137
0
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138 <xml name="family">
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139 <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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140 </xml>
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141
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142 <xml name="lenient">
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143 <param name="lenient" type="boolean" truevalue="--lenient" falsevalue="" checked="False" label="Loosen the restrictions on family structure"/>
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144 </xml>
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145
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146 <xml name="unaffected">
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147 <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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148 </xml>
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149
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150 <xml name="min_kindreds">
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151 <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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152 </xml>
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153
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154 <xml name="min_sequence_depth">
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155 <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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156 help="default: 0 (-d)" />
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157 </xml>
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158
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159 <xml name="min_gq">
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160 <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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161 <validator type="in_range" min="0"/>
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162 </param>
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163 </xml>
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164
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165 <xml name="gt_pl_max">
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166 <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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167 </xml>
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168
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169 <xml name="citations">
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170 <citations>
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171 <citation type="doi">10.1371/journal.pcbi.1003153</citation>
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172 <yield />
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173 </citations>
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174 </xml>
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175
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176 <xml name="infile">
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177 <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." >
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178 <options options_filter_attribute="metadata.gemini_version" >
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179 <filter type="add_value" value="@VERSION@" />
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180 </options>
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181 <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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182 </param>
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183 </xml>
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184
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185 </macros>