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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
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2 <description>Extracting variants from specific regions or genes</description>
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3 <expand macro="requirements" />
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4 <expand macro="version_command" />
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5 <macros>
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6 <import>gemini_macros.xml</import>
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7 <token name="@BINARY@">region</token>
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8 </macros>
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9 <command>
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10 <![CDATA[
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11 gemini @BINARY@
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12
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13 #if $region.region_selector == '--reg':
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14 #if str(${region.region}) != '':
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15 --reg "${region.region}"
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16 #end if
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17 #else:
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18 #if str(${region.gene}) != '':
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19 --gene "${region.gene}"
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20 #end if
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21 #end if
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22
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23 #if $report.report_selector != 'all':
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24 --columns "${report.columns}"
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25 #end if
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26
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4
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27 @CMDLN_SQL_FILTER_FILTER_OPTION@
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0
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28
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29 $header
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30 "${ infile }"
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31 > "${ outfile }"
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32 ]]>
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33 </command>
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34 <expand macro="stdio" />
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35 <inputs>
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2
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36 <expand macro="infile" />
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0
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37
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38 <conditional name="region">
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39 <param name="region_selector" type="select" label="Select by ...?" help="">
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40 <option value="--reg">genomic coordinates</option>
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41 <option value="--gene">gene name</option>
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42 </param>
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43 <when value="--reg">
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44 <param name="region" type="text" label="Specify genomic region" help="e.g. chr1:100-200 (--reg)"/>
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45 </when>
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46 <when value="--gene">
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47 <param name="gene" type="text" label="Specify gene name" help="e.g. PTPN22 (--gene)" />
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48 </when>
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49 </conditional>
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50
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51 <expand macro="column_filter" />
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52 <expand macro="filter" />
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53
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54
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55 <expand macro="add_header_column" />
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56
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57 </inputs>
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58 <outputs>
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2
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59 <data name="outfile" format="tabular" />
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0
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60 </outputs>
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61 <tests>
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62 <test>
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63 </test>
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64 </tests>
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65 <help>
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66 **What it does**
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67
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68 One often is concerned with variants found solely in a particular gene or genomic region.
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69
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70 @CITATION@
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71 </help>
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72 <expand macro="citations"/>
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73 </tool>
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