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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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27 #if $filter.filter_selector == 'yes':
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28 --filter "${filter.filter}"
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29 #end if
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30
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31 $header
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32 "${ infile }"
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33 > "${ outfile }"
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34 ]]>
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35 </command>
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36 <expand macro="stdio" />
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37 <inputs>
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38 <param name="infile" type="data" format="sqlite" label="GEMINI database" />
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39
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40 <conditional name="region">
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41 <param name="region_selector" type="select" label="Select by ...?" help="">
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42 <option value="--reg">genomic coordinates</option>
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43 <option value="--gene">gene name</option>
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44 </param>
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45 <when value="--reg">
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46 <param name="region" type="text" label="Specify genomic region" help="e.g. chr1:100-200 (--reg)"/>
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47 </when>
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48 <when value="--gene">
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49 <param name="gene" type="text" label="Specify gene name" help="e.g. PTPN22 (--gene)" />
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50 </when>
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51 </conditional>
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52
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53 <expand macro="column_filter" />
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54 <expand macro="filter" />
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55
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56
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57 <expand macro="add_header_column" />
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58
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59 </inputs>
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60 <outputs>
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61 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
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62 </outputs>
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63 <tests>
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64 <test>
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65 </test>
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66 </tests>
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67 <help>
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68 **What it does**
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69
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70 One often is concerned with variants found solely in a particular gene or genomic region.
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71
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72 @CITATION@
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73 </help>
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74 <expand macro="citations"/>
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75 </tool>
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