Mercurial > repos > iuc > gemini_gene_wise

annotate gemini_gene_wise.xml @ 0:ee0f11e786d2 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
author iuc
date Tue, 16 Feb 2016 05:55:08 -0500
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children 39688d137011
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ee0f11e786d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
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2 <description>Custom genotype filtering by gene</description>
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3 <macros>
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4 <import>gemini_macros.xml</import>
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5 <token name="@BINARY@">gene_wise</token>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command>
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11 <![CDATA[
ee0f11e786d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
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12 gemini @BINARY@
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ee0f11e786d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
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15 #if int($min_filters) > 0:
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16 --min_filters $min_filters
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17 #end if
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19 #if $gt_filter.strip():
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20 --gt-filter "${gt_filter}"
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21 #end if
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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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27 @CMDLN_SQL_FILTER_FILTER_OPTION@
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29 "${ infile }"
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30 > "${ outfile }"
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31 ]]>
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32 </command>
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33 <inputs>
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34 <expand macro="infile" />
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36 <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values" help="(--gt-filter)">
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37 <expand macro="sanitize_query" />
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38 </param>
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39 <param name="min_filters" type="integer" value="0" min="0" label="Minimum number of filters" help="(--min-filters)" />
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40 <expand macro="column_filter" />
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41 <expand macro="filter" />
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44 </inputs>
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45 <outputs>
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46 <data name="outfile" format="tabular" />
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47 </outputs>
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48 <tests>
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49 <test>
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50 <param name="infile" value="gemini_amend_input.db" ftype="gemini.sqlite" />
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51 <param name="gt_filter" value="((gt_depths).(*).(>=1).(all))" />
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52 <output name="outfile" file="gemini_gene_wise_result.tabular" />
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53 </test>
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54 </tests>
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55 <help>
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56 <![CDATA[
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57 **What it does**
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58
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59 The gemini query tool allows querying by variant and the inheritance tools described above enable querying by gene for fixed inheritance patterns. The gene_wise tool allows querying by gene with custom genotype filters to bridge the gap between these tools.
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60 ]]>
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61 </help>
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62 <expand macro="citations"/>
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63 </tool>