annotate gemini_gene_wise.xml @ 3:d46017ddbf94 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d
author iuc
date Wed, 17 Oct 2018 13:29:48 -0400
parents bc66ebfd4159
children a26f0a30df65
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
99d6e7b1b7f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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2 <description>Custom genotype filtering by gene</description>
99d6e7b1b7f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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3 <macros>
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4 <import>gemini_macros.xml</import>
99d6e7b1b7f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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5 <token name="@BINARY@">gene_wise</token>
99d6e7b1b7f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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6 </macros>
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7 <expand macro="requirements" />
99d6e7b1b7f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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8 <expand macro="stdio" />
99d6e7b1b7f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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9 <expand macro="version_command" />
99d6e7b1b7f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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10 <command>
99d6e7b1b7f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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11 <![CDATA[
99d6e7b1b7f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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12 gemini @BINARY@
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99d6e7b1b7f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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99d6e7b1b7f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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15 #if int($min_filters) > 0:
99d6e7b1b7f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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16 --min_filters $min_filters
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17 #end if
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18
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d46017ddbf94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d
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19 #set $multiline_sql_expr = $gt_filter
d46017ddbf94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d
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20 #set $cmdln_param = "--gt-filter"
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21 @MULTILN_SQL_EXPR_TO_CMDLN@
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bc66ebfd4159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
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23 @COLUMN_SELECT@
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25 @CMDLN_SQL_FILTER_FILTER_OPTION@
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27 "${ infile }"
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28 > "${ outfile }"
99d6e7b1b7f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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29 ]]>
99d6e7b1b7f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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30 </command>
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31 <inputs>
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32 <expand macro="infile" />
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34 <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values" help="(--gt-filter)">
99d6e7b1b7f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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35 <expand macro="sanitize_query" />
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36 </param>
99d6e7b1b7f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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37 <param name="min_filters" type="integer" value="0" min="0" label="Minimum number of filters" help="(--min-filters)" />
99d6e7b1b7f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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38 <expand macro="column_filter" />
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39 <expand macro="filter" />
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99d6e7b1b7f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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42 </inputs>
99d6e7b1b7f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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43 <outputs>
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44 <data name="outfile" format="tabular" />
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="infile" value="gemini_amend_input.db" ftype="gemini.sqlite" />
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49 <param name="gt_filter" value="((gt_depths).(*).(>=1).(all))" />
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50 <output name="outfile" file="gemini_gene_wise_result.tabular" />
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51 </test>
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52 </tests>
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53 <help>
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54 <![CDATA[
99d6e7b1b7f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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55 **What it does**
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56
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57 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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58 ]]>
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59 </help>
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60 <expand macro="citations"/>
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61 </tool>