Mercurial > repos > iuc > gemini_pathways

comparison gemini_pathways.xml @ 7:6352324edcdd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
author iuc
date Fri, 11 Jan 2019 17:30:13 -0500
parents 228263fd9c72
children 2220b0dc7d12
comparison
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6:228263fd9c72 7:6352324edcdd
13 13
14 gemini 14 gemini
15 @BINARY@ 15 @BINARY@
16 -v $ensembl 16 -v $ensembl
17 $lof 17 $lof
18 "${ infile }" 18 '$infile'
19 > "${ outfile }" 19 > '$outfile'
20 ]]> 20 ]]>
21 </command> 21 </command>
22 <inputs> 22 <inputs>
23 <expand macro="infile" /> 23 <expand macro="infile" />
24 24
25 <param name="ensembl" type="integer" value="68" label="Version of ensembl genes to use" 25 <param name="ensembl" type="select"
26 help="Supported versions: 66 to 71. use versions that match the VEP/snpEff versions of the annotated vcf for correctness. For e.g VEP v2.6 and snpEff v3.1 use Ensembl 68 version of the genomes. (-v)"> 26 label="Version of ensembl genes to use"
27 <validator type="in_range" min="66" max="71"/> 27 help="Supported versions: 66 to 71. Use versions that match the VEP/snpEff versions of the annotated vcf for correctness. For e.g VEP v2.6 and snpEff v3.1 use Ensembl 68 version of the genomes. (-v)">
28 <option value="71">Ensembl 71</option>
29 <option value="70">Ensembl 70</option>
30 <option value="69">Ensembl 69</option>
31 <option value="68">Ensembl 68</option>
32 <option value="67">Ensembl 67</option>
33 <option value="66">Ensembl 66</option>
28 </param> 34 </param>
29
30 <param name="lof" type="boolean" truevalue="--lof" falsevalue="" checked="False" 35 <param name="lof" type="boolean" truevalue="--lof" falsevalue="" checked="False"
31 label="Report only pathways with loss-of-function variants" help="(--lof)"/> 36 label="Report only pathways with loss-of-function variants" help="(--lof)"/>
32 <expand macro="annotation_dir" /> 37 <expand macro="annotation_dir" />
33 </inputs> 38 </inputs>
34 <outputs> 39 <outputs>
35 <data name="outfile" format="tabular" /> 40 <data name="outfile" format="tabular" />
36 </outputs> 41 </outputs>
37 <tests> 42 <tests>
38 <test> 43 <test>
39 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" /> 44 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
40 <param name="ensembl" value="68" /> 45 <param name="ensembl" value="71" />
41 <output name="outfile"> 46 <output name="outfile">
42 <assert_contents> 47 <assert_contents>
43 <has_line_matching expression="chrom&#009;start&#009;end&#009;.*pathway.*" /> 48 <has_line_matching expression="chrom&#009;start&#009;end&#009;.*pathway.*" />
44 </assert_contents> 49 </assert_contents>
45 </output> 50 </output>