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comparison gemini_stats.xml @ 4:cdd90678004a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
author iuc
date Fri, 14 Dec 2018 12:47:19 -0500
parents ee894347fcd6
children 86d4303cc3ca
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3:ee894347fcd6 4:cdd90678004a
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
2 <description>Compute useful variant statistics</description> 2 <description>Compute useful variant statistics</description>
3 <macros> 3 <macros>
4 <import>gemini_macros.xml</import> 4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">stats</token> 5 <token name="@BINARY@">stats</token>
6 </macros> 6 </macros>
43 </param> 43 </param>
44 44
45 <param name="summarize" type="text" area="True" size="5x50" label="The query to be issued to the database to summarize" help="(--summarize)"> 45 <param name="summarize" type="text" area="True" size="5x50" label="The query to be issued to the database to summarize" help="(--summarize)">
46 <expand macro="sanitize_query" /> 46 <expand macro="sanitize_query" />
47 </param> 47 </param>
48
49 </inputs> 48 </inputs>
50 <outputs> 49 <outputs>
51 <data name="outfile" format="tabular" /> 50 <data name="outfile" format="tabular" />
52 </outputs> 51 </outputs>
53 <tests> 52 <tests>
54 <test> 53 <test>
55 <param name="infile" value="gemini_burden_input.db" ftype="gemini.sqlite" /> 54 <!-- test vars-by-sample report -->
55 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
56 <param name="stats_type" value="--vars-by-sample" /> 56 <param name="stats_type" value="--vars-by-sample" />
57 <output name="outfile" file="gemini_stats_result.tabular" /> 57 <output name="outfile">
58 <assert_contents>
59 <has_line_matching expression="sample&#009;total" />
60 </assert_contents>
61 </output>
62 </test>
63 <test>
64 <!-- test gts-by-sample report -->
65 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
66 <param name="stats_type" value="--gts-by-sample" />
67 <output name="outfile">
68 <assert_contents>
69 <has_line_matching expression="sample&#009;num_hom_ref&#009;num_het&#009;num_hom_alt&#009;num_unknown&#009;total" />
70 </assert_contents>
71 </output>
58 </test> 72 </test>
59 </tests> 73 </tests>
60 <help><![CDATA[ 74 <help><![CDATA[
61 **What it does** 75 **What it does**
62 76