Mercurial > repos > iuc > gemini_stats
comparison gemini_stats.xml @ 4:cdd90678004a draft
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	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	num_hom_ref	num_het	num_hom_alt	num_unknown	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 |