Mercurial > repos > iuc > gemini_dump

comparison gemini_dump.xml @ 4:7b24461e6bc3 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 85a2af25c79df4758afe9f846e11ef0af16b1c1f
author iuc
date Mon, 17 Dec 2018 12:21:48 -0500
parents a48f00c341dc
children
comparison
equal deleted inserted replaced
3:a48f00c341dc 4:7b24461e6bc3
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1"> 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
2 <description>Extract data from the Gemini DB</description> 2 <description>Extract data from the Gemini DB</description>
3 <macros> 3 <macros>
4 <import>gemini_macros.xml</import> 4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">dump</token> 5 <token name="@BINARY@">dump</token>
6 </macros> 6 </macros>
21 <inputs> 21 <inputs>
22 <expand macro="infile" /> 22 <expand macro="infile" />
23 23
24 <param name="report" type="select" label="The information to be reported" help="(-t)"> 24 <param name="report" type="select" label="The information to be reported" help="(-t)">
25 <option value="--variants">All rows/columns from the variants table (--variants)</option> 25 <option value="--variants">All rows/columns from the variants table (--variants)</option>
26 <option value="--genotypes">All rows/columns from the variants table with one line per sample/genotype (--genotypes)</option> 26 <!-- The genotypes option is broken in gemini v0.20.1.
27 Add this option back in once there is an upstream fix!
28 Remember then to replace all underscores with dashes on the following line. They are only there to not break this comment!
29 <option value="__genotypes">All rows/columns from the variants table with one line per sample/genotype (__genotypes)</option>
30 -->
27 <option value="--samples">All rows/columns from the samples table (--samples)</option> 31 <option value="--samples">All rows/columns from the samples table (--samples)</option>
28 </param> 32 </param>
29 <param argument="--header" type="boolean" label="Include a header of column names" truevalue="--header" falsevalue="" checked="False" /> 33 <param argument="--header" type="boolean" label="Include a header of column names" truevalue="--header" falsevalue="" checked="False" />
30 <param argument="--tfam" type="boolean" label="Output sample information to TFAM information" truevalue="--tfam" falsevalue="" checked="False" /> 34 <param argument="--tfam" type="boolean" label="Output sample information to TFAM information" truevalue="--tfam" falsevalue="" checked="False" />
31 </inputs> 35 </inputs>
32 <outputs> 36 <outputs>
33 <data name="outfile" format="tabular" /> 37 <data name="outfile" format="tabular" />
34 </outputs> 38 </outputs>
35 <tests> 39 <tests>
36 <test> 40 <test>
37 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" /> 41 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
38 <param name="header" value="True" /> 42 <param name="header" value="True" />
39 <param name="report" value="--genotypes" /> 43 <param name="report" value="--samples" />
40 <output name="outfile"> 44 <output name="outfile">
41 <assert_contents> 45 <assert_contents>
42 <has_line_matching expression="chrom&#009;start&#009;end&#009;.*sample&#009;.*genotype.*" /> 46 <has_line_matching expression="sample_id&#009;family_id&#009;name&#009;paternal_id&#009;maternal_id&#009;sex&#009;phenotype" />
43 </assert_contents> 47 </assert_contents>
44 </output> 48 </output>
45 </test> 49 </test>
46 </tests> 50 </tests>
47 <help><![CDATA[ 51 <help><![CDATA[