Mercurial > repos > iuc > vg_convert

comparison convert.xml @ 0:e68d9dfa62a2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
author iuc
date Thu, 09 Apr 2020 04:35:27 -0400
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children 7366704232b6
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-1:000000000000 0:e68d9dfa62a2
1 <tool id="vg_convert" name="vg convert" version="@TOOL_VERSION@">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 ln -s '$infile' ./infile.${infile.ext} &&
9
10 vg convert
11 $output_format
12 ./infile.${infile.ext}
13 > '$output'
14 ]]></command>
15 <inputs>
16 <param name="infile" type="data" format="vg,xg" label="Input file in vg or xg format" />
17 <param name="output_format" type="select" label="Choose your output format">
18 <option value="--xg-out">XG format (--xg-out)</option>
19 <!--option value="- -odgi-out">odgi format (- -odgi-out)</option-->
20 </param>
21 </inputs>
22 <outputs>
23 <data name="output" format="odgi">
24 <change_format>
25 <when input="output_format" value="--xg-out" format="xg"/>
26 </change_format>
27 </data>
28 </outputs>
29 <tests>
30 <test>
31 <param name="infile" value="hla.vg" ftype="vg" />
32 <param name="output_format" value="--xg-out" />
33 <output name="output" file="hla.xg" ftype="xg" compare="sim_size" />
34 </test>
35 <!--test>
36 <param name="infile" value="x.vg" ftype="vg" />
37 <param name="output_format" value="- -odgi-out" />
38 <output name="output" file="x.odgi" ftype="odgi" compare="sim_size" />
39 </test-->
40 </tests>
41 <help><![CDATA[
42
43 variation graph (vg) convert module
44 -----------------------------------
45
46 This module is converting various variant graphs into each format.
47
48 ]]></help>
49 <expand macro="citations" />
50 </tool>