Mercurial > repos > iuc > vg_view

comparison view.xml @ 0:95ec8f978762 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 04:38:19 -0400
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children ee62774bb5bd
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-1:000000000000 0:95ec8f978762
1 <tool id="vg_view" name="vg view" 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 vg view
9 $input_format.input_format_selector
10 '$input_format.infile'
11 $output_format
12 --threads=\${GALAXY_SLOTS:-1}
13 > '$output'
14 ]]></command>
15 <inputs>
16 <conditional name="input_format">
17 <param name="input_format_selector" type="select" label="Your input is in format">
18 <option value="--vg-in" selected="true">variant graph (vg)</option>
19 <option value="--json-in">JSON</option>
20 <option value="--gfa-in">GFA</option>
21 <option value="--bam">BAM</option>
22 </param>
23 <when value="--vg-in">
24 <param name="infile" type="data" format="vg" label="Input file in variant graph format (vg)" />
25 </when>
26 <when value="--gfa-in">
27 <param name="infile" type="data" format="gfa1" label="Input file in Graphical Fragment Assembly (gfa)" />
28 </when>
29 <when value="--json-in">
30 <param name="infile" type="data" format="json" label="Input file in JSON" />
31 </when>
32 <when value="--bam">
33 <param name="infile" type="data" format="bam" label="Input file in BAM" />
34 </when>
35 </conditional>
36
37 <param name="output_format" type="select" label="Choose your output format">
38 <option value="--vg">VG</option>
39 <option value="--json">JSON</option>
40 <option value="--gfa">GFA</option>
41 <option value="--dot">dot</option>
42 </param>
43
44 </inputs>
45 <outputs>
46 <data name="output" format="vg">
47 <change_format>
48 <when input="output_format" value="--dot" format="graph_dot"/>
49 <when input="output_format" value="--json" format="json"/>
50 <when input="output_format" value="--gfa" format="gfa1"/>
51 </change_format>
52 </data>
53 </outputs>
54 <tests>
55 <test>
56 <conditional name="input_format">
57 <param name="input_format_selector" value="--gfa-in" />
58 <param name="infile" value="x.gfa" ftype="gfa1" />
59 </conditional>
60 <param name="output_format" value="--vg" />
61 <output name="output" file="x.vg" ftype="vg" />
62 </test>
63 <test>
64 <conditional name="input_format">
65 <param name="input_format_selector" value="--vg-in" />
66 <param name="infile" value="x.vg" />
67 </conditional>
68 <param name="output_format" value="--json" />
69 <output name="output" file="x.json" ftype="json" />
70 </test>
71 <test>
72 <conditional name="input_format">
73 <param name="input_format_selector" value="--json-in" />
74 <param name="infile" value="x.json" ftype="json" />
75 </conditional>
76 <param name="output_format" value="--vg" />
77 <output name="output" file="x.vg" ftype="vg" />
78 </test>
79 </tests>
80 <help><![CDATA[
81
82 variation graph (vg) view module
83 -----------------------------------
84
85 Inspect and convert variant graphs in different file formats.
86
87 ]]></help>
88 <expand macro="citations" />
89 </tool>