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comparison cooc_tabmut.xml @ 0:ab84c87e56f7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
author iuc
date Thu, 11 Aug 2022 13:47:51 +0000
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children 74328ad6bb70
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-1:000000000000 0:ab84c87e56f7
1 <tool id="cooc_tabmut" name="Cojac: tabmut" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
2 profile="@PROFILE@">
3 <description>
4 export cooccurrence mutations as a table
5 </description>
6 <macros>
7 <import>macros.xml</import>
8 </macros>
9 <expand macro="biotools"/>
10 <expand macro="requirements"/>
11 <expand macro="version"/>
12 <command detect_errors="exit_code"><![CDATA[
13 #for $input_file in $cooc_file
14 #set $cooc_ext = $input_file.ext
15 #end for
16 cooc-tabmut
17 #if $cooc_ext == 'json'
18 -j '$cooc_file'
19 #else if $cooc_ext == 'yaml'
20 -y '$cooc_file'
21 #end if
22 -o cooc-table.csv
23 #if $table_orientation.choice == 'lines'
24 -l
25 #else if $table_orientation.choice == 'multiindex'
26 -m
27 #end if
28 -q
29 ]]></command>
30 <inputs>
31 <param name="cooc_file" type="data" format="json,yaml" multiple="true"
32 label="Results generated by mutbamscan"/>
33 <conditional name="table_orientation">
34 <param name="choice" type="select" label="Output table orientation">
35 <option value="columns">Column-oriented table (default)</option>
36 <option value="lines">Line-oriented table</option>
37 <option value="multiindex">Multi-level indexing (amplicons and counts
38 categories)
39 </option>
40 </param>
41 <when value="columns"/>
42 <when value="lines"/>
43 <when value="multiindex"/>
44 </conditional>
45 </inputs>
46 <outputs>
47 <data name="table" format="csv"
48 label="${tool.name} on ${on_string}: Mutation cooccurrence (CSV table)"
49 from_work_dir="cooc-table.csv">
50 </data>
51 </outputs>
52 <tests>
53 <test expect_num_outputs="1">
54 <param name="cooc_file" value="cooc-test111.json"/>
55 <conditional name="table_orientation">
56 <param name="choice" value="columns"/>
57 </conditional>
58 <output name="table" ftype="csv">
59 <assert_contents>
60 <has_text text="A76_om1.count"/>
61 <has_text text="A76_om1.mut_oneless"/>
62 </assert_contents>
63 </output>
64 </test>
65 </tests>
66 <help><![CDATA[
67 @HELP_HEADER@
68
69 Information about **cooc_tabmut** method
70 ========================================
71
72 The method exports a JSON or YAML file as a CSV/TSV table for downstream analysis (e.g.: RStudio).
73
74 ]]></help>
75 <expand macro="citations"/>
76 </tool>