Mercurial > repos > iuc > cooc_tabmut
comparison cooc_tabmut.xml @ 0:4be399803856 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
author | iuc |
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date | Thu, 11 Aug 2022 13:50:09 +0000 |
parents | |
children | 579538ff939d |
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-1:000000000000 | 0:4be399803856 |
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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> |