Mercurial > repos > iuc > cooc_tabmut
comparison cooc_tabmut.xml @ 1:579538ff939d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
author | iuc |
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date | Mon, 31 Jul 2023 15:23:29 +0000 |
parents | 4be399803856 |
children | eeb5c054ecf8 |
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0:4be399803856 | 1:579538ff939d |
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1 <tool id="cooc_tabmut" name="Cojac: tabmut" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" | 1 <tool id="cooc_tabmut" name="Cojac: tabmut" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" |
2 profile="@PROFILE@"> | 2 profile="@PROFILE@"> |
3 <description> | 3 <description> |
4 export cooccurrence mutations as a table | 4 exports co-occurrence results from mutbamscan as a table |
5 </description> | 5 </description> |
6 <macros> | 6 <macros> |
7 <import>macros.xml</import> | 7 <import>macros.xml</import> |
8 </macros> | 8 </macros> |
9 <expand macro="biotools"/> | 9 <expand macro="biotools"/> |
10 <expand macro="requirements"/> | 10 <expand macro="requirements"/> |
11 <expand macro="version"/> | 11 <expand macro="version"/> |
12 <command detect_errors="exit_code"><![CDATA[ | 12 <command detect_errors="exit_code"><![CDATA[ |
13 #for $input_file in $cooc_file | 13 cojac cooc-tabmut |
14 #set $cooc_ext = $input_file.ext | 14 #if $cooc_data.ext == 'json' |
15 #end for | 15 -j '$cooc_data' |
16 cooc-tabmut | 16 #else |
17 #if $cooc_ext == 'json' | 17 -y '$cooc_data' |
18 -j '$cooc_file' | |
19 #else if $cooc_ext == 'yaml' | |
20 -y '$cooc_file' | |
21 #end if | 18 #end if |
22 -o cooc-table.csv | |
23 #if $table_orientation.choice == 'lines' | 19 #if $table_orientation.choice == 'lines' |
24 -l | 20 -l |
25 #else if $table_orientation.choice == 'multiindex' | 21 #else if $table_orientation.choice == 'multiindex' |
26 -m | 22 -m |
27 #end if | 23 #end if |
24 #if $out_format == 'tsv': | |
25 -o cooc-table.tsv | |
26 #else: | |
27 -o cooc-table.csv | |
28 #end if | |
28 -q | 29 -q |
29 ]]></command> | 30 ]]></command> |
30 <inputs> | 31 <inputs> |
31 <param name="cooc_file" type="data" format="json,yaml" multiple="true" | 32 <param name="cooc_data" type="data" format="json,yaml" label="Results generated by mutbamscan"/> |
32 label="Results generated by mutbamscan"/> | |
33 <conditional name="table_orientation"> | 33 <conditional name="table_orientation"> |
34 <param name="choice" type="select" label="Output table orientation"> | 34 <param name="choice" type="select" label="Output table orientation"> |
35 <option value="columns">Column-oriented table (default)</option> | 35 <option value="columns">Column-oriented table (default)</option> |
36 <option value="lines">Line-oriented table</option> | 36 <option value="lines">Line-oriented table</option> |
37 <option value="multiindex">Multi-level indexing (amplicons and counts | 37 <option value="multiindex">Multi-level indexing (amplicons and counts |
40 </param> | 40 </param> |
41 <when value="columns"/> | 41 <when value="columns"/> |
42 <when value="lines"/> | 42 <when value="lines"/> |
43 <when value="multiindex"/> | 43 <when value="multiindex"/> |
44 </conditional> | 44 </conditional> |
45 <param name="out_format" type="select" label="Type of output to produce"> | |
46 <option value="tsv">Tab-separated (TSV)</option> | |
47 <option value="csv">Comma-separated (CSV)</option> | |
48 </param> | |
45 </inputs> | 49 </inputs> |
46 <outputs> | 50 <outputs> |
47 <data name="table" format="csv" | 51 <data name="table_tsv" format="tsv" label="${tool.name} on ${on_string}: Mutation coo-ccurrence (TSV table)" from_work_dir="cooc-table.tsv"> |
48 label="${tool.name} on ${on_string}: Mutation cooccurrence (CSV table)" | 52 <filter>out_format == 'tsv'</filter> |
49 from_work_dir="cooc-table.csv"> | 53 </data> |
54 <data name="table_csv" format="csv" label="${tool.name} on ${on_string}: Mutation coo-ccurrence (CSV table)" from_work_dir="cooc-table.csv"> | |
55 <filter>out_format == 'csv'</filter> | |
50 </data> | 56 </data> |
51 </outputs> | 57 </outputs> |
52 <tests> | 58 <tests> |
53 <test expect_num_outputs="1"> | 59 <test expect_num_outputs="1"> |
54 <param name="cooc_file" value="cooc-test111.json"/> | 60 <param name="cooc_data" value="cooc-test111.json"/> |
55 <conditional name="table_orientation"> | 61 <conditional name="table_orientation"> |
56 <param name="choice" value="columns"/> | 62 <param name="choice" value="columns"/> |
57 </conditional> | 63 </conditional> |
58 <output name="table" ftype="csv"> | 64 <output name="table_tsv" ftype="tsv"> |
59 <assert_contents> | 65 <assert_contents> |
60 <has_text text="A76_om1.count"/> | 66 <has_text text="A76"/> |
61 <has_text text="A76_om1.mut_oneless"/> | 67 </assert_contents> |
68 </output> | |
69 </test> | |
70 <test expect_num_outputs="1"> | |
71 <param name="cooc_data" value="cooc-test111.json"/> | |
72 <conditional name="table_orientation"> | |
73 <param name="choice" value="columns"/> | |
74 </conditional> | |
75 <param name="out_format" value="csv"/> | |
76 <output name="table_csv" ftype="csv"> | |
77 <assert_contents> | |
78 <has_text text="A76"/> | |
62 </assert_contents> | 79 </assert_contents> |
63 </output> | 80 </output> |
64 </test> | 81 </test> |
65 </tests> | 82 </tests> |
66 <help><![CDATA[ | 83 <help><![CDATA[ |
67 @HELP_HEADER@ | 84 @HELP_HEADER@ |
68 | 85 |
69 Information about **cooc_tabmut** method | 86 Information about **cojac cooc_tabmut** method |
70 ======================================== | 87 ============================================== |
71 | 88 |
72 The method exports a JSON or YAML file as a CSV/TSV table for downstream analysis (e.g.: RStudio). | 89 The method exports a JSON or YAML file as a CSV/TSV table for downstream analysis (e.g.: RStudio). |
73 | 90 |
74 ]]></help> | 91 ]]></help> |
75 <expand macro="citations"/> | 92 <expand macro="citations"/> |