Mercurial > repos > iuc > cat_add_names

comparison cat_add_names.xml @ 0:13192095fd5a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
author iuc
date Tue, 10 Dec 2019 16:04:22 -0500
parents
children acd9fe45eb81
comparison
equal deleted inserted replaced
-1:000000000000 0:13192095fd5a
1 <tool id="cat_add_names" name="CAT add_names" version="@VERSION@.0">
2 <description>annotate with taxonomic names</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version_command" />
8 <command detect_errors="exit_code"><![CDATA[
9 CAT add_names
10 -i '$input'
11 @CAT_TAXONOMY@
12 @ADD_NAMES_OPTIONS@
13 -o 'output_names.txt'
14 && @TXT2TSV@ -i 'output_names.txt' -o '$output'
15 ]]></command>
16 <inputs>
17 <param argument="--input" type="data" format="tabular,txt" label="classification.txt or ORF2LCA.txt from CAT contigs or CAT bins"/>
18 <expand macro="cat_db" />
19 <expand macro="add_names_options" />
20 </inputs>
21 <outputs>
22 <data name="output" format="tabular" label="#set name = $input.name.replace('.txt','.names.txt')# $name"/>
23 </outputs>
24 <tests>
25 <test>
26 <param name="input" ftype="tabular" value="test_contig.contig2classification.txt"/>
27 <expand macro="test_catdb"/>
28 <output name="output">
29 <assert_contents>
30 <has_text text="Firmicutes" />
31 </assert_contents>
32 </output>
33 </test>
34 </tests>
35 <help><![CDATA[
36 **CAT/BAT add_names**
37
38 Add taxonomic names to CAT or BAT output files. Names can be added to ORF2LCA.txt, contig2classification.txt, and bin2classification.txt outputs.
39
40 @COMMON_HELP@
41
42 **INPUT**
43
44 Example: contig2classification.txt from CAT conitgs
45
46 ::
47
48 # contig classification reason lineage lineage scores
49 contig_44250 classified based on 1/2 ORFs 1;131567;2;1224;1236;135623;641;662;666 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00
50 contig_9952 classified based on 1/5 ORFs 1;131567;2;1783272;1239;91061* 1.00;1.00;1.00;1.00;1.00;1.00
51
52
53 **OUTPUT**
54
55 ::
56
57 # contig classification reason lineage lineage scores superkingdom phylum class order family genus species
58 contig_44250 classified based on 1/2 ORFs 1;131567;2;1224;1236;135623;641;662;666 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 Bacteria: 1.00 Proteobacteria: 1.00 Gammaproteobacteria: 1.00 Vibrionales: 1.00 Vibrionaceae: 1.00 Vibrio: 1.00 Vibrio cholerae: 1.00
59 contig_9952 classified based on 1/5 ORFs 1;131567;2;1783272;1239;91061* 1.00;1.00;1.00;1.00;1.00;1.00 Bacteria: 1.00 Firmicutes: 1.00 Bacilli*: 1.00 not classified not classified not classified not classified
60
61
62 Required arguments:
63 -i, --input_file Path to input file. Can be either classification
64 output file or ORF2LCA output file.
65 -t, --taxonomy_folder Path to folder that contains taxonomy files.
66
67 Optional arguments:
68 --only_official Only output official level names.
69 --exclude_scores Do not include bit-score support scores in the
70 lineage.
71
72 ]]></help>
73 <expand macro="citations" />
74 </tool>