comparison cat_summarise.xml @ 0:db1360aae489 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
author iuc
date Tue, 10 Dec 2019 16:04:54 -0500
parents
children 388e6678fa98
comparison
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-1:000000000000 0:db1360aae489
1 <tool id="cat_summarise" name="CAT summarise" version="@VERSION@.0">
2 <description>the number of contigs or bins assigned to each taxonomic name</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 summarise
10 #if $contigs_fasta
11 -c '$contigs_fasta'
12 #end if
13 -i '$input'
14 -o 'output_names_summary.txt'
15 && @TXT2TSV@ -i 'output_names_summary.txt' -o '$output'
16 ]]></command>
17 <inputs>
18 <param argument="--input" type="data" format="tabular" label="classification.names.txt output from CAT add_names"
19 help="The classication must be made with --only_official names"/>
20 <param argument="--contigs_fasta" type="data" format="fasta" optional="true" label="contigs.fasta used for CAT contigs"
21 help="Required if summarising a contig2classification.names output derived from CAT contigs"/>
22 </inputs>
23 <outputs>
24 <data name="output" format="tabular" label="#set name = $input.name.replace('.txt','.summary.txt')# ${tool.name} on ${on_string} $name"/>
25 </outputs>
26 <tests>
27 <test>
28 <param name="input" ftype="tabular" value="test_contig.contig2classification.names.txt"/>
29 <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/>
30 <output name="output">
31 <assert_contents>
32 <has_text text="Firmicutes" />
33 </assert_contents>
34 </output>
35 </test>
36 </tests>
37 <help><![CDATA[
38 **CAT summarise**
39
40 Summarise taxonomic asignemts from a CAT or BAT classification file that has official taxonomic names added by CAT add_names.
41
42 **INPUT**
43
44 ::
45
46 # bin classification reason lineage lineage scores superkingdom phylum class order family genus species
47 genome2.fna classified based on 6/17 ORFs 1;131567;2;1224;1236;135623;641;662;666 1.00;1.00;1.00;0.89;0.89;0.89;0.89;0.89;0.69 Bacteria: 1.00 Proteobacteria: 0.89 Gammaproteobacteria: 0.89 Vibrionales: 0.89 Vibrionaceae: 0.89 Vibrio: 0.89 Vibrio cholerae: 0.69
48 genome3.fna classified based on 4/9 ORFs 1;131567;2;1783272;1239;91061;1385;186820;1637;1639 1.00;1.00;1.00;0.76;0.76;0.76;0.76;0.76;0.76;0.76 Bacteria: 1.00 Firmicutes: 0.76 Bacilli: 0.76 Bacillales: 0.76 Listeriaceae: 0.76 Listeria: 0.76 Listeria monocytogenes: 0.76
49
50
51 **OUTPUT**
52
53 ::
54
55 # total number of bins is 2, of which 2 (100.00%) are classified.
56 #
57 # rank clade number of bins
58 superkingdom Bacteria 2
59 phylum Proteobacteria 1
60 phylum Firmicutes 1
61 class Gammaproteobacteria 1
62 class Bacilli 1
63 order Vibrionales 1
64 order Bacillales 1
65 family Vibrionaceae 1
66 family Listeriaceae 1
67 genus Vibrio 1
68 genus Listeria 1
69 species Vibrio cholerae 1
70 species Listeria monocytogenes 1
71
72
73 Required arguments:
74 -i, --input_file Path to named CAT contig classification file or BAT
75 bin classification file. Currently only official ranks
76 are supported, and only classification files
77 containing a single classification per contig / bin.
78
79 Optional arguments:
80 -c, --contigs_fasta
81 Path to contigs fasta file. This is required if you
82 want to summarise a contig classification file.
83
84 @COMMON_HELP@
85 ]]></help>
86 <expand macro="citations" />
87 </tool>