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comparison cat_bins.xml @ 0:0094893f5001 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
author iuc
date Tue, 10 Dec 2019 16:06:38 -0500
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children 18676df0cb3a
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-1:000000000000 0:0094893f5001
1 <tool id="cat_bins" name="CAT bins" version="@VERSION@.0">
2 <description>annotate with taxonomic classification</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 #set $bin_dir = None
10 #if len($mags) > 1:
11 #set $bin_dir = 'inputs'
12 mkdir -p $bin_dir &&
13 #for mag in $mags:
14 ln -s '$mag' $bin_dir/ &&
15 #end for
16 #end if
17 CAT
18 #if $bin_dir
19 bins -s '.dat' -b '$bin_dir'
20 #else
21 bin -b '$mags'
22 #end if
23 @CAT_DB@
24 @USE_INTERMEDIATES@
25 @CUSTOM_SETTINGS@
26 @DIAMOND_OPTIONS@
27 && @TXT2TSV@ *.ORF2LCA.txt *.bin2classification.txt
28 #if len($mags) > 1:
29 #set pat = '$' + '{i/concatenated./}'
30 && (for i in *.concatenated.*; do ln -s "\$i" "${pat}"; done)
31 #end if
32 @ADD_NAMES@
33 @SUMMARISE@
34 ]]></command>
35 <inputs>
36 <param name="mags" type="data" format="fasta" multiple="true" label="metagenome assembled genomes (MAGs/bins)"/>
37 <expand macro="cat_db" />
38 <expand macro="use_intermediates" />
39 <expand macro="custom_settings" />
40 <expand macro="diamond_options" />
41 <expand macro="add_names" />
42 <expand macro="summarise" />
43 <expand macro="select_bat_outputs" />
44 </inputs>
45 <outputs>
46 <expand macro="outputs" />
47 </outputs>
48 <tests>
49 <test>
50 <param name="mags" ftype="fasta" value="genome2.fna"/>
51 <expand macro="test_catdb"/>
52 <param name="select_outputs" value="bin2classification"/>
53 <output name="bin2classification">
54 <assert_contents>
55 <has_text text="666" />
56 </assert_contents>
57 </output>
58 </test>
59 <test>
60 <param name="mags" ftype="fasta" value="genome3.fna"/>
61 <expand macro="test_catdb"/>
62 <param name="select_outputs" value="bin2classification"/>
63 <output name="bin2classification">
64 <assert_contents>
65 <has_text text="1639" />
66 </assert_contents>
67 </output>
68 </test>
69 <test>
70 <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/>
71 <expand macro="test_catdb"/>
72 <param name="select_outputs" value="bin2classification"/>
73 <output name="bin2classification">
74 <assert_contents>
75 <has_text text="666" />
76 <has_text text="1639" />
77 </assert_contents>
78 </output>
79 </test>
80 <test>
81 <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/>
82 <expand macro="test_catdb"/>
83 <param name="select_outputs" value="bin2classification"/>
84 <param name="select_outputs" value="predicted_proteins_faa"/>
85 <conditional name="names">
86 <param name="add_names" value="both"/>
87 </conditional>
88 <param name="summarise" value="classification"/>
89 <output name="predicted_proteins_faa">
90 <assert_contents>
91 <has_text text="contig_11394" />
92 <has_text text="contig_4403" />
93 </assert_contents>
94 </output>
95 <output name="orf2lca_names">
96 <assert_contents>
97 <has_text text="Listeria" />
98 <has_text text="Vibrio" />
99 </assert_contents>
100 </output>
101 <output name="classification_summary">
102 <assert_contents>
103 <has_text text="Listeria" />
104 </assert_contents>
105 </output>
106 </test>
107
108 </tests>
109 <help><![CDATA[
110 **CAT bin** or **CAT bins**
111
112 Classify metagenomics assembled genomes.
113
114 @COMMON_HELP@
115
116 **INPUTS**
117
118 One or more fasta files of metagenome assembled genomes.
119
120 @OUTPUTS_HELP@
121
122 **CAT bins**
123
124 Run Bin Annotation Tool (BAT) on a set of bins.
125
126 Required arguments:
127 -b, --bin_folder Path to directory containing bins.
128 -d, --database_folder Path to folder that contains database files.
129 -t, --taxonomy_folder Path to folder that contains taxonomy files.
130
131
132 @OPTIONS_HELP@
133
134 ]]></help>
135 <expand macro="citations" />
136 </tool>