Mercurial > repos > jjohnson > contig_annotation_tool

comparison cat_bins.xml @ 0:ad7507073c3f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
author jjohnson
date Sun, 24 Nov 2019 21:56:00 -0500
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children 86cd2e70b0dc
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-1:000000000000 0:ad7507073c3f
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 && @TXT2TSV@ *.ORF2LCA.txt *.bin2classification.txt
27 @ADD_NAMES@
28 @SUMMARISE@
29 ]]></command>
30 <inputs>
31 <param name="mags" type="data" format="fasta" multiple="true" label="metagenome assembled genomes (MAGs/bins)"/>
32 <expand macro="cat_db" />
33 <expand macro="use_intermediates" />
34 <expand macro="custom_settings" />
35 <expand macro="add_names" />
36 <expand macro="summarise" />
37 <expand macro="select_bat_outputs" />
38 </inputs>
39 <outputs>
40 <expand macro="outputs" />
41 </outputs>
42 <tests>
43 <test>
44 <param name="mags" ftype="fasta" value="genome3.fna"/>
45 <expand macro="test_catdb"/>
46 <param name="select_outputs" value="contig2classification"/>
47 <output name="contig2classification">
48 <assert_contents>
49 <has_text text="1639" />
50 </assert_contents>
51 </output>
52 </test>
53 <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/>
54 <expand macro="test_catdb"/>
55 <param name="select_outputs" value="contig2classification"/>
56 <output name="contig2classification">
57 <assert_contents>
58 <has_text text="666" />
59 <has_text text="1639" />
60 </assert_contents>
61 </output>
62 </test>
63 </tests>
64 <help><![CDATA[
65 **CAT bin or bins**
66 Classify metagenomics assembled genomes.
67
68 @COMMON_HELP@
69 ]]></help>
70 <expand macro="citations" />
71 </tool>