Mercurial > repos > jjohnson > contig_annotation_tool

comparison cat_contigs.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 18ece3d5bcde
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-1:000000000000 0:ad7507073c3f
1 <tool id="cat_contigs" name="CAT contigs" 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 CAT contigs -c '$contigs_fasta'
10 @CAT_DB@
11 @USE_INTERMEDIATES@
12 @CUSTOM_SETTINGS@
13 && @TXT2TSV@ *.ORF2LCA.txt *.contig2classification.txt
14 @ADD_NAMES@
15 @SUMMARISE@
16 ]]></command>
17 <inputs>
18 <param name="contigs_fasta" type="data" format="fasta" label="Contigs fasta"/>
19 <expand macro="cat_db" />
20 <expand macro="use_intermediates" />
21 <expand macro="custom_settings" />
22 <expand macro="add_names" />
23 <expand macro="summarise" />
24 <expand macro="select_cat_outputs" />
25 </inputs>
26 <outputs>
27 <expand macro="outputs" />
28 </outputs>
29 <tests>
30 <test>
31 <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/>
32 <expand macro="test_catdb"/>
33 <param name="select_outputs" value="contig2classification"/>
34 <output name="contig2classification">
35 <assert_contents>
36 <has_text text="contig_38063" />
37 </assert_contents>
38 </output>
39 </test>
40 </tests>
41 <help><![CDATA[
42 **CAT contigs**
43 Classifiy metagenomics contigs.
44
45 @COMMON_HELP@
46 ]]></help>
47 <expand macro="citations" />
48 </tool>