Mercurial > repos > jjohnson > contig_annotation_tool

comparison cat_summarise.xml @ 0:ad7507073c3f 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 f80f020c77d04c2e13b89aaea3d784314b940931-dirty
author jjohnson
date Sun, 24 Nov 2019 21:56:00 -0500
parents
children 18ece3d5bcde
comparison
equal deleted inserted replaced
-1:000000000000 0:ad7507073c3f
1 <tool id="cat_summarise" name="CAT summarise" 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 summarise -c '$contigs_fasta' -i '$input'
10 -o output_names_summary.txt
11 && @TXT2TSV@ -i output_names_summary.txt -o $output
12 ]]></command>
13 <inputs>
14 <param name="input" type="data" format="tabular" label="classification.official_names.txt"
15 help="The classication must be made with only_official names"/>
16 <param name="contigs_fasta" type="data" format="fasta" optional="true" label="contigs.fasta"
17 help="Required if a contig2classification.names"/>
18 </inputs>
19 <outputs>
20 <data name="output" format="tabular"/>
21 </outputs>
22 <tests>
23 <test>
24 <param name="input" ftype="tabular" value="test_contig.contig2classification.names.txt"/>
25 <param name="contigs_fasta" ftype="fasta" value="configs.fasta"/>
26 <output name="output">
27 <assert_contents>
28 <has_text text="Firmicutes" />
29 </assert_contents>
30 </output>
31 </test>
32 </tests>
33 <help><![CDATA[
34 **CAT summarise**
35 Produce a summary report of assignments to the ofifcial taxonomic names.
36
37 @COMMON_HELP@
38 ]]></help>
39 <expand macro="citations" />
40 </tool>