Mercurial > repos > jjohnson > contig_annotation_tool

comparison cat_summarise.xml @ 5:226949352e31 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit a1c079107b72dc08612fa664897bb9d627624e52-dirty
author jjohnson
date Wed, 27 Nov 2019 12:11:14 -0500
parents 18ece3d5bcde
children
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4:aaeb63501369 5:226949352e31
9 CAT summarise -c '$contigs_fasta' -i '$input' 9 CAT summarise -c '$contigs_fasta' -i '$input'
10 -o output_names_summary.txt 10 -o output_names_summary.txt
11 && @TXT2TSV@ -i output_names_summary.txt -o $output 11 && @TXT2TSV@ -i output_names_summary.txt -o $output
12 ]]></command> 12 ]]></command>
13 <inputs> 13 <inputs>
14 <param name="input" type="data" format="tabular" label="classification.official_names.txt" 14 <param argument="--input" type="data" format="tabular" label="classification.official_names.txt"
15 help="The classication must be made with only_official names"/> 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" 16 <param argument="--contigs_fasta" type="data" format="fasta" optional="true" label="contigs.fasta"
17 help="Required if a contig2classification.names"/> 17 help="Required if a contig2classification.names"/>
18 </inputs> 18 </inputs>
19 <outputs> 19 <outputs>
20 <data name="output" format="tabular"/> 20 <data name="output" format="tabular"/>
21 </outputs> 21 </outputs>
30 </output> 30 </output>
31 </test> 31 </test>
32 </tests> 32 </tests>
33 <help><![CDATA[ 33 <help><![CDATA[
34 **CAT summarise** 34 **CAT summarise**
35 Produce a summary report of assignments to the ofifcial taxonomic names. 35
36 Summarise taxonomic asignemts from anamed CAT or BAT classification file.
37
38 Required arguments:
39 -i, --input_file Path to named CAT contig classification file or BAT
40 bin classification file. Currently only official ranks
41 are supported, and only classification files
42 containing a single classification per contig / bin.
43
44 Optional arguments:
45 -c, --contigs_fasta
46 Path to contigs fasta file. This is required if you
47 want to summarise a contig classification file.
36 48
37 @COMMON_HELP@ 49 @COMMON_HELP@
38 ]]></help> 50 ]]></help>
39 <expand macro="citations" /> 51 <expand macro="citations" />
40 </tool> 52 </tool>