Mercurial > repos > jjohnson > contig_annotation_tool

comparison cat_add_names.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 ad7507073c3f
children
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4:aaeb63501369 5:226949352e31
11 @ADD_NAMES_OPTIONS@ 11 @ADD_NAMES_OPTIONS@
12 -o output_names.txt 12 -o output_names.txt
13 && @TXT2TSV@ -i output_names.txt -o $output 13 && @TXT2TSV@ -i output_names.txt -o $output
14 ]]></command> 14 ]]></command>
15 <inputs> 15 <inputs>
16 <param name="input" type="data" format="tabular,txt" label="classification.txt or ORF2LCA.txt"/> 16 <param argument="--input" type="data" format="tabular,txt" label="classification.txt or ORF2LCA.txt"/>
17 <expand macro="cat_db" /> 17 <expand macro="cat_db" />
18 <expand macro="add_names_options" /> 18 <expand macro="add_names_options" />
19 </inputs> 19 </inputs>
20 <outputs> 20 <outputs>
21 <data name="output" format="tabular"/> 21 <data name="output" format="tabular"/>
31 </output> 31 </output>
32 </test> 32 </test>
33 </tests> 33 </tests>
34 <help><![CDATA[ 34 <help><![CDATA[
35 **CAT/BAT add_names** 35 **CAT/BAT add_names**
36 Add names for the NCBI taxomy IDs. 36
37 Add taxonomic names to CAT or BAT output files.
38
39 Required arguments:
40 -i, --input_file Path to input file. Can be either classification
41 output file or ORF2LCA output file.
42 -t, --taxonomy_folder Path to folder that contains taxonomy files.
43
44 Optional arguments:
45 --only_official Only output official level names.
46 --exclude_scores Do not include bit-score support scores in the
47 lineage.
37 48
38 @COMMON_HELP@ 49 @COMMON_HELP@
39 ]]></help> 50 ]]></help>
40 <expand macro="citations" /> 51 <expand macro="citations" />
41 </tool> 52 </tool>