Mercurial > repos > jjohnson > contig_annotation_tool

diff 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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--- a/cat_add_names.xml	Wed Nov 27 10:27:23 2019 -0500
+++ b/cat_add_names.xml	Wed Nov 27 12:11:14 2019 -0500
@@ -13,7 +13,7 @@
     && @TXT2TSV@ -i output_names.txt -o $output
     ]]></command>
     <inputs>
-        <param name="input" type="data" format="tabular,txt" label="classification.txt or ORF2LCA.txt"/>
+        <param argument="--input" type="data" format="tabular,txt" label="classification.txt or ORF2LCA.txt"/>
         <expand macro="cat_db" />
         <expand macro="add_names_options" />
     </inputs>
@@ -33,7 +33,18 @@
     </tests>
     <help><![CDATA[
 **CAT/BAT add_names** 
-Add names for the NCBI taxomy IDs.
+
+Add taxonomic names to CAT or BAT output files.
+
+Required arguments:
+  -i, --input_file       Path to input file. Can be either classification
+                         output file or ORF2LCA output file.
+  -t, --taxonomy_folder  Path to folder that contains taxonomy files.
+
+Optional arguments:
+  --only_official        Only output official level names.
+  --exclude_scores       Do not include bit-score support scores in the
+                         lineage.
 
 @COMMON_HELP@
     ]]></help>