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

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit a1c079107b72dc08612fa664897bb9d627624e52-dirty

--- a/cat_summarise.xml	Wed Nov 27 10:27:23 2019 -0500
+++ b/cat_summarise.xml	Wed Nov 27 12:11:14 2019 -0500
@@ -11,9 +11,9 @@
     && @TXT2TSV@ -i output_names_summary.txt -o $output
     ]]></command>
     <inputs>
-        <param name="input" type="data" format="tabular" label="classification.official_names.txt"
+        <param argument="--input" type="data" format="tabular" label="classification.official_names.txt"
             help="The classication must be made with only_official names"/>
-        <param name="contigs_fasta" type="data" format="fasta" optional="true" label="contigs.fasta" 
+        <param argument="--contigs_fasta" type="data" format="fasta" optional="true" label="contigs.fasta" 
             help="Required if a contig2classification.names"/>
     </inputs>
     <outputs>
@@ -32,7 +32,19 @@
     </tests>
     <help><![CDATA[
 **CAT summarise** 
-Produce a summary report of assignments to the ofifcial taxonomic names. 
+
+Summarise taxonomic asignemts from anamed CAT or BAT classification file. 
+
+Required arguments:
+  -i, --input_file     Path to named CAT contig classification file or BAT
+                       bin classification file. Currently only official ranks
+                       are supported, and only classification files
+                       containing a single classification per contig / bin.
+
+Optional arguments:
+  -c, --contigs_fasta
+                        Path to contigs fasta file. This is required if you
+                        want to summarise a contig classification file.
 
 @COMMON_HELP@
     ]]></help>