--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cat_add_names.xml	Tue Dec 10 16:04:22 2019 -0500
@@ -0,0 +1,74 @@
+<tool id="cat_add_names" name="CAT add_names" version="@VERSION@.0">
+    <description>annotate with taxonomic names</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code"><![CDATA[
+    CAT add_names 
+    -i '$input'
+    @CAT_TAXONOMY@
+    @ADD_NAMES_OPTIONS@
+    -o 'output_names.txt'
+    && @TXT2TSV@ -i 'output_names.txt' -o '$output'
+    ]]></command>
+    <inputs>
+        <param argument="--input" type="data" format="tabular,txt" label="classification.txt or ORF2LCA.txt from CAT contigs or CAT bins"/>
+        <expand macro="cat_db" />
+        <expand macro="add_names_options" />
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular"  label="#set name = $input.name.replace('.txt','.names.txt')# $name"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" ftype="tabular" value="test_contig.contig2classification.txt"/>
+            <expand macro="test_catdb"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="Firmicutes" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**CAT/BAT add_names** 
+
+Add taxonomic names to CAT or BAT output files.  Names can be added to ORF2LCA.txt, contig2classification.txt, and bin2classification.txt outputs. 
+
+@COMMON_HELP@
+
+**INPUT**
+
+Example: contig2classification.txt from CAT conitgs
+
+::
+
+  # contig        classification  reason  lineage lineage scores
+  contig_44250    classified      based on 1/2 ORFs       1;131567;2;1224;1236;135623;641;662;666 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00
+  contig_9952     classified      based on 1/5 ORFs       1;131567;2;1783272;1239;91061*  1.00;1.00;1.00;1.00;1.00;1.00
+
+
+**OUTPUT**
+
+::
+
+  # contig        classification  reason  lineage lineage scores  superkingdom    phylum  class   order   family  genus   species
+  contig_44250    classified      based on 1/2 ORFs       1;131567;2;1224;1236;135623;641;662;666 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00    Bacteria: 1.00  Proteobacteria: 1.00    Gammaproteobacteria: 1.00       Vibrionales: 1.00       Vibrionaceae: 1.00      Vibrio: 1.00    Vibrio cholerae: 1.00
+  contig_9952     classified      based on 1/5 ORFs       1;131567;2;1783272;1239;91061*  1.00;1.00;1.00;1.00;1.00;1.00   Bacteria: 1.00  Firmicutes: 1.00        Bacilli*: 1.00  not classified  not classified  not classified  not classified
+
+
+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.
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>