--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cat_bins.xml	Tue Dec 10 16:06:38 2019 -0500
@@ -0,0 +1,136 @@
+<tool id="cat_bins" name="CAT bins" version="@VERSION@.0">
+    <description>annotate with taxonomic classification</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code"><![CDATA[
+    #set $bin_dir = None
+    #if len($mags) > 1:
+        #set $bin_dir = 'inputs'
+        mkdir -p $bin_dir &&
+        #for mag in $mags:
+            ln -s '$mag' $bin_dir/ &&
+        #end for
+    #end if
+    CAT 
+    #if $bin_dir
+        bins -s '.dat' -b '$bin_dir'
+    #else
+        bin -b '$mags'
+    #end if 
+    @CAT_DB@
+    @USE_INTERMEDIATES@
+    @CUSTOM_SETTINGS@
+    @DIAMOND_OPTIONS@
+    && @TXT2TSV@ *.ORF2LCA.txt *.bin2classification.txt
+    #if len($mags) > 1:
+        #set pat = '$' + '{i/concatenated./}'
+        && (for i in *.concatenated.*; do ln -s "\$i" "${pat}"; done)
+    #end if
+    @ADD_NAMES@
+    @SUMMARISE@
+    ]]></command>
+    <inputs>
+        <param name="mags" type="data" format="fasta" multiple="true" label="metagenome assembled genomes (MAGs/bins)"/>
+        <expand macro="cat_db" />
+        <expand macro="use_intermediates" />
+        <expand macro="custom_settings" />
+        <expand macro="diamond_options" />
+        <expand macro="add_names" />
+        <expand macro="summarise" />
+        <expand macro="select_bat_outputs" />
+    </inputs>
+    <outputs>
+        <expand macro="outputs" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="mags" ftype="fasta" value="genome2.fna"/>
+            <expand macro="test_catdb"/>
+            <param name="select_outputs" value="bin2classification"/>
+            <output name="bin2classification">
+                <assert_contents>
+                    <has_text text="666" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="mags" ftype="fasta" value="genome3.fna"/>
+            <expand macro="test_catdb"/>
+            <param name="select_outputs" value="bin2classification"/>
+            <output name="bin2classification">
+                <assert_contents>
+                    <has_text text="1639" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/>
+            <expand macro="test_catdb"/>
+            <param name="select_outputs" value="bin2classification"/>
+            <output name="bin2classification">
+                <assert_contents>
+                    <has_text text="666" />
+                    <has_text text="1639" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/>
+            <expand macro="test_catdb"/>
+            <param name="select_outputs" value="bin2classification"/>
+           <param name="select_outputs" value="predicted_proteins_faa"/>
+            <conditional name="names">
+                <param name="add_names" value="both"/>
+            </conditional>
+            <param name="summarise" value="classification"/>
+            <output name="predicted_proteins_faa">
+                <assert_contents>
+                    <has_text text="contig_11394" />
+                    <has_text text="contig_4403" />
+                </assert_contents>
+            </output>
+            <output name="orf2lca_names">
+                <assert_contents>
+                    <has_text text="Listeria" />
+                    <has_text text="Vibrio" />
+                </assert_contents>
+            </output>
+            <output name="classification_summary">
+                <assert_contents>
+                    <has_text text="Listeria" />
+                </assert_contents>
+            </output>
+        </test>
+
+    </tests>
+    <help><![CDATA[
+**CAT bin** or **CAT bins**
+
+Classify metagenomics assembled genomes. 
+
+@COMMON_HELP@
+
+**INPUTS**
+
+One or more fasta files of metagenome assembled genomes.
+
+@OUTPUTS_HELP@
+
+**CAT bins**
+
+Run Bin Annotation Tool (BAT) on a set of bins.
+
+Required arguments:
+  -b, --bin_folder       Path to directory containing bins.
+  -d, --database_folder  Path to folder that contains database files.
+  -t, --taxonomy_folder  Path to folder that contains taxonomy files.
+
+
+@OPTIONS_HELP@
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>