# HG changeset patch
# User iuc
# Date 1678395672 0
# Node ID 31853794ace2f0945404aa9b2d2e74d16c3da193
# Parent  18676df0cb3a151f7d1a04356bcd22f7c9c46d28
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 2948f114101aeefa951f47df8ee3b25656d9680e

diff -r 18676df0cb3a -r 31853794ace2 cat_bins.xml
--- a/cat_bins.xml	Wed Jan 08 13:03:51 2020 -0500
+++ b/cat_bins.xml	Thu Mar 09 21:01:12 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="cat_bins" name="CAT bins" version="@VERSION@.1">
+<tool id="cat_bins" name="CAT bins" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>annotate with taxonomic classification</description>
     <macros>
         <import>macros.xml</import>
@@ -6,19 +6,24 @@
     <expand macro="requirements" />
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
+    #import re
     #set $bin_dir = None
     #if len($mags) > 1:
         #set $bin_dir = 'inputs'
         mkdir -p $bin_dir &&
         #for mag in $mags:
-            ln -s '$mag' $bin_dir/ &&
+            #set input_identifier = re.sub('[^\s\w\-]', '_', str($mag.element_identifier))
+            ln -s '$mag' '${bin_dir}/${input_identifier}.FASTA' &&
         #end for
+    #else
+        #set $bin_file = re.sub('[^\s\w\-]', '_', str($mags[0].element_identifier))
+        ln -s $mags[0] '$bin_file' &&
     #end if
     CAT 
     #if $bin_dir
-        bins -s '.dat' -b '$bin_dir'
+        bins -s '.FASTA' -b '$bin_dir'
     #else
-        bin -b '$mags'
+        bin -b '$bin_file'
     #end if 
     @CAT_DB@
     @USE_INTERMEDIATES@
@@ -81,7 +86,8 @@
             <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"/>
+            <param name="select_outputs" value="predicted_proteins_faa"/>
+            <param name="fraction" value="0.6"/>
             <conditional name="names">
                 <param name="add_names" value="both"/>
             </conditional>
@@ -94,13 +100,13 @@
             </output>
             <output name="orf2lca_names">
                 <assert_contents>
-                    <has_text text="Listeria" />
+                    <has_text text="Vibrionaceae" />
                     <has_text text="Vibrio" />
                 </assert_contents>
             </output>
             <output name="classification_summary">
                 <assert_contents>
-                    <has_text text="Listeria" />
+                    <has_text text="Gammaproteobacteria" />
                 </assert_contents>
             </output>
         </test>
diff -r 18676df0cb3a -r 31853794ace2 macros.xml
--- a/macros.xml	Wed Jan 08 13:03:51 2020 -0500
+++ b/macros.xml	Thu Mar 09 21:01:12 2023 +0000
@@ -1,8 +1,9 @@
 <macros>
-    <token name="@VERSION@">5.0.3</token>
+    <token name="@TOOL_VERSION@">5.2.3</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@VERSION@">cat</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">cat</requirement>
             <yield/>
         </requirements>
     </xml>