# HG changeset patch
# User iuc
# Date 1690288059 0
# Node ID 6501b5b339886117bf0eefdb3c241366abd2e289
# Parent  dbf1798c0dcc0b30a22c52ded002000c92281db9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk commit fab39612473d91e048868d9c122d7dd61a2bd9d4

diff -r dbf1798c0dcc -r 6501b5b33988 gtdbtk_classify_wf.xml
--- a/gtdbtk_classify_wf.xml	Thu Feb 16 23:35:55 2023 +0000
+++ b/gtdbtk_classify_wf.xml	Tue Jul 25 12:27:39 2023 +0000
@@ -9,9 +9,6 @@
 
 mkdir input_dir &&
 mkdir output_dir &&
-mkdir output_tsv_dir &&
-mkdir output_newick_dir &&
-mkdir output_fasta_dir &&
 #for $i in $input:
     ## gtdbtk uses the file extension to determine the input format.
     #set ext = "." + $i.ext
@@ -53,38 +50,38 @@
         <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)">
             <filter>advanced['output_process_log'] == 'yes'</filter>
         </data>
-        <collection name="output_tsv" type="list" format="tsv" label="${tool.name} on ${on_string} (tsv)">
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tsv" ext="tsv" directory="output_dir"/>
+        <collection name="output_align" type="list" format="fasta.gz" label="${tool.name} on ${on_string} (align)">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fasta.gz" ext="fasta.gz" directory="output_dir/align"/>
+        </collection>
+        <collection name="output_identfy" type="list" format="tsv" label="${tool.name} on ${on_string} (identify)">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tsv" ext="tsv" directory="output_dir/identify"/>
         </collection>
-        <collection name="output_newick" type="list" format="newick" label="${tool.name} on ${on_string} (newick)">
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tree" ext="newick" directory="output_dir"/>
+        <collection name="output_classify" type="list" format="newick" label="${tool.name} on ${on_string} (classify)">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tree" ext="newick" directory="output_dir/classify"/>
         </collection>
-        <collection name="output_fasta" type="list" format="fasta" label="${tool.name} on ${on_string} (fasta)">
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fasta" ext="fasta" directory="output_dir"/>
+        <collection name="output_summary" type="list" format="tsv" label="${tool.name} on ${on_string} (summary)">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tsv" ext="tsv" directory="output_dir"/>
         </collection>
     </outputs>
     <tests>
         <!-- The commented test here is valid if we could store the GTDB-Tk database -->
         <!--
-        <test expect_num_outputs="3">
+        <test expect_num_outputs="4">
             <param name="input" value="genome_1.fna.gz" ftype="fasta.gz"/>
             <param name="gtdbtk_db" value="gtdbtk202"/>
-            <output_collection name="output_tsv" type="list" count="6">
-                <element name="gtdbtk.ar122.filtered" ftype="tsv">
+            <output_collection name="output_summary" type="list" count="1">
+                <element name="gtdbtk.ar122.summary" ftype="tsv">
                     <assert_contents>
-                        <has_size value="0"/>
+                        <has_text text="user_genome"/>
                     </assert_contents>
                 </element>
+            </output_collection>
+            <output_collection name="output_identfy" type="list" count="4">
                 <element name="gtdbtk.ar122.markers_summary" ftype="tsv">
                     <assert_contents>
                         <has_text text="number_unique_genes"/>
                     </assert_contents>
                 </element>
-                <element name="gtdbtk.ar122.summary" ftype="tsv">
-                    <assert_contents>
-                        <has_text text="genome_1_fna_gz"/>
-                    </assert_contents>
-                </element>
                 <element name="gtdbtk.bac120.markers_summary" ftype="tsv">
                     <assert_contents>
                         <has_text text="genome_1_fna_gz"/>
@@ -101,15 +98,25 @@
                     </assert_contents>
                 </element>
             </output_collection>
-            <output_collection name="output_newick" type="list" count="1">
-                <element name="gtdbtk.ar122.classify" ftype="newick">
+            <output_collection name="output_classify" type="list" count="3">
+                <element name="gtdbtk.ar122.classify.tree.6" ftype="newick">
+                    <assert_contents>
+                        <has_text text="GB_GCA_"/>
+                    </assert_contents>
+                </element>
+                <element name="gtdbtk.ar122" ftype="newick">
+                    <assert_contents>
+                        <has_text text="user_genome"/>
+                    </assert_contents>
+                </element>
+                <element name="gtdbtk.backbone.ar122.classify" ftype="newick">
                     <assert_contents>
                         <has_text text="GB_GCA_"/>
                     </assert_contents>
                 </element>
             </output_collection>
-            <output_collection name="output_fasta" type="list" count="2">
-                <element name="gtdbtk.ar122.msa" ftype="fasta">
+            <output_collection name="output_align" type="list" count="2">
+                <element name="gtdbtk.ar122.msa" ftype="fasta.gz">
                     <assert_contents>
                         <has_text text="GB_GCA_000008085"/>
                     </assert_contents>
@@ -158,3 +165,4 @@
     ]]></help>
     <expand macro="citations"/>
 </tool>
+
diff -r dbf1798c0dcc -r 6501b5b33988 macros.xml
--- a/macros.xml	Thu Feb 16 23:35:55 2023 +0000
+++ b/macros.xml	Tue Jul 25 12:27:39 2023 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">2.2.2</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">20.09</token>
     <xml name="requirements">
         <requirements>