Mercurial > repos > iuc > gtdbtk_classify_wf

changeset 4:65d52c693b8e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk commit 94a1996b09d7597793f823307cbac6208e20f1d1
author iuc
date Fri, 01 Mar 2024 07:19:45 +0000
parents f8f56dd6449f
children a68b985913ab
files gtdbtk_classify_wf.xml macros.xml test-data/gtdbtk_database.loc
diffstat 3 files changed, 11 insertions(+), 21 deletions(-) [+]
line wrap: on
line diff
--- a/gtdbtk_classify_wf.xml	Fri Feb 09 21:40:53 2024 +0000
+++ b/gtdbtk_classify_wf.xml	Fri Mar 01 07:19:45 2024 +0000
@@ -71,16 +71,16 @@
         <!--
         <test expect_num_outputs="4">
             <param name="input" value="genome_1.fna.gz" ftype="fasta.gz"/>
-            <param name="gtdbtk_db" value="gtdbtk202"/>
+            <param name="gtdbtk_db" value="gtdbtk214"/>
             <output_collection name="output_summary" type="list" count="1">
-                <element name="gtdbtk.ar122.summary" ftype="tsv">
+                <element name="gtdbtk.ar53.summary" ftype="tsv">
                     <assert_contents>
                         <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">
+                <element name="gtdbtk.ar53.markers_summary" ftype="tsv">
                     <assert_contents>
                         <has_text text="number_unique_genes"/>
                     </assert_contents>
@@ -101,30 +101,20 @@
                     </assert_contents>
                 </element>
             </output_collection>
-            <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">
+            <output_collection name="output_classify" type="list" count="1">
+                <element name="gtdbtk.ar53.classify" ftype="newick">
                     <assert_contents>
                         <has_text text="GB_GCA_"/>
                     </assert_contents>
                 </element>
             </output_collection>
             <output_collection name="output_align" type="list" count="2">
-                <element name="gtdbtk.ar122.msa" ftype="fasta.gz">
+                <element name="gtdbtk.ar53.msa" ftype="fasta.gz" decompress="true">
                     <assert_contents>
                         <has_text text="GB_GCA_000008085"/>
                     </assert_contents>
                 </element>
-                <element name="gtdbtk.ar122.user_msa" ftype="fasta">
+                <element name="gtdbtk.ar53.user_msa" ftype="fasta.gz" decompress="true">
                     <assert_contents>
                         <has_text text="genome_1_fna_gz"/>
                     </assert_contents>
--- a/macros.xml	Fri Feb 09 21:40:53 2024 +0000
+++ b/macros.xml	Fri Mar 01 07:19:45 2024 +0000
@@ -1,7 +1,7 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.2.2</token>
-    <token name="@VERSION_SUFFIX@">1</token>
-    <token name="@PROFILE@">20.09</token>
+    <token name="@TOOL_VERSION@">2.3.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">22.05</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">gtdbtk</requirement>
--- a/test-data/gtdbtk_database.loc	Fri Feb 09 21:40:53 2024 +0000
+++ b/test-data/gtdbtk_database.loc	Fri Mar 01 07:19:45 2024 +0000
@@ -23,4 +23,4 @@
 #drwxr-sr-x  4 gvk G-824019    4096 Apr 21  2021 pplacer/
 #drwxr-sr-x  2 gvk G-824019    4096 Apr 20  2021 radii/
 #drwxr-sr-x  2 gvk G-824019    4096 Apr 20  2021 taxonomy/
-gtdbtk202	GTDB-Tk database v202	${__HERE__}/gtdbtk202
+gtdbtk214	GTDB-Tk database v214	${__HERE__}/gtdbtk214/