diff do-partition.xml @ 6:e562293ee5ec draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"

--- a/do-partition.xml	Fri Sep 07 11:02:11 2018 -0400
+++ b/do-partition.xml	Wed Dec 18 16:03:58 2019 -0500
@@ -1,5 +1,5 @@
-<tool id="khmer_partition" name="Sequence partition all-in-one" version="@WRAPPER_VERSION@.0">
-    <description>Load, partition, and annotate FAST[AQ] sequences</description>
+<tool id="khmer_partition" name="khmer: Sequence partition all-in-one" version="@WRAPPER_VERSION@@TOOL_VERSION@">
+    <description>Load, partition, and annotate sequences</description>
     <macros>
         <token name="@BINARY@">do-partition.py</token>
         <import>macros.xml</import>
@@ -8,16 +8,14 @@
     <expand macro="stdio" />
     <expand macro="version" />
     <command><![CDATA[
-set -xu &&
-#for $num, $input in enumerate($inputs)
-    ln -s ${input} sequence-${num} &&
-#end for
+set -u &&
+@LINK_SEQUENCES@
 mkdir -p output && cd output &&
 @BINARY@
 @TABLEPARAMS@
 @THREADS@
 output
-../sequence-*
+@USE_SEQUENCES@
 ]]>
     </command>
     <inputs>
@@ -25,21 +23,18 @@
         <expand macro="tableinputs" />
     </inputs>
     <outputs>
-        <data name="information" format="txt" from_work_dir="output.info" label="${tool.name} summary." />
-        <collection name="annotated_sequence_files" type="list">
-            <discover_datasets pattern="__name__" directory="output" />
-        </collection>
+        <data name="information" format="txt" from_work_dir="output.info" label="${tool.name} on ${on_string}: summary." />
+        <expand macro="output_sequences" extension="part"/>
     </outputs>
     <tests>
         <test>
             <param name="inputs" value="random-20-a.fa"/>
-            <output_collection name="annotated_sequence_files" type="list">
-                <element name="sequence-0.part" file="random-20-a.fa.part" />
+            <output_collection name="sequences" type="list">
+                <element name="random-20-a.fa" file="random-20-a.fa.part" />
             </output_collection>
         </test>
     </tests>
     <help><![CDATA[
-
 Load in a set of sequences, partition them, merge the partitions, and
 annotate the original sequences files with the partition information.