diff tn93_cluster.xml @ 1:112d80c9ccca draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"

--- a/tn93_cluster.xml	Fri Apr 23 03:04:15 2021 +0000
+++ b/tn93_cluster.xml	Wed Apr 20 17:00:11 2022 +0000
@@ -1,12 +1,11 @@
-<tool id="tn93_cluster" name="TN93 Cluster" version="@VERSION@">
+<tool id="tn93_cluster" name="TN93 Cluster" version="@TOOL_VERSION@+galaxy1">
     <description>sequences that lie within a specific distance of each other</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <requirements>
-        <requirement type="package" version="@VERSION@">tn93</requirement>
+    <expand macro="requirements">
         <requirement type="package" version="3.9">python</requirement>
-    </requirements>
+    </expand>
     <version_command><![CDATA[tn93 --version]]></version_command>
     <command detect_errors="exit_code"><![CDATA[
     python '$__tool_directory__/tn93_cluster.py' --input '$input_fasta' --reference '$reference' --output '$tn93_clusters'
@@ -25,7 +24,7 @@
         <param name="reference" type="data" format="fasta" label="Reference in FASTA format" />
         <param argument="--compress" type="boolean" truevalue="--compress" falsevalue="" label="Output additional fasta dataset with compressed clusters" />
         <param argument="--cluster-count" type="integer" value="200" label="Only retain this many clusters" />
-        <param argument="--threshold" type="float" min="0" value="0.0005" label="Distance threshold" help="Sequences which lie within this distance will be clustered" />
+        <param argument="--threshold" type="float" value="0.0005" min="0" max="1" label="Distance threshold" help="Sequences which lie within this distance will be clustered" />
         <param argument="--ambigs" type="select" label="Strategy for ambiguous nucleotides">
             <option value="resolve" selected="true">resolve</option>
             <option value="average">average</option>
@@ -42,8 +41,8 @@
             label="Maximum tolerated fraction of ambiguous characters" />
     </inputs>
     <outputs>
-        <data format="json" name="tn93_clusters" />
-        <data format="fasta" name="tn93_compressed_clusters">
+        <data format="json" name="tn93_clusters" from_work_dir="clusters.json" />
+        <data format="fasta" name="tn93_compressed_clusters" from_work_dir="clusters.fa">
             <filter>compress</filter>
         </data>
     </outputs>