diff eventaligncollapse.xml @ 1:ad011fc670d6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"

--- a/eventaligncollapse.xml	Thu Apr 30 05:56:29 2020 -0400
+++ b/eventaligncollapse.xml	Tue May 12 17:08:45 2020 -0400
@@ -1,12 +1,11 @@
 <?xml version="1.0"?>
-<tool id="nanopolishcomp_eventaligncollapse" name="Eventalign Collapse" version="@TOOL_VERSION@+@WRAPPER_VERSION@">
+<tool id="nanopolishcomp_eventaligncollapse" name="NanopolishComp: EventalignCollapse" version="@TOOL_VERSION@+@WRAPPER_VERSION@">
     <description>by kmers rather than by event</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
-    <stdio></stdio>
-    <version_command>NanopolishComp --version</version_command>
+    <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
         ## initialize
         ## requires a minimum of 3 threads
@@ -18,9 +17,9 @@
             -i '$i'
             -s
             -r $r
-            -f 
+            -f
             #for $current in $f
-                $current 
+                $current
             #end for
             -o 'results'
             -p 'out'
@@ -38,7 +37,7 @@
             <option value="mad">Mad</option>
             <option value="num_signals" selected="true">Number of signals</option>
         </param>
-        <param name="out" type="select" multiple="true" label="Select output file(s)" help="">
+        <param name="out" type="select" multiple="true" label="Select output file(s)">
             <option value="eventalign_collapse" selected="true">Eventalign Collapse</option>
             <option value="index" selected="true">Index</option>
             <option value="log">Log</option>
@@ -51,14 +50,14 @@
         <data name="out_index" format="tabular" from_work_dir="results/out_eventalign_collapse.tsv.idx" label="${tool.name} on ${on_string}: Index">
             <filter>'index' in out</filter>
         </data>
-        <data name="out_log" format="txt" from_work_dir="results/out_eventalign_collapse.log" label="${tool.name} on ${on_string}: log">
+        <data name="out_log" format="txt" from_work_dir="results/out_eventalign_collapse.log" label="${tool.name} on ${on_string}: Log">
             <filter>'log' in out</filter>
         </data>
     </outputs>
     <tests>
         <!-- #1 default -->
         <test expect_num_outputs="3">
-            <param name="i" value="sample.tsv"/>
+            <param name="i" value="sample_event.tsv"/>
             <param name="out" value="eventalign_collapse,index,log"/>
             <output name="out_eventalign_collapse">
                 <assert_contents>
@@ -83,7 +82,7 @@
         </test>
         <!-- #2 -->
         <test expect_num_outputs="2">
-            <param name="i" value="sample.tsv"/>
+            <param name="i" value="sample_event.tsv"/>
             <param name="s" value="true"/>
             <param name="r" value="10"/>
             <param name="f" value="mean,std,median,mad,num_signals"/>
@@ -115,7 +114,7 @@
 
 **Input**
 
-A nanopolish eventalign tabular output file. 
+A nanopolish eventalign tabular output file.
 
 **Output**