Mercurial > repos > iuc > hmmer_alimask

diff alimask.xml @ 3:819d044451ed draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
author iuc
date Sat, 07 Apr 2018 03:48:26 -0400
parents a20b2c7c5eee
children b4dc65565864
line wrap: on
line diff
--- a/alimask.xml	Wed Apr 04 13:59:34 2018 -0400
+++ b/alimask.xml	Sat Apr 07 03:48:26 2018 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hmmer_alimask" name="alimask" version="@WRAPPER_VERSION@.0">
+<tool id="hmmer_alimask" name="alimask" version="@TOOL_VERSION@">
   <description>append modelmask line to a multiple sequence alignments</description>
   <macros>
     <import>macros.xml</import>
@@ -7,7 +7,6 @@
   <expand macro="requirements"/>
   <expand macro="stdio"/>
   <command><![CDATA[
-
 alimask
 
 #if $range_type.range_type_select == "model":
@@ -23,9 +22,9 @@
 @ARSWS@
 @SEED@
 
-$msafile
-$output
-      ]]></command>
+'$msafile'
+'$output'
+  ]]></command>
   <inputs>
     <expand macro="input_msa" />
     <conditional name="range_type">
@@ -35,15 +34,15 @@
             <option value="ali">Range in alignment coordinates</option>
         </param>
         <when value="model">
-            <repeat min="1" name="modelranges" title="Model Ranges">
-                <param label="Model Range Start" name="modelrangestart" type="integer" value="10" />
-                <param label="Model Range End" name="modelrangeend" type="integer" value="20" />
+            <repeat name="modelranges" min="1" title="Model Ranges">
+                <param name="modelrangestart" type="integer" value="10" label="Model Range Start" />
+                <param name="modelrangeend" type="integer" value="20" label="Model Range End" />
             </repeat>
         </when>
         <when value="ali">
-            <repeat min="1" name="aliranges" title="Alignment Ranges">
-                <param label="Alignment Range Start" name="alirangestart" type="integer" value="10" />
-                <param label="Alignment Range End" name="alirangeend" type="integer" value="20" />
+            <repeat name="aliranges" min="1" title="Alignment Ranges">
+                <param name="alirangestart" type="integer" value="10" label="Alignment Range Start" />
+                <param name="alirangeend" type="integer" value="20" label="Alignment Range End" />
             </repeat>
         </when>
     </conditional>
@@ -55,7 +54,7 @@
     <expand macro="seed"/>
   </inputs>
   <outputs>
-    <data format="stockholm" name="output" label="Output MSA"/>
+    <data name="output" format="stockholm" label="Output MSA"/>
   </outputs>
   <tests>
     <test>
@@ -110,6 +109,6 @@
 @SEED_HELP@
 
 @ATTRIBUTION@
-]]></help>
+  ]]></help>
   <expand macro="citation"/>
 </tool>