Mercurial > repos > iuc > crossmap_bam

diff macros.xml @ 1:8e5feca6a518 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
author iuc
date Fri, 20 Oct 2017 02:48:57 -0400
parents d04d5afec2e0
children 083774cc8472
line wrap: on
line diff
--- a/macros.xml	Tue Sep 26 05:44:53 2017 -0400
+++ b/macros.xml	Fri Oct 20 02:48:57 2017 -0400
@@ -2,12 +2,11 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="324">ucsc-wigtobigwig</requirement>
-            <requirement type="package" version="0.2.2">crossmap</requirement>
+            <requirement type="package" version="0.2.5">crossmap</requirement>
             <yield/>
         </requirements>
     </xml>
-    <token name="@WRAPPER_VERSION@">0.2.2</token>
+    <token name="@WRAPPER_VERSION@">0.2.5</token>
     <xml name="stdio">
         <stdio>
             <regex match="Aborted (core dumped)" source="stdout" level="fatal"/>
@@ -16,7 +15,9 @@
         </stdio>
     </xml>
     <xml name="version_command">
-        <version_command>CrossMap.py 2&gt;&amp;1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command>
+        <version_command><![CDATA[
+CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*'
+        ]]></version_command>
     </xml>
     <xml name="chain">
         <conditional name="chain_source">
@@ -26,25 +27,18 @@
             </param>
             <when value="cached">
                 <param name="input_chain" type="select" label="Lift Over To">
-                    <options from_file="liftOver.loc">
-                        <column name="dbkey" index="0"/><!-- species/build 'from' -->
-                        <column name="name" index="1"/><!-- species/build 'to' -->
-                        <column name="value" index="2"/><!-- path of chain file -->
+                    <options from_data_table="liftOver">
+                        <!--
                         <filter type="data_meta" ref="input" key="dbkey" column="0"/>
+                        -->
                     </options>
                 </param>
             </when>
             <when value="history">
-                <param type="data" format="csv" name="input_chain" label="LiftOver chain file"/>
+                <param name="input_chain" type="data" format="csv" label="LiftOver chain file"/>
             </when>
         </conditional>
     </xml>
-    <xml name="source">
-        <param name="index_source" type="select" label="Source for Input Data">
-            <option value="cached">Local data (in galaxy)</option>
-            <option value="history">From History</option>
-        </param>
-    </xml>
     <token name="@HELP_GENERAL@">
 CrossMap
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