Mercurial > repos > iuc > mageck_gsea

diff mageck_macros.xml @ 2:82a180e6b582 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
author iuc
date Wed, 04 Apr 2018 11:03:05 -0400
parents d95eae71878e
children 3b22ff50a362
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--- a/mageck_macros.xml	Sat Feb 17 10:41:13 2018 -0500
+++ b/mageck_macros.xml	Wed Apr 04 11:03:05 2018 -0400
@@ -1,27 +1,34 @@
 <?xml version="1.0"?>
 <macros>
+
     <token name="@VERSION@">0.5.7</token>
+
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">mageck</requirement>
-            <!-- needed for pdf report outputs -->
+            <requirement type="package" version="1.14.2">numpy</requirement>
             <requirement type="package" version="3.0.1">r-gplots</requirement>
             <requirement type="package" version="1.8_2">r-xtable</requirement>
             <yield/>
         </requirements>
     </xml>
+
     <xml name="version">
-        <version_command>mageck -v </version_command>
+        <version_command><![CDATA[
+            echo $(mageck -v )", numpy version" $([python -c "import numpy; numpy.version.version"])", gplots version" $(R --vanilla --slave -e "library(gplots); cat(sessionInfo()\$otherPkgs\$gplots\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", xtable version" $(R --vanilla --slave -e "library(xtable); cat(sessionInfo()\$otherPkgs\$xtable\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+        ]]></version_command>
     </xml>
+
+    <xml name="sort_criteria">
+        <param name="sort_criteria" argument="--sort-criteria" type="select" optional="true" label="Sorting criteria">
+            <option value="neg" selected="True">Negative selection</option>
+            <option value="pos">positive selection</option>
+        </param>
+      </xml>
+
     <xml name="citations">
         <citations>
             <citation type="doi">10.1186/s13059-014-0554-4</citation>
         </citations>
     </xml>
-    <xml name="sort_criteria">
-        <param name="sort_criteria" argument="--sort-criteria" type="select" label="Sorting criteria">
-            <option value="neg" selected="True">Negative selection</option>
-            <option value="pos">positive selection</option>
-        </param>
-      </xml>
 </macros>