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changeset 8:1624dcf79877

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test update
author Bjoern Gruening <bjoern.gruening@gmail.com>
date Mon, 27 May 2013 01:38:34 +0200
parents 63f3b73bf005
children fbcbcd9b5de0
files osra.xml tool_dependencies.xml
diffstat 2 files changed, 14 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- a/osra.xml	Mon May 27 01:38:19 2013 +0200
+++ b/osra.xml	Mon May 27 01:38:34 2013 +0200
@@ -3,7 +3,7 @@
     <requirements>
         <requirement type="package" version="2.0.0">osra</requirement>
     </requirements>
-    <command interpreter='python'>
+    <command interpreter="python">
         ## OSRA_DATA_FILES is set during the toolshed Installation
         ## if it is not set, use the standard configuration and hope the best
         osra.py -f $oformat $infile 
@@ -12,27 +12,27 @@
         ## further additions of OSRA parameter should go after -l and -a
         ## because -l and -a can be removed by the python wrapper
         
-        > $outfile
+        &gt; $outfile
     </command>
     <inputs>
-        <param name="infile" type="data" format="png,pdf" label="Image or PDF with molecules"/>
-        <param name="oformat" type="select" label="Output molecule format">
+        <param format="png,pdf" label="Image or PDF with molecules" name="infile" type="data" />
+        <param label="Output molecule format" name="oformat" type="select">
             <option value="can">SMILES</option>
             <option value="sdf">SDF</option>
         </param>
     </inputs>
     <outputs>
-        <data name="outfile" type="data" format="sdf">
+        <data format="sdf" name="outfile" type="data">
             <change_format>
-                <when input="oformat" value="can" format="smi"/>
+                <when format="smi" input="oformat" value="can" />
             </change_format>
         </data>
     </outputs>
     <tests>
         <test>
-            <param name="infile" ftype="png" value="CID_2244.png"/>
-            <param name="oformat" value="sdf"/>
-            <output name="outfile" ftype="sdf" file="osra_on_CID2244.sdf"/>
+            <param ftype="png" name="infile" value="CID_2244.png" />
+            <param name="oformat" value="sdf" />
+            <output file="osra_on_CID2244.sdf" ftype="sdf" name="outfile" />
         </test>
     </tests>
     <help>
--- a/tool_dependencies.xml	Mon May 27 01:38:19 2013 +0200
+++ b/tool_dependencies.xml	Mon May 27 01:38:34 2013 +0200
@@ -1,10 +1,9 @@
-<?xml version="1.0"?>
 <tool_dependency>
     <package name="openbabel" version="2.3.2">
-        <repository changeset_revision="efffcee80e03" name="package_openbabel_2_3" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="ccda1b8ebc72" name="package_openbabel_2_3" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="graphicsmagick" version="1.3.18">
-        <repository changeset_revision="34f511310435" name="package_graphicsmagick_1_3" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="34f511310435" name="package_graphicsmagick_1_3" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="osra" version="2.0.0">
         <install version="1.0">
@@ -14,10 +13,10 @@
 
                 
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="efffcee80e03" name="package_openbabel_2_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="ccda1b8ebc72" name="package_openbabel_2_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/">
                         <package name="openbabel" version="2.3.2" />
                     </repository>
-                    <repository changeset_revision="34f511310435" name="package_graphicsmagick_1_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="34f511310435" name="package_graphicsmagick_1_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/">
                         <package name="graphicsmagick" version="1.3.18" />
                     </repository>
                 </action>
@@ -68,4 +67,4 @@
         </install>
         <readme>We still have a handfull of requirements</readme>
     </package>
-</tool_dependency>
\ No newline at end of file
+</tool_dependency>