changeset 1:731ad135ddb4 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty

Binary file confab.tar.bz2 has changed

--- a/confab.xml	Thu Aug 15 03:31:39 2013 -0400
+++ b/confab.xml	Sun Nov 01 10:28:54 2015 -0500
@@ -4,15 +4,18 @@
     <requirements>
         <requirement type="package" version="1.0.1">confab</requirement>
     </requirements>
-    <command> confab 
+    <command>
+<![CDATA[
+    confab
         -i ${infile.ext}
         -o sdf
-        -r $RMSD 
-        -e $energy 
-        -c $conformers 
-        $first_conformer 
+        -r $RMSD
+        -e $energy
+        -c $conformers
+        $first_conformer
         $infile
-        $outfile 2>&#38;1
+        $outfile 2>&1
+]]>
     </command>
     <inputs>
         <param name="infile" type="data" format="sdf,mol2" label="Input molecule with 3D coordinates" help="Dataset missing? See TIP below"/>
@@ -32,9 +35,10 @@
             <param name='conformers' value='100000' />
             <param name='first_conformer' value='-a' />
             <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' />
-        </test>	
+        </test>
     </tests>
 <help>
+<![CDATA[
 
 .. class:: infomark
 
@@ -51,7 +55,7 @@
 **Input**
 
 * Example::
-	
+
 	21.2060    9.9350   63.0810 C   0  0  0  0  0  0  0  0  0  0  0  0
 	21.2410    9.4460   64.5510 C   0  0  0  0  0  0  0  0  0  0  0  0
 	22.0000    8.1250   64.6300 C   0  0  0  0  0  0  0  0  0  0  0  0
@@ -133,6 +137,6 @@
 .. _Confab: https://code.google.com/p/confab/
 
 
- </help>
-
+]]>
+    </help>
 </tool>

--- a/repository_dependencies.xml	Thu Aug 15 03:31:39 2013 -0400
+++ b/repository_dependencies.xml	Sun Nov 01 10:28:54 2015 -0500
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format).">
-    <repository changeset_revision="85eca06eefc6" name="molecule_datatypes" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="85eca06eefc6" name="molecule_datatypes" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
 </repositories>

--- a/tool_dependencies.xml	Thu Aug 15 03:31:39 2013 -0400
+++ b/tool_dependencies.xml	Sun Nov 01 10:28:54 2015 -0500
@@ -1,16 +1,16 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="eigen2" version="2.0.17">
-        <repository changeset_revision="a66c1f4d3c68" name="package_eigen_2_0" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="a270fba04f3a" name="package_eigen_2_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="confab" version="1.0.1">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">http://confab.googlecode.com/files/Confab-1.0.1.tar.gz</action>
+                <action type="download_by_url">https://github.com/bgruening/confab/archive/1.0.1.tar.gz</action>
 
                 <!-- populate the environment variables from the dependend repos -->
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="a66c1f4d3c68" name="package_eigen_2_0" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="a270fba04f3a" name="package_eigen_2_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                         <package name="eigen2" version="2.0.17" />
                     </repository>
                 </action>