diff confab.xml @ 24:e8462e1fb27e draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit 573c8fb0102ba3ab52fd998494a1b4be3e440620

--- a/confab.xml	Sun Nov 01 10:33:40 2015 -0500
+++ b/confab.xml	Sun May 22 18:43:28 2016 -0400
@@ -1,20 +1,23 @@
-<tool id="ctb_confab" name="Conformer calculation" version="0.1">
+<tool id="ctb_confab" name="Conformer calculation" version="0.3">
     <description>for molecules (confab)</description>
-    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile"></parallelism>
+    <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <requirements>
-        <requirement type="package" version="1.0.1">confab</requirement>
+         <requirement type="package" version="2.3.90dev7d621d9">openbabel</requirement>
     </requirements>
-    <command>
+    <command detect_errors="aggressive">
 <![CDATA[
-    confab
+
+    obabel
+        "${infile}"
+        -O "${outfile}"
         -i ${infile.ext}
         -o sdf
-        -r $RMSD
-        -e $energy
-        -c $conformers
+        --confab
+        --rcutoff $RMSD
+        --ecutoff $energy
+        --conf $conformers
         $first_conformer
-        $infile
-        $outfile 2>&1
+
 ]]>
     </command>
     <inputs>
@@ -22,7 +25,8 @@
         <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (in Angstrom)' />
         <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' />
         <param name='conformers' type='integer' value='100' label='Max number of conformers to test' />
-        <param name='first_conformer' type='boolean' truevalue='-a' falsevalue='' label='Include the input conformation as the first conformer' />
+        <param name='first_conformer' type='boolean' truevalue='--original' falsevalue=''
+            label='Include the input conformation as the first conformer' />
     </inputs>
     <outputs>
         <data format="sdf" name="outfile" label="${tool.name} on ${on_string}"/>
@@ -33,8 +37,8 @@
             <param name='RMSD'  value='0.5' />
             <param name='energy' value='50.0' />
             <param name='conformers' value='100000' />
-            <param name='first_conformer' value='-a' />
-            <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' />
+            <param name='first_conformer' value="True" />
+            <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' lines_diff="4"/>
         </test>
     </tests>
 <help>
@@ -126,17 +130,12 @@
   9  8  1  6  0  0  0
  10  9  1  1  0  0  0
 
------
-
-.. class:: infomark
-
-**Cite**
-
-Confab_
-
-.. _Confab: https://code.google.com/p/confab/
 
 
 ]]>
     </help>
+    <citations>
+        <citation type="doi">10.1186/1758-2946-3-33</citation>
+        <citation type="doi">10.1186/1758-2946-3-8</citation>
+    </citations>
 </tool>