# HG changeset patch
# User Bjoern Gruening <bjoern.gruening@gmail.com>
# Date 1370032335 -7200
# Node ID 62897185a8038988afc465876fabd98510a362b6
# Parent  4fe6069549ef3fca10e5727bf539f67f3832941b
ChemicalToolBoX update.

diff -r 4fe6069549ef -r 62897185a803 align-it/align-it.xml
--- a/align-it/align-it.xml	Wed May 29 20:24:02 2013 +0200
+++ b/align-it/align-it.xml	Fri May 31 22:32:15 2013 +0200
@@ -1,4 +1,4 @@
-<tool id="ctb_alignit" name="Pharmacophore Alignment">
+<tool id="ctb_alignit" name="Pharmacophore Alignment" version="0.1">
     <description>and Optimization (Align-it)</description>
     <requirements>
         <requirement type="package" version="1.0.0">silicos_it</requirement>
diff -r 4fe6069549ef -r 62897185a803 align-it/align-it_create_db.xml
--- a/align-it/align-it_create_db.xml	Wed May 29 20:24:02 2013 +0200
+++ b/align-it/align-it_create_db.xml	Fri May 31 22:32:15 2013 +0200
@@ -1,4 +1,4 @@
-<tool id="ctb_alignit_create_db" name="Pharmacophore">
+<tool id="ctb_alignit_create_db" name="Pharmacophore" version="0.1">
     <description>generation (Align-it)</description>
     <requirements>
         <requirement type="package" version="1.0.0">silicos_it</requirement>
diff -r 4fe6069549ef -r 62897185a803 shape-it/shape-it.xml
--- a/shape-it/shape-it.xml	Wed May 29 20:24:02 2013 +0200
+++ b/shape-it/shape-it.xml	Fri May 31 22:32:15 2013 +0200
@@ -1,21 +1,45 @@
-<tool id="shapeit" name="Shape-it">
-    <description> alignment of a reference molecule against a database of molecules using the shape of the molecules</description>
+<tool id="shapeit" name="Shape alignment" version="0.1">
+    <description>against a database of molecules (Shape-it)</description>
     <requirements>
         <requirement type="package" version="1.0.0">silicos_it</requirement>
         <requirement type="package" version="2.3.2">openbabel</requirement>
     </requirements>
     <command >
-        shape-it --Format ${database.ext}  --dbase $database --reference $reference --addIterations $addIterations --best $best --out $output  2>&#38;1
+        shape-it 
+        --format ${database.ext}
+        --dbase $database
+        --reference $reference
+        --addIterations $addIterations
+        --best $best
+        --cutoff $cutoff
+        #if $scores == 'yes':
+            --scores $output_scores
+        #end if
+        --rankBy $rankBy
+        $noref
+        --out $output  2>&#38;1
     </command>
     <inputs>
-        <param name="database" type="data" format='sdf,mol,mol2,smi' label="database" />
-        <param name="reference" type="data" format='sdf,mol,mol2,smi' label="refrence" />
-        <param name="cutoff" type="float" value="0.0" />
+        <param name="reference" type="data" format='sdf,mol,mol2,smi' label="Refrence molecule" />
+        <param name="database" type="data" format='sdf,mol,mol2' label="Database of Molecules (needs 3D coordinates)" />
+        <param name="cutoff" type="float" value="0.0">
+            <validator type="in_range" min="0.0" />
+        </param>
         <param name='addIterations' type='integer' value='0' label='Perform N additional optimization steps with the simulated annealing procedure' />
-        <param name='best' type='integer' value='0' label='the N best scoring molecules are reported' />
+        <param name='best' type='integer' value='0' label='The N best scoring molecules are reported' />
+        <param name='scores' type='boolean' truevalue='yes' falsevalue='' label='Output a Tab-delimited text file with the scores of molecules' checked="false" />
+        <param name='noref' type='boolean' truevalue='--noRef' falsevalue='' label='The reference molecule is not written into the output files' checked="false" />
+        <param name='rankBy' type='select' format='text' label="This option defines the used scoring scheme">
+            <option value='TANIMOTO'>Tanimoto</option>
+            <option value='TVERSKY_REF'>TVERSKY_REF</option>
+            <option value='TVERSKY_DB'>TVERSKY_DB</option>
+        </param>
     </inputs>
     <outputs>
         <data name="output" format_source='database' />
+        <data name="output_scores" format="tabular">
+            <filter>scores == "yes"</filter>
+         </data>
     </outputs>
     <tests>
         <test>
diff -r 4fe6069549ef -r 62897185a803 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed May 29 20:24:02 2013 +0200
+++ b/tool_dependencies.xml	Fri May 31 22:32:15 2013 +0200
@@ -7,20 +7,23 @@
         <repository changeset_revision="3a993ff17df5" name="package_openbabel_2_3" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="rdkit" version="2012_12_1">
-        <repository changeset_revision="8df0530b1c1c" name="package_rdkit_2012_12" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+        <repository changeset_revision="5b30ea84ba25" name="package_rdkit_2012_12" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="silicos_it" version="1.0.0">
         <install version="1.0">
             <actions>
-                
                 <action type="download_by_url">http://www.silicos-it.com/_php/download.php?file=strip-it-1.0.1.tar.gz</action>
 
+                <!-- populate the environment variables from the dependend repos 
+                    $OPENBABEL_INCLUDE_DIR and $OPENBABEL_LIB_DIR
+                -->
                 <action type="set_environment_for_install">
                     <repository changeset_revision="3a993ff17df5" name="package_openbabel_2_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/">
                         <package name="openbabel" version="2.3.2" />
                     </repository>
                 </action>
 
+                <!--compiling strip-it -->
                 <action type="shell_command">
                     cd strip-it-1.0.1 &amp;&amp;
                     cmake . -DOPENBABEL2_INCLUDE_DIRS=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/strip-it/ -DOPENBABEL2_LIBRARIES=$OPENBABEL_LIB_DIR/libopenbabel.so &amp;&amp; 
@@ -30,6 +33,7 @@
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/strip-it/bin</environment_variable>
                 </action>
 
+                <!-- compiling align-it -->
                 <action type="shell_command">wget http://www.silicos-it.com/_php/download.php?file=align-it-1.0.3.tar.gz</action>
                 <action type="shell_command">tar xfvz download.php?file=align-it-1.0.3.tar.gz &amp;&amp; 
                     cd align-it-1.0.3 &amp;&amp; 
@@ -40,6 +44,7 @@
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/align-it/bin</environment_variable>
                 </action>
 
+                <!-- compiling shape-it -->
                 <action type="shell_command">wget http://www.silicos-it.com/_php/download.php?file=shape-it-1.0.1.tar.gz</action>
                 <action type="shell_command">tar xfvz download.php?file=shape-it-1.0.1.tar.gz &amp;&amp; 
                     cd shape-it-1.0.1 &amp;&amp;