diff CADDSuite-1.0.1/galaxyconfigs/tools/MolFilter.xml @ 5:e30a41af9d2b

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/galaxyconfigs/tools/MolFilter.xml	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,64 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="molfilter" name="MolFilter" version="0.9">
+    <description>filter molecule files</description>
+    <command interpreter="bash"><![CDATA[../../MolFilter 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $min_logP ) != ''  and str( $min_logP ) != 'None' :
+   -min_logP "$min_logP"
+#end if
+#if str( $max_logP ) != ''  and str( $max_logP ) != 'None' :
+   -max_logP "$max_logP"
+#end if
+#if str( $min_MW ) != ''  and str( $min_MW ) != 'None' :
+   -min_MW "$min_MW"
+#end if
+#if str( $max_MW ) != ''  and str( $max_MW ) != 'None' :
+   -max_MW "$max_MW"
+#end if
+#if str( $q ) != ''  and str( $q ) != 'None' :
+   -q "$q"
+#end if
+#if str( $min_sim ) != ''  and str( $min_sim ) != 'None' :
+   -min_sim "$min_sim"
+#end if
+#if str( $max_sim ) != ''  and str( $max_sim ) != 'None' :
+   -max_sim "$max_sim"
+#end if
+#if str( $smarts ) != ''  and str( $smarts ) != 'None' :
+   -smarts "$smarts"
+#end if
+#if str( $smarts_file ) != ''  and str( $smarts_file ) != 'None' :
+   -smarts_file "$smarts_file"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+-quiet 
+#if str( $rm ) != ''  and str( $rm ) != 'None' :
+   -rm
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" optional="false" label="input molecule-file" type="data" format="mol2/sdf/drf"/>
+        <param name="q" optional="true" label="query molecules for similarity searching" type="data" format="txt"/>
+        <param name="smarts_file" optional="true" label="SMARTS pattern" type="data" format="txt"/>
+        <param name="min_logP" optional="true" label="Optional: minimal logP value" type="text" area="true" size="1x5" value=""/>
+        <param name="max_logP" optional="true" label="Optional: maximal logP value" type="text" area="true" size="1x5" value=""/>
+        <param name="min_MW" optional="true" label="Optional: minimal molecular weight" type="text" area="true" size="1x5" value=""/>
+        <param name="max_MW" optional="true" label="Optional: maximal molecular weight" type="text" area="true" size="1x5" value=""/>
+        <param name="min_sim" optional="true" label="Optional: minimal average similarity" type="text" area="true" size="1x5" value=""/>
+        <param name="max_sim" optional="true" label="Optional: maximal similarity" type="text" area="true" size="1x5" value=""/>
+        <param name="smarts" optional="true" label="Optional: SMARTS pattern" area="true" type="text" size="1x15"/>
+        <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>MolFilter can filter molecules from a molecule input file according to SMARTS expressions, logP, molecular weight, or similarity to query molecule(s).
+
+Output of this tool is a molecule file that contains all compounds that fulfilled the specified search criteria.</help>
+</tool>
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