diff CADDSuite-1.6/galaxyconfigs/tools/PDBCutter.xml @ 8:dbb480e39d95 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.6/galaxyconfigs/tools/PDBCutter.xml	Sat Dec 15 13:15:46 2012 -0500
@@ -0,0 +1,59 @@
+
+<!--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="pdbcutter" name="PDBCutter" version="1.6">
+    <description>separate ligand and receptor</description>
+    <command interpreter="bash"><![CDATA[../../PDBCutter 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $rec ) != ''  and str( $rec ) != 'None' :
+   -rec "$rec"
+#end if
+#if str( $lig ) != ''  and str( $lig ) != 'None' :
+   -lig "$lig"
+#end if
+#if str( $lig_chain ) != ''  and str( $lig_chain ) != 'None' :
+   -lig_chain "$lig_chain"
+#end if
+#if str( $lig_name ) != ''  and str( $lig_name ) != 'None' :
+   -lig_name "$lig_name"
+#end if
+#if str( $rm_ch ) != ''  and str( $rm_ch ) != 'None' :
+   -rm_ch "$rm_ch"
+#end if
+#if str( $id ) != ''  and str( $id ) != 'None' :
+   -id "$id"
+#end if
+#if str( $p ) != ''  and str( $p ) != 'None' :
+   -p "$p"
+#end if
+#if str( $rm_res ) != ''  and str( $rm_res ) != 'None' :
+   -rm_res "$rm_res"
+#end if
+#if str( $auto ) != ''  and str( $auto ) != 'None' :
+   -auto
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" optional="false" label="input pdb-file" type="data" format="pdb"/>
+        <param name="lig_chain" optional="false" label="chain-name of ligand" area="true" type="text" size="1x15"/>
+        <param name="lig_name" optional="false" label="ligand name" area="true" type="text" size="1x15"/>
+        <param name="rm_ch" optional="true" label="Optional: protein chains that are to be deleted" area="true" type="text" size="1x15"/>
+        <param name="id" optional="true" label="Optional: PDB ID for download of ligand as sdf from PDB server, if desired" area="true" type="text" size="1x15"/>
+        <param name="p" optional="true" label="Optional: proxy for ligand download, if required" area="true" type="text" size="1x15"/>
+        <param name="rm_res" optional="true" label="Optional: pdb-residues that are to be deleted (e.g. water or ions)" area="true" type="text" size="1x15"/>
+        <param name="auto" optional="true" label="extract largest heterosystem as ligand (ignore specified lig. def.)" type="boolean" truevalue="true" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="rec" format="pdb"/>
+        <data name="lig" format="pdb"/>
+    </outputs>
+    <help>This tool splits a given pdb-file into two files containing receptor and reference ligand, respectively.
+
+The name of the reference ligand (exactly as it appears in the pdb-file) and the name of its chain need to be specified by '-lig_name' and '-lig_chain'.
+If desired, the correct topology of the reference ligand can be downloaded by this tool from the Protein Data Bank as an sd-file and stored in the specified ligand output file.
+Optionally, chains (e.g. in case of multimers) or pdb-residues (e.g. water or ions) that you don't need can be deleted from the receptor. In this case, specify their names with '-rm_ch' or '-rm_res'.
+
+Output of this tool is one pdb-file containing the receptor-structure, i.e. the protein w/o reference ligand and w/o undesired chains/residues (if any were specified), and one file containing the reference ligand.</help>
+</tool>
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