diff galaxy_stubs/PDBCutter.xml @ 2:605370bc1def draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_stubs/PDBCutter.xml	Tue Jul 12 12:33:33 2016 -0400
@@ -0,0 +1,104 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
+<!--Proposed Tool Section: [Preparation]-->
+<tool id="PDBCutter" name="PDBCutter" version="1.1.0">
+  <description>separate ligand and receptor  </description>
+  <macros>
+    <token name="@EXECUTABLE@">PDBCutter</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>PDBCutter
+
+#if $param_i:
+  -i $param_i
+#end if
+#if $param_rec:
+  -rec $param_rec
+#end if
+#if $param_lig:
+  -lig $param_lig
+#end if
+#if $param_lig_chain:
+  -lig_chain     "$param_lig_chain"
+#end if
+#if $param_lig_name:
+  -lig_name     "$param_lig_name"
+#end if
+
+#if $rep_param_rm_ch:
+-rm_ch
+  #for token in $rep_param_rm_ch:
+    #if " " in str(token):
+      "$token.param_rm_ch"
+    #else
+      $token.param_rm_ch
+    #end if
+  #end for
+#end if
+
+#if $rep_param_rm_res:
+-rm_res
+  #for token in $rep_param_rm_res:
+    #if " " in str(token):
+      "$token.param_rm_res"
+    #else
+      $token.param_rm_res
+    #end if
+  #end for
+#end if
+</command>
+  <inputs>
+    <param name="param_i" type="data" format="pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input pdb-file" help="(-i) "/>
+    <param name="param_lig_chain" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="chain-name of ligand" help="(-lig_chain) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_lig_name" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="ligand name" help="(-lig_name) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <repeat name="rep_param_rm_ch" min="0" max="1" title="param_rm_ch">
+      <param name="param_rm_ch" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="protein chains that are to be deleted" help="(-rm_ch) ">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
+    <repeat name="rep_param_rm_res" min="0" max="1" title="param_rm_res">
+      <param name="param_rm_res" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="pdb-residues that are to be deleted (" help="(-rm_res) e.g. water or ions)">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
+  </inputs>
+  <expand macro="advanced_options"/>
+  <outputs>
+    <data name="param_rec" format="pdb"/>
+    <data name="param_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'.
+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 pdb-file containing the reference ligand.
+
+</help>
+</tool>