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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_stubs/LigandFileSplitter.xml	Tue Jul 12 12:33:33 2016 -0400
@@ -0,0 +1,91 @@
+<?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="LigandFileSplitter" name="LigandFileSplitter" version="1.1.0">
+  <description>split molecule files</description>
+  <macros>
+    <token name="@EXECUTABLE@">LigandFileSplitter</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>LigandFileSplitter
+
+#if $param_i:
+  -i $param_i
+#end if
+#if $param_no:
+  -no $param_no
+#end if
+#if $param_mpf:
+  -mpf $param_mpf
+#end if
+#if $param_outname_pattern:
+  -outname_pattern     "$param_outname_pattern"
+#end if
+
+#if $rep_param_o:
+-o
+  #for token in $rep_param_o:
+    #if " " in str(token):
+      "$token.param_o"
+    #else
+      $token.param_o
+    #end if
+  #end for
+#end if
+</command>
+  <inputs>
+    <param name="param_i" type="data" format="mol2,sdf,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input molecule file" help="(-i) "/>
+    <param name="param_no" type="integer" value="0" label="Number of output files to be created" help="(-no) "/>
+    <param name="param_mpf" type="integer" value="0" label="Number of molecules per output file" help="(-mpf) "/>
+    <param name="param_outname_pattern" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="Pattern that will be used to generate the names of the output files, see notes and examples below" help="(-outname_pattern) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+  </inputs>
+  <expand macro="advanced_options"/>
+  <outputs>
+    <data name="param_o" metadata_source="param_i" format="input"/>
+  </outputs>
+  <help>LigandFileSplitter splits a molecule file into a given number of subsets.
+
+Examples:
+
+$ LigandFileSplitter -i Trypsin_actives.sdf -o batch_1 batch_2
+  will split the input file Trypsin_actives.sdf in the two output files batch_1.sdf and batch_2.sdf.
+
+$ LigandFileSplitter -i Trypsin_actives.sdf -no 3
+  will split the input file Trypsin_actives.sdf in three files named Trypsin_actives_0.sdf, Trypsin_actives_1.sdf and Trypsin_actives_2.sdf
+
+$ LigandFileSplitter -i ligands.sdf -ligands_per_file 4
+  will split the input file ligands.sdf in as many files needed to fit at most 4 ligands per file.
+  The files will be named ligands_0.sdf, ligands_1.sdf ... ligands_N.sdf
+
+$ LigandFileSplitter -i ligands.sdf -ligands_per_file 5 -outname_pattern split_ligands-%d.sdf
+  will split the input file ligands.sdf in as many files needed to fit at most 5 ligands per file.
+  The files will be named split_ligands-0.sdf, split_ligands-1.sdf, ... , split_ligands-N.sdf.
+
+$ LigandFileSplitter -i ligands.sdf -outname_pattern split_ligands_%d.sdf -no 100
+  will split the input file ligands.sdf in 100 files using the following names:
+  split_ligands_0.sdf, split_ligands_1.sdf, ... , split_ligands_99.sdf.
+
+NOTES:
+- Molecules are not sorted in any way.
+- The tool is no format converter and the format of the output files will be the same as of the input file.
+- Output_name_pattern accepts a printf-like pattern, expecting exactly one decimal integer placeholder, %d.
+- The following are valid patterns: output_ligand.sdf_%d, split_%d.mol, %d_lig.drf
+- The following are invalid patterns: output_%f.sdf, ligands.drf_%u, %d_lig_%d.mol, molecules.sdf
+
+WARNING:
+- If the parameter outname_pattern is specified, the user is responsible for the occurrence of a valid file extension
+  in the outname_pattern, which has to be of the same file format as the input file.
+
+
+
+</help>
+</tool>