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

Uploaded

<?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>