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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Preparation]-->
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4 <tool id="LigandFileSplitter" name="LigandFileSplitter" version="1.1.0">
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5 <description>split molecule files</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">LigandFileSplitter</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="stdio"/>
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11 <expand macro="requirements"/>
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12 <command>LigandFileSplitter
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13
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14 #if $param_i:
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15 -i $param_i
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16 #end if
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17 #if $param_no:
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18 -no $param_no
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19 #end if
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20 #if $param_mpf:
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21 -mpf $param_mpf
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22 #end if
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23 #if $param_outname_pattern:
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24 -outname_pattern "$param_outname_pattern"
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25 #end if
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26
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27 #if $rep_param_o:
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28 -o
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29 #for token in $rep_param_o:
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30 #if " " in str(token):
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31 "$token.param_o"
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32 #else
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33 $token.param_o
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34 #end if
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35 #end for
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36 #end if
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37 </command>
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38 <inputs>
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39 <param name="param_i" type="data" format="mol2,sdf,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input molecule file" help="(-i) "/>
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40 <param name="param_no" type="integer" value="0" label="Number of output files to be created" help="(-no) "/>
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41 <param name="param_mpf" type="integer" value="0" label="Number of molecules per output file" help="(-mpf) "/>
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42 <param name="param_outname_pattern" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="Pattern that will be used to generate the names of the output files, see notes and examples below" help="(-outname_pattern) ">
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43 <sanitizer>
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44 <valid initial="string.printable">
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45 <remove value="'"/>
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46 <remove value="""/>
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47 </valid>
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48 </sanitizer>
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49 </param>
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50 </inputs>
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51 <expand macro="advanced_options"/>
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52 <outputs>
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53 <data name="param_o" metadata_source="param_i" format="input"/>
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54 </outputs>
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55 <help>LigandFileSplitter splits a molecule file into a given number of subsets.
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56
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57 Examples:
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58
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59 $ LigandFileSplitter -i Trypsin_actives.sdf -o batch_1 batch_2
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60 will split the input file Trypsin_actives.sdf in the two output files batch_1.sdf and batch_2.sdf.
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61
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62 $ LigandFileSplitter -i Trypsin_actives.sdf -no 3
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63 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
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64
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65 $ LigandFileSplitter -i ligands.sdf -ligands_per_file 4
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66 will split the input file ligands.sdf in as many files needed to fit at most 4 ligands per file.
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67 The files will be named ligands_0.sdf, ligands_1.sdf ... ligands_N.sdf
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68
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69 $ LigandFileSplitter -i ligands.sdf -ligands_per_file 5 -outname_pattern split_ligands-%d.sdf
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70 will split the input file ligands.sdf in as many files needed to fit at most 5 ligands per file.
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71 The files will be named split_ligands-0.sdf, split_ligands-1.sdf, ... , split_ligands-N.sdf.
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72
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73 $ LigandFileSplitter -i ligands.sdf -outname_pattern split_ligands_%d.sdf -no 100
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74 will split the input file ligands.sdf in 100 files using the following names:
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75 split_ligands_0.sdf, split_ligands_1.sdf, ... , split_ligands_99.sdf.
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76
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77 NOTES:
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78 - Molecules are not sorted in any way.
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79 - The tool is no format converter and the format of the output files will be the same as of the input file.
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80 - Output_name_pattern accepts a printf-like pattern, expecting exactly one decimal integer placeholder, %d.
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81 - The following are valid patterns: output_ligand.sdf_%d, split_%d.mol, %d_lig.drf
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82 - The following are invalid patterns: output_%f.sdf, ligands.drf_%u, %d_lig_%d.mol, molecules.sdf
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83
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84 WARNING:
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85 - If the parameter outname_pattern is specified, the user is responsible for the occurrence of a valid file extension
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86 in the outname_pattern, which has to be of the same file format as the input file.
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87
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88
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89
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90 </help>
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91 </tool>
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