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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: [Convert, combine and store]-->
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4 <tool id="Converter" name="Converter" version="1.1.0">
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5 <description>interconvert molecular file-formats</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">Converter</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>Converter
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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 $param_if:
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18 -if
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19 #if " " in str($param_if):
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20 "$param_if"
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21 #else
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22 $param_if
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23 #end if
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24 #end if
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25 #if $param_o:
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26 -o $param_o
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27 #end if
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28 #if $param_of:
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29 -of
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30 #if " " in str($param_of):
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31 "$param_of"
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32 #else
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33 $param_of
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34 #end if
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35 #end if
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36 #if $param_rm:
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37 -rm $param_rm
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38 #end if
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39 </command>
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40 <inputs>
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41 <param name="param_i" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input filename" help="(-i) "/>
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42 <param name="param_if" type="select" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input format" help="(-if) ">
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43 <option value="mol2">mol2</option>
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44 <option value=" sdf"> sdf</option>
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45 <option value=" drf"> drf</option>
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46 <option value=" pdb"> pdb</option>
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47 <option value=" ac"> ac</option>
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48 <option value=" ent"> ent</option>
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49 <option value=" brk"> brk</option>
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50 <option value=" hin"> hin</option>
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51 <option value=" mol"> mol</option>
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52 <option value=" xyz"> xyz</option>
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53 <option value=" mol2.gz"> mol2.gz</option>
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54 <option value=" sdf.gz"> sdf.gz</option>
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55 <option value=" drf.gz"> drf.gz</option>
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56 <option value=" pdb.gz"> pdb.gz</option>
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57 <option value=" ac.gz"> ac.gz</option>
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58 <option value=" ent.gz"> ent.gz</option>
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59 <option value=" brk.gz"> brk.gz</option>
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60 <option value=" hin.gz"> hin.gz</option>
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61 <option value=" mol.gz"> mol.gz</option>
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62 <option value=" xyz.gz"> xyz.gz</option>
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63 </param>
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64 <param name="param_of" type="select" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="output format" help="(-of) ">
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65 <option value="mol2">mol2</option>
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66 <option value=" sdf"> sdf</option>
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67 <option value=" drf"> drf</option>
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68 <option value=" pdb"> pdb</option>
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69 <option value=" ac"> ac</option>
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70 <option value=" ent"> ent</option>
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71 <option value=" brk"> brk</option>
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72 <option value=" hin"> hin</option>
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73 <option value=" mol"> mol</option>
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74 <option value=" xyz"> xyz</option>
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75 <option value=" mol2.gz"> mol2.gz</option>
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76 <option value=" sdf.gz"> sdf.gz</option>
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77 <option value=" drf.gz"> drf.gz</option>
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78 <option value=" pdb.gz"> pdb.gz</option>
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79 <option value=" ac.gz"> ac.gz</option>
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80 <option value=" ent.gz"> ent.gz</option>
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81 <option value=" brk.gz"> brk.gz</option>
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82 <option value=" hin.gz"> hin.gz</option>
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83 <option value=" mol.gz"> mol.gz</option>
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84 <option value=" xyz.gz"> xyz.gz</option>
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85 </param>
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86 <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input file when finished" help="(-rm) "/>
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87 </inputs>
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88 <expand macro="advanced_options"/>
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89 <outputs>
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90 <data name="param_o" metadata_source="param_i" format="input"/>
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91 </outputs>
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92 <help>This tool can be used to convert between different molecular file-formats.
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93 Supported formats are mol2,sdf,drf,pdb,ac,ent,brk,hin,mol,xyz,mol2.gz,sdf.gz,drf.gz,pdb.gz,ac.gz,ent.gz,brk.gz,hin.gz,mol.gz,xyz.gz. File extensions of input and output filenames are ignored.
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94
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95 </help>
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96 </tool>
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