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1 <tool id="compound_convert" name="Compound Convert">
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2 <description>Converts various chemistry and molecular modeling data files</description>
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3 <!--<parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
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4 We can't use that currently, because a few output-datatypes, like the fastsearch index do not support merging. We need to patch galaxy to not abort in such a case
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5 and run the job in non.multi mode.
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6 -->
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7 <requirements>
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8 <requirement type="package" version="2.3.2">openbabel</requirement>
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9 </requirements>
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10 <command>
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11 ## The command is a Cheetah template which allows some Python based syntax.
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12 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
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13
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14 #if str($out_format) == 'fs':
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15 ## For the fastsearch index we need to copy the original molecule files to the composite datatype of obfs.
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16 ## Because openbabel likes file extensions, we give the molecule file a proper file extension.
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17 mkdir $outfile.extra_files_path;
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18 cp "${infile}" ${os.path.join($outfile.extra_files_path, 'molecule.%s' % $infile.ext )};
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19 #end if
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20
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21 obabel -i "${infile.ext}"
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22 #if str($out_format) == 'fs':
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23 ${os.path.join($outfile.extra_files_path, 'molecule.%s' % $infile.ext )}
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24 -o "${out_format}" -e
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25 -O ${os.path.join($outfile.extra_files_path,'molecule.fs')}
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26 #else:
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27 "${infile}"
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28 -o "${out_format}" -e
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29 -O "${outfile}"
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30 #end if
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31
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32 $remove_h
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33 #if $iso_chi or $can or $exp_h:
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34 -x$iso_chi$exp_h$can
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35 #end if
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36 #if $dative_bonds:
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37 -b
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38 #end if
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39 #if int($ph) >= 0:
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40 -p $ph
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41 #end if
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42 2>&1
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43 </command>
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44 <inputs>
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45 <param name="infile" type="data" format="sdf,mol2,cml,inchi,smi" label="Select input file with molecules"/>
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46 <param name="out_format" type="select" label="Output format">
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47 <option value="acr">Carine ASCI Crystal</option>
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48 <option value="alc">Alchemy format</option>
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49 <option value="bgf">MSI BGF format</option>
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50 <option value="box">Dock 3.5 Box format</option>
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51 <option value="bs">Ball and Stick format</option>
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52 <option value="c3d1">Chem3D Cartesian 1 format</option>
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53 <option value="c3d2">Chem3D Cartesian 2 format</option>
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54 <option value="caccrt">Cacao Cartesian format</option>
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55 <option value="cache">CAChe MolStruct format</option>
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56 <option value="cacint">Cacao Internal format</option>
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57 <option value="can">Canonical SMILES format (can)</option>
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58 <option value="cdxml">ChemDraw CDXML format</option>
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59 <option value="cht">Chemtool format</option>
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60 <option value="cif">Crystallographic Information File</option>
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61 <option value="cml">Chemical Markup Language</option>
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62 <option value="cmlr">CML Reaction format</option>
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63 <option value="com">Gaussian 98/03 Cartesian Input</option>
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64 <option value="copy">Copies raw text</option>
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65 <option value="crk2d">Chemical Resource Kit 2D diagram format</option>
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66 <option value="crk3d">Chemical Resource Kit 3D format</option>
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67 <option value="csr">Accelrys/MSI Quanta CSR format</option>
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68 <option value="cssr">CSD CSSR format</option>
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69 <option value="ct">ChemDraw Connection Table format</option>
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70 <option value="dmol">DMol3 coordinates format</option>
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71 <!--<option value="ent">Protein Data Bank format</option>
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72 <option value="fa">FASTA format</option>-->
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73 <option value="fasta">FASTA format</option>
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74 <option value="feat">Feature format</option>
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75 <option value="fh">Fenske-Hall Z-Matrix format</option>
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76 <option value="fix">SMILES FIX format</option>
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77 <option value="fpt">Fingerprint format</option>
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78 <option value="fract">Free Form Fractional format</option>
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79 <option value="fs">Open Babel FastSearching database (fs)</option>
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80 <!--<option value="fsa">FASTA format</option>-->
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81 <option value="gamin">GAMESS Input</option>
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82 <option value="gau">Gaussian 98/03 Cartesian Input</option>
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83 <!--<option value="gjc">Gaussian 98/03 Cartesian Input</option>
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84 <option value="gjf">Gaussian 98/03 Cartesian Input</option>-->
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85 <option value="gpr">Ghemical format</option>
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86 <option value="gr96">GROMOS96 format</option>
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87 <option value="hin">HyperChem HIN format</option>
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88 <option value="inchi">IUPAC InChI</option>
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89 <option value="inp">GAMESS Input</option>
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90 <option value="jin">Jaguar input format</option>
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91 <!--<option value="mdl">MDL MOL format (mol)</option>-->
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92 <option value="mmd">MacroModel format</option>
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93 <option value="mmod">MacroModel format</option>
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94 <option value="mol">MDL MOL format (mol)</option>
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95 <option value="mol2">Sybyl Mol2 format (mol2)</option>
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96 <option value="molreport">Open Babel molecule report</option>
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97 <option value="mop">MOPAC Cartesian format</option>
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98 <option value="mopcrt">MOPAC Cartesian format</option>
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99 <option value="mopin">MOPAC Internal</option>
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100 <option value="mpc">MOPAC Cartesian format</option>
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101 <option value="mpd">Sybyl descriptor format</option>
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102 <option value="mpqcin">MPQC simplified input format</option>
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103 <option value="nw">NWChem input format</option>
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104 <option value="pcm">PCModel format</option>
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105 <option value="pdb">Protein Data Bank format (pdb)</option>
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106 <option value="pov">POV-Ray input format</option>
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107 <option value="pqs">Parallel Quantum Solutions format</option>
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108 <option value="qcin">Q-Chem input format</option>
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109 <option value="report">Open Babel report format</option>
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110 <option value="rxn">MDL RXN format</option>
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111 <!--<option value="sd">MDL MOL format</option>-->
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112 <option value="sdf">MDL MOL format (sdf)</option>
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113 <option value="smi">SMILES format (smi)</option>
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114 <!--<option value="sy2">Sybyl Mol2 format</option>-->
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115 <option value="tdd">Thermo format</option>
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116 <option value="test">Test format</option>
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117 <option value="therm">Thermo format</option>
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118 <option value="tmol">TurboMole Coordinate format</option>
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119 <option value="txyz">Tinker MM2 format</option>
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120 <option value="unixyz">UniChem XYZ format</option>
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121 <option value="vmol">ViewMol format</option>
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122 <option value="xed">XED format</option>
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123 <option value="xyz">XYZ cartesian coordinates format</option>
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124 <option value="yob">YASARA.org YOB format</option>
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125 <option value="zin">ZINDO input format</option>
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126 </param>
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127 <param name="iso_chi" type="boolean" label="Do not include isotopic or chiral markings (-xi)" truevalue="i" falsevalue="" checked="false" />
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128 <param name="can" type="boolean" label="Output in canonical form (-xc)" truevalue="c" falsevalue="" checked="false" />
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129 <param name="exp_h" type="boolean" label="Output explicit hydrogens as such (-xh)" truevalue="h" falsevalue="" checked="false" />
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130 <param name="remove_h" type="boolean" label="Delete hydrogen atoms (-d)" truevalue="-d" falsevalue="" />
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131 <param name="ph" size="3" type="float" value="-1" label="Add hydrogens appropriate for pH (-p)" help="-1 means deactivated"/>
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132 <param name="dative_bonds" type="boolean" label="Convert dative bonds (e.g. [N+]([O-])=O to N(=O)=O) (-b)" truevalue="-b" falsevalue="" />
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133 </inputs>
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134 <outputs>
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135 <data name="outfile" type="data" format="text" label="Convert to ${out_format.input.value_label} from ${on_string}">
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136 <change_format>
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137 <when input="out_format" value="sdf" format="sdf"/>
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138 <when input="out_format" value="smi" format="smi"/>
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139 <when input="out_format" value="mol2" format="mol2"/>
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140 <when input="out_format" value="inchi" format="inchi"/>
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141 <when input="out_format" value="cml" format="cml"/>
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142 <when input="out_format" value="mol" format="mol"/>
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143 <when input="out_format" value="pdb" format="pdb"/>
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144 <when input="out_format" value="fs" format="obfs"/>
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145 </change_format>
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146 </data>
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147 </outputs>
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148 <help>
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149
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150 **What it does**
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151
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152 OpenBabel is a cross-platform program designed to interconvert between many file formats used in molecular modeling and computational chemistry and related areas.
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153
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154 -----
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155
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156
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157 </help>
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158 </tool>
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