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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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7
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14 #set $format = $oformat.oformat_opts_selector
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15
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16 #if $format == "fs":
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17 ## For the fastsearch index we need to copy the original molecule files to the composite datatype of obfs.
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18 ## Because openbabel likes file extensions, we give the molecule file a proper file extension.
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19 mkdir $outfile.extra_files_path;
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20 cp "${infile}" ${os.path.join($outfile.extra_files_path, 'molecule.%s' % $infile.ext )};
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21 #end if
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22
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23 obabel -i "${infile.ext}"
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24
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25 #if $format == "fs":
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26 ## the fs filetype need his own symlink path, all others can take the original ones
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27 ${os.path.join($outfile.extra_files_path, 'molecule.%s' % $infile.ext )}
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28 -o "$format" -e
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29 -O ${os.path.join($outfile.extra_files_path,'molecule.fs')}
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7
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30 #if int($oformat.fs_fold) > 0:
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31 -xN$oformat.fs_fold
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32 #end if
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33 ${oformat.fs_fptype}
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34 #else:
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35 "${infile}"
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36 -o "$format"
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37 -O "${outfile}"
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38 -e
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39 #end if
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40
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41
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42 #if $format == 'cml':
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43 $oformat.cml_array
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44 $oformat.cml_cml1
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45 $oformat.cml_aromatic
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46 $oformat.cml_hydrogen
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47 $oformat.cml_metadata
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48 $oformat.cml_omit
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49 $oformat.cml_continuous
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50 $oformat.cml_properties
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51 $oformat.cml_gen2d
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52 $oformat.cml_gen3d
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53 #elif $format == 'inchi':
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54 ##ignore less import warnings
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55 -w
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56 #if $oformat.inchi_truncate:
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57 #set $truncate = ''.join( str( $oformat.inchi_truncate ).split( ',' ) )
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58 -xT ${truncate}
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59 #end if
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60
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61 #if $oformat.inchi_additional:
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62 #set $additional = ' '.join( str( $oformat.inchi_additional ).split( ',' ) )
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63 -xX '${additional}'
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64 #end if
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65
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66 $oformat.inchi_key
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67 $oformat.inchi_name
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68 $oformat.inchi_unique
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69 $oformat.inchi_unique_sort
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70 #elif $format == 'can':
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71 $oformat.can_exp_h
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72 $oformat.can_iso_chi
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73 $oformat.can_rad
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74 $oformat.can_atomclass_out
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75 #elif $format == 'smi':
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76 $oformat.smi_exp_h
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77 $oformat.smi_iso_chi
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78 $oformat.smi_rad
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79 $oformat.smi_atomclass_out
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80 $oformat.smi_can
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81 $oformat.smi_coordinates
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82 #elif $format == 'sdf':
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83 $oformat.sdf_exp_h
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84 $oformat.sdf_no_prop
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85 $oformat.sdf_wedge_bonds
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86 $oformat.sdf_alias_out
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87 $oformat.sdf_gen2d
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88 $oformat.sdf_gen3d
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89 #elif $format == 'fpt':
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90 $oformat.fpt_fptype
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91 #if int($oformat.fpt_fold) > 0:
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92 $oformat.fpt_fold
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93 #end if
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94 $oformat.fpt_hex_multiple
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95 $oformat.fpt_hex
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96 $oformat.fpt_set
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97 $oformat.fpt_unset
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98 #elif $format == 'mol2':
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99 $oformat.mol2_ignore_res
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100 $oformat.mol2_gen2d
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101 $oformat.mol2_gen3d
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102 #end if
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103
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104 ## Uniqueness according to stripped InChI's or canonical SMILES
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105 #if str($unique.unique_opts_selector):
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106 #if $unique.unique_opts_selector == 'inchi':
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107 #if $unique.truncate:
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108 #set $truncate = ''.join( str( $unique.truncate ).split( ',' ) )
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109 --unique $truncate
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110 #end if
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111 #else
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112 --unique $unique.unique_opts_selector
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113 #end if
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114 #end if
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115
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116
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117 #if str($appendtotitle).strip():
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118 --addtotitle '${appendtotitle}'
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119 #end if
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120
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121 $remove_h
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122 $dative_bonds
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123
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124 #if int($ph) >= 0:
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125 -p $ph
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126 #end if
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127
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128 2>&1
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129 </command>
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130 <inputs>
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131 <param name="infile" type="data" format="sdf,mol2,cml,inchi,smi" label="Select input file with molecules"/>
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132 <conditional name="oformat">
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133 <param name="oformat_opts_selector" type="select" label="Output format">
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134 <option value="acr">Carine ASCI Crystal</option>
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135 <option value="alc">Alchemy format</option>
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136 <option value="bgf">MSI BGF format</option>
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137 <option value="box">Dock 3.5 Box format</option>
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138 <option value="bs">Ball and Stick format</option>
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139 <option value="c3d1">Chem3D Cartesian 1 format</option>
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140 <option value="c3d2">Chem3D Cartesian 2 format</option>
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141 <option value="caccrt">Cacao Cartesian format</option>
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142 <option value="cache">CAChe MolStruct format</option>
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143 <option value="cacint">Cacao Internal format</option>
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144 <option value="can" selected="True">Canonical SMILES format (can)</option>
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145 <option value="cdxml">ChemDraw CDXML format</option>
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146 <option value="cht">Chemtool format</option>
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147 <option value="cif">Crystallographic Information File</option>
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148 <option value="cml">Chemical Markup Language</option>
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149 <option value="cmlr">CML Reaction format</option>
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150 <option value="com">Gaussian 98/03 Cartesian Input</option>
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151 <option value="copy">Copies raw text</option>
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152 <option value="crk2d">Chemical Resource Kit 2D diagram format</option>
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153 <option value="crk3d">Chemical Resource Kit 3D format</option>
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154 <option value="csr">Accelrys/MSI Quanta CSR format</option>
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155 <option value="cssr">CSD CSSR format</option>
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156 <option value="ct">ChemDraw Connection Table format</option>
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157 <option value="dmol">DMol3 coordinates format</option>
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158 <!--<option value="ent">Protein Data Bank format</option>
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159 <option value="fa">FASTA format</option>-->
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160 <option value="fasta">FASTA format</option>
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161 <option value="feat">Feature format</option>
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162 <option value="fh">Fenske-Hall Z-Matrix format</option>
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163 <option value="fix">SMILES FIX format</option>
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164 <option value="fpt">Fingerprint format (fpt)</option>
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165 <option value="fract">Free Form Fractional format</option>
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166 <option value="fs">Open Babel FastSearching database (fs)</option>
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167 <!--<option value="fsa">FASTA format</option>-->
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168 <option value="gamin">GAMESS Input</option>
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169 <option value="gau">Gaussian 98/03 Cartesian Input</option>
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170 <!--<option value="gjc">Gaussian 98/03 Cartesian Input</option>
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171 <option value="gjf">Gaussian 98/03 Cartesian Input</option>-->
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172 <option value="gpr">Ghemical format</option>
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173 <option value="gr96">GROMOS96 format</option>
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174 <option value="hin">HyperChem HIN format</option>
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175 <option value="inchi">IUPAC InChI</option>
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176 <option value="inp">GAMESS Input</option>
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177 <option value="jin">Jaguar input format</option>
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178 <!--<option value="mdl">MDL MOL format (mol)</option>-->
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179 <option value="mmd">MacroModel format</option>
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180 <option value="mmod">MacroModel format</option>
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181 <!--<option value="mol">MDL MOL format (mol)</option> use SDF-->
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182 <option value="mol2">Sybyl Mol2 format (mol2)</option>
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183 <option value="molreport">Open Babel molecule report</option>
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184 <option value="mop">MOPAC Cartesian format</option>
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185 <option value="mopcrt">MOPAC Cartesian format</option>
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186 <option value="mopin">MOPAC Internal</option>
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187 <option value="mpc">MOPAC Cartesian format</option>
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188 <option value="mpd">Sybyl descriptor format</option>
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189 <option value="mpqcin">MPQC simplified input format</option>
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190 <option value="nw">NWChem input format</option>
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191 <option value="pcm">PCModel format</option>
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192 <option value="pdb">Protein Data Bank format (pdb)</option>
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193 <option value="pov">POV-Ray input format</option>
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194 <option value="pqs">Parallel Quantum Solutions format</option>
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195 <option value="qcin">Q-Chem input format</option>
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196 <option value="report">Open Babel report format</option>
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197 <option value="rxn">MDL RXN format</option>
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198 <!--<option value="sd">MDL MOL format</option>-->
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199 <option value="sdf">MDL MOL format (sdf, mol)</option>
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200 <option value="smi">SMILES format (smi)</option>
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201 <!--<option value="sy2">Sybyl Mol2 format</option>-->
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202 <option value="tdd">Thermo format</option>
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203 <option value="test">Test format</option>
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204 <option value="therm">Thermo format</option>
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205 <option value="tmol">TurboMole Coordinate format</option>
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206 <option value="txyz">Tinker MM2 format</option>
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207 <option value="unixyz">UniChem XYZ format</option>
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208 <option value="vmol">ViewMol format</option>
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209 <option value="xed">XED format</option>
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210 <option value="xyz">XYZ cartesian coordinates format</option>
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211 <option value="yob">YASARA.org YOB format</option>
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212 <option value="zin">ZINDO input format</option>
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213 </param>
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214 <when value="acr" />
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215 <when value="alc" />
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216 <when value="bgf" />
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217 <when value="box" />
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218 <when value="bs" />
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219 <when value="c3d1" />
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220 <when value="c3d2" />
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221 <when value="caccrt" />
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222 <when value="cache" />
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223 <when value="cacint" />
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224 <when value="can">
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225 <param name="can_exp_h" type="boolean" label="Output explicit hydrogens as such (-xh)" truevalue="-xh" falsevalue="" checked="false" />
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226 <param name="can_iso_chi" type="boolean" label="Do not include isotopic or chiral markings (-xi)" truevalue="-xi" falsevalue="" checked="false" />
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227 <param name="can_rad" type="boolean" label="Radicals lower case eg ethyl is Cc (-xr)" truevalue="-xr" falsevalue="" checked="false" />
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228 <param name="can_atomclass_out" type="boolean" label="Output atomclass like [C:2] (-xa)" truevalue="-xa" falsevalue="" checked="false" />
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229 </when>
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230 <when value="cdxml" />
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231 <when value="cht" />
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232 <when value="cif" />
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233 <when value="cml">
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234 <param name="cml_cml1" type="boolean" label="convert to CML 1 (rather than CML 2) (-x1)" truevalue="-x1" falsevalue="" checked="false" />
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235 <param name="cml_array" type="boolean" label="write array format for atoms and bonds (-xa)" truevalue="-xa" falsevalue="" checked="false" />
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236 <param name="cml_aromatic" type="boolean" label="write aromatic bonds as such, not Kekule form (-xA)" truevalue="-xA" falsevalue="" checked="false" />
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237 <param name="cml_hydrogen" type="boolean" label="use hydrogen Count for all hydrogens (-xh)" truevalue="-xh" falsevalue="" checked="false" />
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238 <param name="cml_metadata" type="boolean" label="write metadata (-xm)" truevalue="-xm" falsevalue="" checked="false" />
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239 <param name="cml_omit" type="boolean" label="omit XML and namespace declarations (-xx)" truevalue="-xx" falsevalue="" checked="false" />
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240 <param name="cml_continuous" type="boolean" label="continuous output: no formatting (-xc)" truevalue="-xc" falsevalue="" checked="false" />
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241 <param name="cml_properties" type="boolean" label="write properties (-xp)" truevalue="-xp" falsevalue="" checked="false" />
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242 <param name="cml_gen2d" type="boolean" label="Generate 2D coordinates (--gen2d)" truevalue="--gen2d" falsevalue="" checked="false" />
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243 <param name="cml_gen3d" type="boolean" label="Generate 3D coordinates (--gen3d)" truevalue="--gen3d" falsevalue="" checked="false" />
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244 </when>
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245 <when value="cmlr" />
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246 <when value="com" />
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247 <when value="copy" />
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248 <when value="crk2d" />
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249 <when value="crk3d" />
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250 <when value="csr" />
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251 <when value="cssr" />
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252 <when value="ct" />
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253 <when value="dmol" />
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254 <when value="fa" />
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255 <when value="fasta" />
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256 <when value="feat" />
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257 <when value="fh" />
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258 <when value="fix" />
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259 <when value="fpt">
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260 <param name="fpt_fptype" type="select" label="Fingerprint type">
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261 <option value="-xfFP2" selected="True">FP2</option>
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262 <option value="-xfFP3">FP3</option>
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263 <option value="-xfFP4">FP4</option>
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264 <option value="-xfMACCS">MACCS</option>
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265 </param>
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266 <param name="fpt_fold" type="integer" value="0" size="20" label="Fold fingerprint to the number of specifed bits (32, 64, 128, etc.)" help="Use zero for default">
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267 <validator type="in_range" min="0" />
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268 </param>
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269 <param name="fpt_hex_multiple" type="boolean" label="hex output when multiple molecules (-xh)" truevalue="-xh" falsevalue="" checked="false" />
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270 <param name="fpt_hex" type="boolean" label="hex output only (-xo)" truevalue="-xo" falsevalue="" checked="false" />
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271 <param name="fpt_set" type="boolean" label="describe each set bit (-xs)" truevalue="-xs" falsevalue="" checked="false" />
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272 <param name="fpt_unset" type="boolean" label="describe each unset bit (-xu)" truevalue="-xu" falsevalue="" checked="false" />
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273 </when>
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274 <when value="fract" />
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275 <when value="fs">
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276 <param name="fs_fptype" type="select" label="Fingerprint type">
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277 <option value="-xfFP2" selected="True">FP2</option>
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278 <option value="-xfFP3">FP3</option>
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279 <option value="-xfFP4">FP4</option>
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280 <option value="-xfMACCS">MACCS</option>
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281 </param>
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282 <param name="fs_fold" type="integer" value="0" size="20" label="Fold fingerprint to the number of specifed bits (32, 64, 128, etc.)" help="Use zero for default">
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283 <validator type="in_range" min="0" />
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284 </param>
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285 </when>
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286 <when value="gamin" />
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287 <when value="gau" />
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288 <when value="gjf" />
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289 <when value="gpr" />
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290 <when value="gr96" />
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291 <when value="hin" />
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292 <when value="inchi">
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293 <param name="inchi_key" type="boolean" label="output InChIKey only (-xK)" truevalue="-xK" falsevalue="" checked="false" />
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294 <param name="inchi_name" type="boolean" label="add molecule name after InChI (-xt)" truevalue="-xt" falsevalue="" checked="true" />
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295 <param name="inchi_unique" type="boolean" label="output only unique molecules (-xu)" truevalue="-xu" falsevalue="" checked="false" />
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296 <param name="inchi_unique_sort" type="boolean" label="output only unique molecules and sort them (-xU)" truevalue="-xU" falsevalue="" checked="false" />
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297 <param name="inchi_truncate" type="select" multiple="True" display="checkboxes" label="truncate InChI according to various parameters">
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298 <option value="/formula">formula only</option>
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299 <option value="/connect">formula and connectivity only</option>
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300 <option value="/nostereo">ignore E/Z and sp3 stereochemistry</option>
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301 <option value="/sp3">ignore sp3 stereochemistry</option>
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302 <option value="/noEZ">ignore E/Z steroeochemistry</option>
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303 <option value="/nochg">ignore charge and protonation</option>
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304 <option value="/noiso">ignore isotopes</option>
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305 </param>
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306
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307 <param name="inchi_additional" type="select" multiple="True" display="checkboxes" label="Additional InChI options" help="For more information please see the InChI documentation (http://www.inchi-trust.org/fileadmin/user_upload/html/inchifaq/inchi-faq.html).">
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308 <option value="NEWPSOFF">Narrow End of Wedge Points to Stereo is OFF (NEWPSOFF - stdInChI)</option>
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309 <option value="DoNotAddH">Skip the addition of hydrogen atoms (DoNotAddH - stdInChI)</option>
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310 <option value="SNon">Exclude stereo (SNon - stdInChI)</option>
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311 <option value="SRel">Relative stereo (SRel)</option>
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312 <option value="SRac">Racemic stereo (SRac)</option>
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313 <option value="SUCF">Use Chiral Flag (SUCF)</option>
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314 <option value="ChiralFlagON">Set Chiral Flag (ChrialFlagON)</option>
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315 <option value="ChiralFlagOFF">Set Not-Chiral Flag (ChrialFlagOFF)</option>
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316 <option value="SUU">Include omitted unknown/undefined stereo (SUU)</option>
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317 <option value="SLUUD">Stereo labels for "unknown" and "undefined" are different, 'u' and '?', respectively (SLUUD) </option>
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318 <option value="FixedH">Mobile H Perception Off (FixedH)</option>
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319 <option value="RecMet">Include reconnected bond to metal results (RecMet)</option>
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320 <option value="KET">Keto-enol tautomerism (KET)</option>
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321 <option value="15T">1,5-tautomerism (15T)</option>
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322 </param>
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323 </when>
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324 <when value="inp" />
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325 <when value="jin" />
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326 <when value="mmd" />
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327 <when value="mmod" />
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328 <when value="mol2">
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329 <param name="mol2_ignore_res" type="boolean" label="Output ignores residue information for ligands (-xl)" truevalue="-xl" falsevalue="" checked="false" />
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9
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330 <param name="mol2_gen2d" type="boolean" label="Generate 2D coordinates (--gen2d)" truevalue="--gen2d" falsevalue="" checked="false" />
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331 <param name="mol2_gen3d" type="boolean" label="Generate 3D coordinates (--gen3d)" truevalue="--gen3d" falsevalue="" checked="false" />
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7
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332 </when>
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333 <when value="molreport" />
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334 <when value="mop" />
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335 <when value="mopcrt" />
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336 <when value="mopin" />
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337 <when value="mpc" />
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338 <when value="mpd" />
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339 <when value="mpqcin" />
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340 <when value="nw" />
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341 <when value="pcm" />
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342 <when value="pdb" />
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343 <when value="pov" />
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344 <when value="pqs" />
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345 <when value="qcin" />
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346 <when value="report" />
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347 <when value="rxn" />
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348 <when value="sdf">
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349 <param name="sdf_exp_h" type="boolean" label="output V3000 not V2000 (used for >999 atoms/bonds) (-x3)" truevalue="-x3" falsevalue="" checked="false" />
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350 <param name="sdf_no_prop" type="boolean" label="write no properties (-xm)" truevalue="-xm" falsevalue="" checked="false" />
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351 <param name="sdf_wedge_bonds" type="boolean" label="use wedge and hash bonds from input (2D structures only) (-xw)" truevalue="-xw" falsevalue="" checked="false" />
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352 <param name="sdf_alias_out" type="boolean" label="output in Alias form, e.g. Ph (-xA)" truevalue="-xA" falsevalue="" checked="false" />
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9
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353 <param name="sdf_gen2d" type="boolean" label="Generate 2D coordinates (--gen2d)" truevalue="--gen2d" falsevalue="" checked="false" />
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354 <param name="sdf_gen3d" type="boolean" label="Generate 3D coordinates (--gen3d)" truevalue="--gen3d" falsevalue="" checked="false" />
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7
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355 </when>
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356 <when value="smi">
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357 <param name="smi_exp_h" type="boolean" label="Output explicit hydrogens as such (-xh)" truevalue="-xh" falsevalue="" checked="false" />
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358 <param name="smi_iso_chi" type="boolean" label="Do not include isotopic or chiral markings (-xi)" truevalue="-xi" falsevalue="" checked="false" />
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359 <param name="smi_rad" type="boolean" label="Radicals lower case eg ethyl is Cc (-xr)" truevalue="-xr" falsevalue="" checked="false" />
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360 <param name="smi_atomclass_out" type="boolean" label="Output atomclass like [C:2] (-xa)" truevalue="-xa" falsevalue="" checked="false" />
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361 <param name="smi_can" type="boolean" label="Output in canonical form (-xc)" truevalue="-xc" falsevalue="" checked="false" />
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362 <param name="smi_coordinates" type="boolean" label="append X/Y coordinates in canonical-SMILES order (-xx)" truevalue="-xx" falsevalue="" checked="false" />
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363 </when>
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364 <when value="tdd" />
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365 <when value="test" />
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366 <when value="therm" />
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367 <when value="tmol" />
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368 <when value="txyz" />
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369 <when value="unixyz" />
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370 <when value="vmol" />
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371 <when value="xed" />
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372 <when value="xyz" />
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373 <when value="yob" />
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374 <when value="zin" />
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375 </conditional>
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376
|
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377
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378 <!-- Options for all formats.-->
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379 <param name="remove_h" type="boolean" label="Delete hydrogen atoms, make all hydrogen implicit (-d)" truevalue="-d" falsevalue="" />
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380 <param name="ph" size="5" type="float" value="-1" label="Add hydrogens appropriate for pH (-p)" help="-1 means deactivated"/>
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381 <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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382
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383 <param name="appendtotitle" type="text" value="" size="20" label="Append the specified text after each molecule title"/>
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384
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385 <!-- Uniqueness -->
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386 <conditional name="unique">
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387 <param name="unique_opts_selector" type="select" label="Uniqueness according to">
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388 <option value="" selected="True">No unique filter</option>
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389 <option value="inchi">InChI</option>
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390 <option value="cansmi">canonical SMILES with stereochemical information</option>
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391 <option value="cansmiNS">canonical SMILES without stereochemical information</option>
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392 <option value="title">title</option>
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|
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393 </param>
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|
|
394 <when value="" />
|
|
|
395 <when value="cansmi" />
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|
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396 <when value="cansmiNS" />
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|
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397 <when value="title" />
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|
|
398 <when value="inchi">
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|
|
399 <param name="truncate" type="select" multiple="True" display="checkboxes" label="Uniqueness defined as truncated InChI">
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|
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400 <option value="/formula">formula only</option>
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|
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401 <option value="/connect">formula and connectivity only</option>
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|
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402 <option value="/nostereo">ignore E/Z and sp3 stereochemistry</option>
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|
|
403 <option value="/sp3">ignore sp3 stereochemistry</option>
|
|
|
404 <option value="/noEZ">ignore E/Z steroeochemistry</option>
|
|
|
405 <option value="/nochg">ignore charge and protonation</option>
|
|
|
406 <option value="/noiso">ignore isotopes</option>
|
|
|
407 </param>
|
|
|
408 </when>
|
|
|
409 </conditional>
|
|
0
|
410 </inputs>
|
|
7
|
411
|
|
|
412
|
|
0
|
413 <outputs>
|
|
7
|
414 <data name="outfile" type="data" format="text" label="Convert to ${oformat.oformat_opts_selector} from ${on_string}">
|
|
0
|
415 <change_format>
|
|
7
|
416 <when input="oformat.oformat_opts_selector" value="sdf" format="sdf"/>
|
|
|
417 <when input="oformat.oformat_opts_selector" value="can" format="smi"/>
|
|
|
418 <when input="oformat.oformat_opts_selector" value="smi" format="smi"/>
|
|
|
419 <when input="oformat.oformat_opts_selector" value="mol2" format="mol2"/>
|
|
|
420 <when input="oformat.oformat_opts_selector" value="inchi" format="inchi"/>
|
|
|
421 <when input="oformat.oformat_opts_selector" value="cml" format="cml"/>
|
|
|
422 <when input="oformat.oformat_opts_selector" value="mol" format="mol"/>
|
|
|
423 <when input="oformat.oformat_opts_selector" value="pdb" format="pdb"/>
|
|
|
424 <when input="oformat.oformat_opts_selector" value="fs" format="obfs"/>
|
|
0
|
425 </change_format>
|
|
|
426 </data>
|
|
|
427 </outputs>
|
|
|
428 <help>
|
|
|
429
|
|
|
430 **What it does**
|
|
|
431
|
|
|
432 OpenBabel is a cross-platform program designed to interconvert between many file formats used in molecular modeling and computational chemistry and related areas.
|
|
|
433
|
|
|
434 -----
|
|
|
435
|
|
|
436
|
|
|
437 </help>
|
|
|
438 </tool>
|
