Mercurial > repos > bgruening > openbabel_compound_convert

annotate ob_convert.xml @ 7:a9df9aae60bb draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:37:52 -0400
parents edb576416262
children a072cb207571
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a9df9aae60bb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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1 <tool id="openbabel_compound_convert" name="Compound conversion" version="@VERSION@.0">
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2 <description>- interconvert between various chemistry and molecular modeling data files</description>
0
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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 <macros>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="requirements"/>
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11 <command detect_errors="aggressive">
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12 <![CDATA[
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13
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14 #set $format = $oformat.oformat_opts_selector
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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 $outfile.files_path;
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20 cp "${infile}" ${os.path.join($outfile.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.files_path, 'molecule.%s' % $infile.ext )}
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28 -o "$format" -e
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29 -O ${os.path.join($outfile.files_path,'molecule.fs')}
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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 #if $format == 'cml':
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42 $oformat.cml_array
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43 $oformat.cml_cml1
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44 $oformat.cml_aromatic
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45 $oformat.cml_hydrogen
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46 $oformat.cml_metadata
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47 $oformat.cml_omit
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48 $oformat.cml_continuous
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49 $oformat.cml_properties
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50 $oformat.gen2d
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51 $oformat.gen3d
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52 #elif $format == 'inchi':
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53 ## Ignore less import warnings
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54 -w
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55 #if $oformat.inchi_truncate:
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56 #set $truncate = ''.join( str( $oformat.inchi_truncate ).split( ',' ) )
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57 -xT ${truncate}
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58 #end if
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59
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60 #if $oformat.inchi_additional:
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61 #set $additional = ' '.join( str( $oformat.inchi_additional ).split( ',' ) )
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62 -xX '${additional}'
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63 #end if
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64
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65 $oformat.inchi_key
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66 $oformat.inchi_name
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67 $oformat.inchi_unique
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68 $oformat.inchi_unique_sort
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69 #elif $format == 'can':
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70 $oformat.can_exp_h
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71 $oformat.can_iso_chi
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72 $oformat.can_rad
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73 $oformat.can_atomclass_out
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74 #elif $format == 'smi':
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75 $oformat.smi_exp_h
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76 $oformat.smi_iso_chi
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77 $oformat.smi_rad
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78 $oformat.smi_atomclass_out
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79 $oformat.smi_can
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80 $oformat.smi_coordinates
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81 #elif $format == 'sdf':
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82 $oformat.sdf_exp_h
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83 $oformat.sdf_no_prop
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84 $oformat.sdf_wedge_bonds
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85 $oformat.sdf_alias_out
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86 $oformat.gen2d
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87 $oformat.gen3d
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88 #elif $format == 'fpt':
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89 $oformat.fpt_fptype
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90 #if int($oformat.fpt_fold) > 0:
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91 $oformat.fpt_fold
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92 #end if
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93 $oformat.fpt_hex_multiple
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94 $oformat.fpt_hex
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95 $oformat.fpt_set
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96 $oformat.fpt_unset
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97 #elif $format == 'mol2':
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98 $oformat.mol2_ignore_res
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99 $oformat.gen2d
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100 $oformat.gen3d
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101 #end if
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102
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103 ## Uniqueness according to stripped InChI's or canonical SMILES
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104 #if str($unique.unique_opts_selector):
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105 #if $unique.unique_opts_selector == 'inchi':
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106 #if $unique.truncate:
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107 #set $truncate = ''.join( str( $unique.truncate ).split( ',' ) )
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108 --unique $truncate
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109 #end if
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110 #else
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111 --unique $unique.unique_opts_selector
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112 #end if
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113 #end if
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114
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115 #if str($appendtotitle).strip():
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116 --addtotitle '${appendtotitle}'
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117 #end if
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118
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119 $remove_h
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120 $dative_bonds
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121
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122 #if float($ph) >= 0:
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123 -p $ph
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124 #end if
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125
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126 ]]>
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127 </command>
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128 <inputs>
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129 <expand macro="infile_all_types"/>
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130 <conditional name="oformat">
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131 <param name="oformat_opts_selector" type="select" label="Output format">
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132 <option value="acr">Carine ASCI Crystal</option>
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133 <option value="alc">Alchemy format</option>
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134 <option value="bgf">MSI BGF format</option>
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135 <option value="box">Dock 3.5 Box format</option>
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136 <option value="bs">Ball and Stick format</option>
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137 <option value="c3d1">Chem3D Cartesian 1 format</option>
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138 <option value="c3d2">Chem3D Cartesian 2 format</option>
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139 <option value="caccrt">Cacao Cartesian format</option>
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140 <option value="cache">CAChe MolStruct format</option>
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141 <option value="cacint">Cacao Internal format</option>
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142 <option value="can" selected="True">Canonical SMILES format (can)</option>
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143 <option value="cdxml">ChemDraw CDXML format</option>
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144 <option value="cht">Chemtool format</option>
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145 <option value="cif">Crystallographic Information File</option>
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146 <option value="cml">Chemical Markup Language (CML)</option>
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147 <option value="cmlr">CML Reaction format</option>
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148 <option value="com">Gaussian 98/03 Cartesian Input</option>
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149 <option value="copy">Copies raw text</option>
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150 <option value="crk2d">Chemical Resource Kit 2D diagram format</option>
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151 <option value="crk3d">Chemical Resource Kit 3D format</option>
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152 <option value="csr">Accelrys/MSI Quanta CSR format</option>
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153 <option value="cssr">CSD CSSR format</option>
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154 <option value="ct">ChemDraw Connection Table format</option>
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155 <option value="dmol">DMol3 coordinates format</option>
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156 <!--<option value="ent">Protein Data Bank format</option>
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157 <option value="fa">FASTA format</option>-->
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158 <option value="fasta">FASTA format</option>
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159 <option value="feat">Feature format</option>
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160 <option value="fh">Fenske-Hall Z-Matrix format</option>
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161 <option value="fix">SMILES FIX format</option>
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162 <option value="fpt">Fingerprint format (fpt)</option>
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163 <option value="fract">Free Form Fractional format</option>
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164 <option value="fs">Open Babel FastSearching database (fs)</option>
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165 <!--<option value="fsa">FASTA format</option>-->
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166 <option value="gamin">GAMESS Input</option>
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167 <option value="gau">Gaussian 98/03 Cartesian Input</option>
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168 <!--<option value="gjc">Gaussian 98/03 Cartesian Input</option>
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169 <option value="gjf">Gaussian 98/03 Cartesian Input</option>-->
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170 <option value="gpr">Ghemical format</option>
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171 <option value="gr96">GROMOS96 format</option>
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172 <option value="hin">HyperChem HIN format</option>
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173 <option value="inchi">IUPAC InChI</option>
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174 <option value="inp">GAMESS Input</option>
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175 <option value="jin">Jaguar input format</option>
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176 <!--<option value="mdl">MDL MOL format (mol)</option>-->
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177 <option value="mmd">MacroModel format</option>
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178 <option value="mmod">MacroModel format</option>
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179 <!--<option value="mol">MDL MOL format (mol)</option> use SDF-->
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180 <option value="mol2">Sybyl Mol2 format (mol2)</option>
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181 <option value="molreport">Open Babel molecule report</option>
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182 <option value="mop">MOPAC Cartesian format</option>
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183 <option value="mopcrt">MOPAC Cartesian format</option>
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184 <option value="mopin">MOPAC Internal</option>
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185 <option value="mpc">MOPAC Cartesian format</option>
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186 <option value="mpd">Sybyl descriptor format</option>
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187 <option value="mpqcin">MPQC simplified input format</option>
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188 <option value="nw">NWChem input format</option>
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189 <option value="pcm">PCModel format</option>
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190 <option value="pdb">Protein Data Bank format (pdb)</option>
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191 <option value="pov">POV-Ray input format</option>
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192 <option value="pqs">Parallel Quantum Solutions format</option>
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193 <option value="qcin">Q-Chem input format</option>
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194 <option value="report">Open Babel report format</option>
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195 <option value="rxn">MDL RXN format</option>
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196 <!--<option value="sd">MDL MOL format</option>-->
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197 <option value="sdf">MDL MOL format (sdf, mol)</option>
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198 <option value="smi">SMILES format (smi)</option>
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199 <!--<option value="sy2">Sybyl Mol2 format</option>-->
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200 <option value="tdd">Thermo format</option>
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201 <option value="test">Test format</option>
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202 <option value="therm">Thermo format</option>
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203 <option value="tmol">TurboMole Coordinate format</option>
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204 <option value="txyz">Tinker MM2 format</option>
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205 <option value="unixyz">UniChem XYZ format</option>
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206 <option value="vmol">ViewMol format</option>
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207 <option value="xed">XED format</option>
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208 <option value="xyz">XYZ cartesian coordinates format</option>
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209 <option value="yob">YASARA.org YOB format</option>
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210 <option value="zin">ZINDO input format</option>
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211 </param>
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212 <when value="acr" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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213 <when value="alc" />
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214 <when value="bgf" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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215 <when value="box" />
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216 <when value="bs" />
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217 <when value="c3d1" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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218 <when value="c3d2" />
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219 <when value="caccrt" />
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220 <when value="cache" />
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221 <when value="cacint" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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222 <when value="can">
7
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223 <param name="can_exp_h" type="boolean" label="Explicitly include hydrogens in output (-xh)" truevalue="-xh" falsevalue="" checked="false" />
0
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224 <param name="can_iso_chi" type="boolean" label="Do not include isotopic or chiral markings (-xi)" truevalue="-xi" falsevalue="" checked="false" />
7
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225 <param name="can_rad" type="boolean" label="Show radicals in lower case (e.g. ethyl as Cc) (-xr)" truevalue="-xr" falsevalue="" checked="false" />
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226 <param name="can_atomclass_out" type="boolean" label="Output atomclass (e.g. [C:2]) (-xa)" truevalue="-xa" falsevalue="" checked="false" />
0
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227 </when>
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228 <when value="cdxml" />
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229 <when value="cht" />
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230 <when value="cif" />
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231 <when value="cml">
7
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232 <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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233 <param name="cml_array" type="boolean" label="Write array format for atoms and bonds (-xa)" truevalue="-xa" falsevalue="" checked="false" />
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234 <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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235 <param name="cml_hydrogen" type="boolean" label="Use hydrogen count for all hydrogens (-xh)" truevalue="-xh" falsevalue="" checked="false" />
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236 <param name="cml_metadata" type="boolean" label="Write metadata (-xm)" truevalue="-xm" falsevalue="" checked="false" />
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237 <param name="cml_omit" type="boolean" label="Omit XML and namespace declarations (-xx)" truevalue="-xx" falsevalue="" checked="false" />
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238 <param name="cml_continuous" type="boolean" label="Continuous output: no formatting (-xc)" truevalue="-xc" falsevalue="" checked="false" />
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239 <param name="cml_properties" type="boolean" label="Write properties (-xp)" truevalue="-xp" falsevalue="" checked="false" />
0
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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240 <expand macro="2D_3D_opts" />
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241 </when>
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242 <when value="cmlr" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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243 <when value="com" />
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244 <when value="copy" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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245 <when value="crk2d" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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246 <when value="crk3d" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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247 <when value="csr" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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248 <when value="cssr" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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249 <when value="ct" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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250 <when value="dmol" />
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251 <when value="fasta" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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252 <when value="feat" />
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253 <when value="fh" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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254 <when value="fix" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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255 <when value="fpt">
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256 <param name="fpt_fptype" type="select" label="Fingerprint type">
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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257 <option value="-xfFP2" selected="True">FP2</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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258 <option value="-xfFP3">FP3</option>
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259 <option value="-xfFP4">FP4</option>
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260 <option value="-xfMACCS">MACCS</option>
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261 </param>
7
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262 <param name="fpt_fold" type="integer" value="0" label="Fold fingerprint to the number of specified bits (32, 64, 128, etc.)" help="Use zero for default">
0
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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263 <validator type="in_range" min="0" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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264 </param>
7
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265 <param name="fpt_hex_multiple" type="boolean" label="Hex output when multiple molecules (-xh)" truevalue="-xh" falsevalue="" checked="false" />
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266 <param name="fpt_hex" type="boolean" label="Hex output only (-xo)" truevalue="-xo" falsevalue="" checked="false" />
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267 <param name="fpt_set" type="boolean" label="Describe each set bit (-xs)" truevalue="-xs" falsevalue="" checked="false" />
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268 <param name="fpt_unset" type="boolean" label="Describe each unset bit (-xu)" truevalue="-xu" falsevalue="" checked="false" />
0
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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269 </when>
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270 <when value="fract" />
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271 <when value="fs">
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272 <param name="fs_fptype" type="select" label="Fingerprint type">
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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273 <option value="-xfFP2" selected="True">FP2</option>
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274 <option value="-xfFP3">FP3</option>
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275 <option value="-xfFP4">FP4</option>
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276 <option value="-xfMACCS">MACCS</option>
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277 </param>
7
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278 <param name="fs_fold" type="integer" value="0" label="Fold fingerprint to the number of specified bits (32, 64, 128, etc.)" help="Use zero for default">
0
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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279 <validator type="in_range" min="0" />
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280 </param>
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281 </when>
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282 <when value="gamin" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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283 <when value="gau" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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284 <when value="gpr" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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285 <when value="gr96" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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286 <when value="hin" />
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287 <when value="inchi">
7
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288 <param name="inchi_key" type="boolean" label="Output InChIKey only (-xK)" truevalue="-xK" falsevalue="" checked="false" />
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289 <param name="inchi_name" type="boolean" label="Add molecule name after InChI (-xt)" truevalue="-xt" falsevalue="" checked="true" />
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290 <param name="inchi_unique" type="boolean" label="Output only unique molecules (-xu)" truevalue="-xu" falsevalue="" checked="false" />
a9df9aae60bb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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291 <param name="inchi_unique_sort" type="boolean" label="Output only unique molecules and sort them (-xU)" truevalue="-xU" falsevalue="" checked="false" />
a9df9aae60bb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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292 <param name="inchi_truncate" type="select" multiple="True" display="checkboxes" label="Truncate InChI according to various parameters">
0
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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293 <option value="/formula">formula only</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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294 <option value="/connect">formula and connectivity only</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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295 <option value="/nostereo">ignore E/Z and sp3 stereochemistry</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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296 <option value="/sp3">ignore sp3 stereochemistry</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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297 <option value="/noEZ">ignore E/Z steroeochemistry</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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298 <option value="/nochg">ignore charge and protonation</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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299 <option value="/noiso">ignore isotopes</option>
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300 </param>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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301
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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302 <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).">
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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303 <option value="NEWPSOFF">Narrow End of Wedge Points to Stereo is OFF (NEWPSOFF - stdInChI)</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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304 <option value="DoNotAddH">Skip the addition of hydrogen atoms (DoNotAddH - stdInChI)</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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305 <option value="SNon">Exclude stereo (SNon - stdInChI)</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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306 <option value="SRel">Relative stereo (SRel)</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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307 <option value="SRac">Racemic stereo (SRac)</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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308 <option value="SUCF">Use Chiral Flag (SUCF)</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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309 <option value="ChiralFlagON">Set Chiral Flag (ChrialFlagON)</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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310 <option value="ChiralFlagOFF">Set Not-Chiral Flag (ChrialFlagOFF)</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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311 <option value="SUU">Include omitted unknown/undefined stereo (SUU)</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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312 <option value="SLUUD">Stereo labels for "unknown" and "undefined" are different, 'u' and '?', respectively (SLUUD) </option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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313 <option value="FixedH">Mobile H Perception Off (FixedH)</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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314 <option value="RecMet">Include reconnected bond to metal results (RecMet)</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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315 <option value="KET">Keto-enol tautomerism (KET)</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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316 <option value="15T">1,5-tautomerism (15T)</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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317 </param>
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318 </when>
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319 <when value="inp" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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320 <when value="jin" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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321 <when value="mmd" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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322 <when value="mmod" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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323 <when value="mol2">
7
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324 <param name="mol2_ignore_res" type="boolean" label="Output ignores residue information for ligands?" help="(-xl)"
0
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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325 truevalue="-xl" falsevalue="" checked="false" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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326 <expand macro="2D_3D_opts" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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327 </when>
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328 <when value="molreport" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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329 <when value="mop" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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330 <when value="mopcrt" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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331 <when value="mopin" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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332 <when value="mpc" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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333 <when value="mpd" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
334 <when value="mpqcin" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
335 <when value="nw" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
336 <when value="pcm" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
337 <when value="pdb" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
338 <when value="pov" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
339 <when value="pqs" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
340 <when value="qcin" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
341 <when value="report" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
342 <when value="rxn" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
343 <when value="sdf">
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
344 <param name="sdf_exp_h" type="boolean" truevalue="-x3" falsevalue="" checked="false"
7
a9df9aae60bb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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parents: 0
diff changeset
345 label="Output V3000 not V2000 (used for >999 atoms/bonds)" help="(-x3)" />
0
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
346 <param name="sdf_no_prop" type="boolean" truevalue="-xm" falsevalue="" checked="false"
7
a9df9aae60bb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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parents: 0
diff changeset
347 label="Do not write properties" help="(-xm)" />
0
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
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348 <param name="sdf_wedge_bonds" type="boolean" truevalue="-xw" falsevalue="" checked="false"
7
a9df9aae60bb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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parents: 0
diff changeset
349 label="Use wedge and hash bonds from input (2D structures only)" help="(-xw)"/>
0
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
350 <param name="sdf_alias_out" type="boolean" truevalue="-xA" falsevalue="" checked="false"
7
a9df9aae60bb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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parents: 0
diff changeset
351 label="Output in alias form, e.g. Ph for phenyl" help="(-xA)" />
0
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
352 <expand macro="2D_3D_opts" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
353 </when>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
354 <when value="smi">
7
a9df9aae60bb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 0
diff changeset
355 <param name="smi_exp_h" type="boolean" label="Explicitly include hydrogens in output" help="(-xh)"
0
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
356 truevalue="-xh" falsevalue="" checked="false" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
357 <param name="smi_iso_chi" type="boolean" label="Do not include isotopic or chiral markings" help="(-xi)"
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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parents:
diff changeset
358 truevalue="-xi" falsevalue="" checked="false" />
7
a9df9aae60bb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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parents: 0
diff changeset
359 <param name="smi_rad" type="boolean" label="Show radicals in lower case (e.g. ethyl as Cc)" help="(-xr)" truevalue="-xr"
0
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
360 falsevalue="" checked="false" />
7
a9df9aae60bb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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parents: 0
diff changeset
361 <param name="smi_atomclass_out" type="boolean" label="Output atomclass (e.g. [C:2])" help="(-xa)"
0
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
362 truevalue="-xa" falsevalue="" checked="false" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
363 <param name="smi_can" type="boolean" label="Output in canonical form" help="(-xc)"
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
364 truevalue="-xc" falsevalue="" checked="false" />
7
a9df9aae60bb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 0
diff changeset
365 <param name="smi_coordinates" type="boolean" label="Append X/Y coordinates in canonical-SMILES order" help="(-xx)"
0
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
366 truevalue="-xx" falsevalue="" checked="false" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
367 </when>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
368 <when value="tdd" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
369 <when value="test" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
370 <when value="therm" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
371 <when value="tmol" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
372 <when value="txyz" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
373 <when value="unixyz" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
374 <when value="vmol" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
375 <when value="xed" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
376 <when value="xyz" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
377 <when value="yob" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
378 <when value="zin" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
379 </conditional>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
380
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
381 <!-- Options for all formats.-->
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
382 <param name="remove_h" type="boolean" truevalue="-d" falsevalue=""
7
a9df9aae60bb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 0
diff changeset
383 label="Delete hydrogen atoms, make all hydrogens implicit" help="(-d)" />
0
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
384 <param name="ph" type="float" value="-1" label="Add hydrogens appropriate for pH" help="-1 means deactivated (-p)"/>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
385 <param name="dative_bonds" type="boolean" truevalue="-b" falsevalue=""
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
386 label="Convert dative bonds" help="e.g. [N+]([O-])=O to N(=O)=O (-b)" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
387 <param name="appendtotitle" type="text" value="" label="Append the specified text after each molecule title"/>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
388
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
389 <!-- Uniqueness -->
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
390 <conditional name="unique">
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
391 <param name="unique_opts_selector" type="select" label="Uniqueness according to">
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
392 <option value="" selected="True">No unique filter</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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parents:
diff changeset
393 <option value="inchi">InChI</option>
7
a9df9aae60bb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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parents: 0
diff changeset
394 <option value="cansmi">Canonical SMILES with stereochemical information</option>
a9df9aae60bb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 0
diff changeset
395 <option value="cansmiNS">Canonical SMILES without stereochemical information</option>
a9df9aae60bb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 0
diff changeset
396 <option value="title">Title</option>
0
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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parents:
diff changeset
397 </param>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
398 <when value="" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
399 <when value="cansmi" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
400 <when value="cansmiNS" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
401 <when value="title" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
402 <when value="inchi">
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
403 <param name="truncate" type="select" multiple="True" display="checkboxes" label="Uniqueness defined as truncated InChI">
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
404 <option value="/formula">formula only</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
405 <option value="/connect">formula and connectivity only</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
406 <option value="/nostereo">ignore E/Z and sp3 stereochemistry</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
407 <option value="/sp3">ignore sp3 stereochemistry</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
408 <option value="/noEZ">ignore E/Z steroeochemistry</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
409 <option value="/nochg">ignore charge and protonation</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
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410 <option value="/noiso">ignore isotopes</option>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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parents:
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411 </param>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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parents:
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412 </when>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
413 </conditional>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
414 </inputs>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
415
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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416 <outputs>
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417 <data name="outfile" format="text" label="Convert to ${oformat.oformat_opts_selector} from ${on_string}">
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418 <change_format>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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419 <when input="oformat.oformat_opts_selector" value="sdf" format="sdf"/>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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420 <when input="oformat.oformat_opts_selector" value="can" format="smi"/>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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421 <when input="oformat.oformat_opts_selector" value="smi" format="smi"/>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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422 <when input="oformat.oformat_opts_selector" value="mol2" format="mol2"/>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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423 <when input="oformat.oformat_opts_selector" value="inchi" format="inchi"/>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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424 <when input="oformat.oformat_opts_selector" value="cml" format="cml"/>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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425 <when input="oformat.oformat_opts_selector" value="mol" format="mol"/>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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426 <when input="oformat.oformat_opts_selector" value="pdb" format="pdb"/>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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427 <when input="oformat.oformat_opts_selector" value="fs" format="obfs"/>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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428 </change_format>
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429 </data>
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430 </outputs>
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431 <tests>
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432 <test>
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433 <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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434 <param name="oformat_opts_selector" value="cml" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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435 <output name="outfile" ftype="cml" file="ob_convert_on_CID2244.cml" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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436 </test>
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437 <test>
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438 <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
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439 <param name="oformat_opts_selector" value="fs" />
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440 <output name="outfile" compare="contains" file="ob_convert_on_CID2244_obfs.txt" ftype="obfs">
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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441 <extra_files type="file" value="molecule.sdf" name="molecule.sdf" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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442 <extra_files type="file" value="molecule.fs" name="molecule.fs" compare="sim_size" />
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443 </output>
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444 </test>
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445 <test>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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446 <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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447 <param name="oformat_opts_selector" value="inchi" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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448 <output name="outfile" ftype="inchi" file="ob_convert_on_CID2244.inchi" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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449 </test>
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450 <test>
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451 <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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452 <param name="oformat_opts_selector" value="pdb" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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453 <output name="outfile" ftype="pdb" file="ob_convert_on_CID2244.pdb" lines_diff="4" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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454 </test>
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455 <test>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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456 <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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457 <param name="oformat_opts_selector" value="can" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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458 <output name="outfile" ftype="smi" file="ob_convert_on_CID2244.smi" />
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459 </test>
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460 <test>
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461 <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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462 <param name="oformat_opts_selector" value="sdf" />
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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463 <output name="outfile" ftype="sdf" file="ob_convert_on_CID2244.sdf" lines_diff="2"/>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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464 </test>
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465 </tests>
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466 <help>
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467 <![CDATA[
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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468
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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469 .. class:: infomark
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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470
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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471 **What this tool does**
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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472
7
a9df9aae60bb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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473 The compound converter combines several Open Babel command prompt converters into a single easy-to-use tool. It interconverts various chemistry and molecular modeling data files. The output format can be specified as well as several parameters. Some parameters are available for all tools (e.g. protonation state and pH) while others are specific for a given output format (e.g. exclude isotopes for conversion to canSMI).
0
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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474
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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475 -----
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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476
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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477 .. class:: infomark
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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478
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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479 **Output**
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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480
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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481 Can be specified manually.
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482
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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483
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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484 ]]>
edb576416262 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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485 </help>
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486 <expand macro="citations"/>
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487 </tool>