Mercurial > repos > bgruening > shape_it

annotate shape-it.xml @ 1:d7ecb50b2b66 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:41:43 -0400
parents 31f5b5421a02
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31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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1 <tool id="ctb_shapeit" name="Shape alignment" version="1.0.1.0">
1
d7ecb50b2b66 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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2 <description>against a database of molecules (shape-it)</description>
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31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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3 <requirements>
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4 <requirement type="package" version="1.0.1">shape_it</requirement>
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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5 </requirements>
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6 <command detect_errors="aggressive">
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7 <![CDATA[
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31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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9 ln -s ${database} ./database.${database.ext} &&
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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10 ln -s ${reference} ./reference.${reference.ext} &&
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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11
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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12 shape-it
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13 --format ${database.ext}
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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14 --dbase ./database.${database.ext}
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15 --reference ./reference.${reference.ext}
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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16 --addIterations $addIterations
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17 #if int($best) > 0:
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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18 --best $best
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19 #end if
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20 --cutoff $cutoff
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21 #if $scores:
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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22 --scores $output_scores
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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23 #end if
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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24 --rankBy $rankBy
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25 $noref
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26 $scoreonly
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27 --out ./result.${database.ext}
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28
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29 &&
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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30 mv ./result.${database.ext} '$output'
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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31 ]]>
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32 </command>
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33 <inputs>
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34 <param name="reference" type="data" format='sdf,mol,mol2' label="Reference molecule (with 3D coordinates)" />
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35 <param name="database" type="data" format='sdf,mol,mol2' label="Database of molecules (with 3D coordinates)" />
1
d7ecb50b2b66 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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36 <param name="cutoff" type="float" value="0.0" label="Cutoff"
d7ecb50b2b66 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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37 help="Only molecules with a score higher than the cutoff are reported; the scoring function is defined by the scoring scheme.">
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38 <validator type="in_range" min="0.0" />
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39 </param>
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40 <param name='addIterations' type='integer' value='0' label='Perform N additional optimization steps with the simulated annealing procedure'
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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41 help="The default value is set to 0, which refers to only a local gradient ascent."/>
1
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42 <param name='best' type='integer' value='0' label='Number of best-scoring molecules to report' help="The N best scoring molecules are reported; 0 means all molecules are reported"/>
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43 <param name='scores' type='boolean' truevalue='yes' falsevalue='' label='Output a tab-delimited text file with the molecule scores' checked="false" />
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44 <param name='noref' type='boolean' truevalue='--noRef' falsevalue='' label='Do not write reference molecule into the output files' checked="false" />
0
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45 <param name='scoreonly' type='boolean' truevalue='--scoreOnly' falsevalue=''
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46 label='Only the volume overlap between the reference and the given pose is computed' checked="false" />
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47 <param name='rankBy' type='select' format='text' label="Scoring scheme">
0
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48 <option value='TANIMOTO'>Tanimoto</option>
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49 <option value='TVERSKY_REF'>TVERSKY_REF</option>
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50 <option value='TVERSKY_DB'>TVERSKY_DB</option>
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51 </param>
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52 </inputs>
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53 <outputs>
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54 <data name="output" format_source='database' />
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55 <data name="output_scores" format="tabular">
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56 <filter>scores is True</filter>
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57 </data>
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58 </outputs>
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59 <tests>
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60 <test>
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61 <param name="database" ftype='sdf' value="CID_3033.sdf" />
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62 <param name="reference" ftype="sdf" value='CID_3037.sdf' />
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63 <param name="cutoff" value="0.0" />
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64 <param name='addIterations' value='0' />
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65 <param name='best' value='0' />
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66 <param name='scoreonly' value="true" />
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67 <output name="output" ftype='sdf' file="shapeit_on_CID3033_and_CID3037.sdf" lines_diff="4" />
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68 </test>
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69 </tests>
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70 <help>
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71 <![CDATA[
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72
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73
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74 .. class:: infomark
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75
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76 **What this tool does**
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77
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78 Shape-it_ is a tool that aligns a reference molecule against a set of database
1
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79 molecules using the shape of the molecules as the alignment criterion.
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80 It is based on the use of `gaussian volumes as descriptor for molecular shape`_ as was introduced by Grant and Pickup.
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81
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82 The program expects one reference molecule with
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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83 its three-dimensional coordinates and one database files containing one
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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84 or more molecules in three dimensions. The results are either the alignment
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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85 of all database molecules and their respective scores or the N best
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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86 scoring molecules of the complete database.
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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87
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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88 .. _gaussian volumes as descriptor for molecular shape: http://pubs.acs.org/doi/abs/10.1021/j100011a016
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89 .. _Shape-it: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/shape-it/1.0.1/shape-it.html
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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90
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91 -----
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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92
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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93 .. class:: infomark
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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94
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95 **Input**
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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96
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97
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98 `3D formats recognized by OpenBabel`_ - either SDF, MOL, or MOL2
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99
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100 .. _3D formats recognized by OpenBabel: http://openbabel.org/wiki/Category:Formats
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101
1
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102 * Example (SDF)::
0
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103
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104 - database
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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105 27 28 0 0 0 0 0 0 0999 V2000
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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106 -4.8550 1.3401 0.2120 Cl 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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107 4.8529 -1.3406 0.2121 Cl 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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108 -0.1809 -2.1668 -0.3789 O 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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109 0.1788 2.1664 -0.3787 O 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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110 -0.0011 -0.0002 1.4744 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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111 -1.2222 -0.2738 0.6597 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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112 1.2377 0.2772 0.6480 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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113 -1.2586 -1.3462 -0.2316 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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114 1.2565 1.3457 -0.2314 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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115 -2.3343 0.5568 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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116 2.3322 -0.5574 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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117 -2.4069 -1.5879 -0.9855 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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118 2.4048 1.5875 -0.9852 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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119 -3.4827 0.3152 0.0433 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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120 3.4807 -0.3156 0.0435 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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121 -3.5190 -0.7571 -0.8481 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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122 3.5170 0.7568 -0.8478 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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123 -0.1548 0.8649 2.1342 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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124 0.1601 -0.8435 2.1593 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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125 -2.3089 1.3938 1.4913 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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126 2.3053 -1.3909 1.4943 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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127 -2.4415 -2.4213 -1.6818 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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128 2.4469 2.4191 -1.6835 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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129 -4.4070 -0.9574 -1.4422 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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130 4.4050 0.9570 -1.4418 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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131 0.2961 -2.2262 0.4641 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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132 0.3872 2.8487 -1.0397 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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133 1 14 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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134 2 15 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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135 3 8 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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136 3 26 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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137 4 9 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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138 4 27 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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139 5 6 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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140 5 7 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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141 .....
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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142
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143 - reference
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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144
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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145 30 31 0 0 0 0 0 0 0999 V2000
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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146 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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147 1.1377 -1.6392 2.1136 Cl 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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148 -3.2620 -2.9284 -1.0647 O 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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149 -2.7906 -1.9108 0.9092 O 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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150 0.2679 -0.2051 -0.3990 N 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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151 -2.0640 0.5139 -0.3769 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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152 -0.7313 0.7178 -0.0192 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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153 -2.4761 -0.6830 -1.1703 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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154 1.6571 -0.2482 -0.1795 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
155 -3.0382 1.4350 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
156 -0.3728 1.8429 0.7234 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
157 -2.6797 2.5600 0.7506 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
158 -1.3470 2.7640 1.1083 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
159 2.5353 0.3477 -1.0918 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
160 2.1740 -0.8865 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
161 -2.8480 -1.8749 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
162 3.9124 0.3058 -0.8739 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
163 3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
164 4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
165 -1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
166 -3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
167 -0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
168 -4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
169 0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
170 -3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
171 -1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
172 4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
173 3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
174 5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
175 -3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
176 1 14 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
177 2 15 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
178 3 16 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
179 3 30 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
180 4 16 2 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
181 5 7 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
182 5 9 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
183 5 22 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
184 6 7 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
185 6 8 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
186 ......
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
187
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
188 - cutoff : 0.0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
189
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
190 -----
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
191
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
192 .. class:: infomark
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
193
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
194 **Output**
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
195
1
d7ecb50b2b66 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 0
diff changeset
196 The output file contains first the reference molecule, followed by the molecules
d7ecb50b2b66 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 0
diff changeset
197 aligned to the reference molecule. If the 'Number of best-scoring molecules' option
d7ecb50b2b66 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 0
diff changeset
198 is set only the top-best scoring molecules will be reported in the output file,
d7ecb50b2b66 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 0
diff changeset
199 otherwise all molecules are written to the output file.
d7ecb50b2b66 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 0
diff changeset
200
0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
201 * Example::
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
202
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
203 27 28 0 0 0 0 0 0 0 0999 V2000
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
204 -4.8550 1.3401 0.2120 Cl 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
205 4.8529 -1.3406 0.2121 Cl 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
206 -0.1809 -2.1668 -0.3789 O 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
207 0.1788 2.1664 -0.3787 O 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
208 -0.0011 -0.0002 1.4744 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
209 -1.2222 -0.2738 0.6597 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
210 1.2377 0.2772 0.6480 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
211 -1.2586 -1.3462 -0.2316 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
212 1.2565 1.3457 -0.2314 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
213 -2.3343 0.5568 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
214 2.3322 -0.5574 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
215 -2.4069 -1.5879 -0.9855 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
216 2.4048 1.5875 -0.9852 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
217 -3.4827 0.3152 0.0433 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
218 3.4807 -0.3156 0.0435 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
219 -3.5190 -0.7571 -0.8481 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
220 3.5170 0.7568 -0.8478 C 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
221 -0.1548 0.8649 2.1342 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
222 0.1601 -0.8435 2.1593 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
223 -2.3089 1.3938 1.4913 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
224 2.3053 -1.3909 1.4943 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
225 -2.4415 -2.4213 -1.6818 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
226 2.4469 2.4191 -1.6835 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
227 -4.4070 -0.9574 -1.4422 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
228 4.4050 0.9570 -1.4418 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
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229 0.2961 -2.2262 0.4641 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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230 0.3872 2.8487 -1.0397 H 0 0 0 0 0 0 0 0 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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231 1 14 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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232 2 15 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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233 3 8 1 0 0 0 0
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234 3 26 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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235 4 9 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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236 4 27 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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237 5 6 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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238 5 7 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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239 5 18 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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240 5 19 1 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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241 6 8 2 0 0 0 0
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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242 ......
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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243
1
d7ecb50b2b66 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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244 In addition, if the option to output scores is selected, a tabular file will be created.
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245 Each line represents a molecule from the database, with columns describing the volumes
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246 of the reference and database molecules, overlap volumes, and Shape-it scores produced
d7ecb50b2b66 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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247 by the three scoring schemes.
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248
d7ecb50b2b66 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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249 * Example::
d7ecb50b2b66 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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250
d7ecb50b2b66 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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251 dbName refName Shape-it::Tanimoto Shape-it::Tversky_Ref Shape-it::Tversky_Db overlap refVolume dbVolume
d7ecb50b2b66 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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252 3033 3037 0.562 0.754 0.688 128.56 169.59 187.87
d7ecb50b2b66 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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253
0
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254
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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255 ]]>
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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256 </help>
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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257 <citations>
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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258 <citation type="doi">10.1021/j100011a016</citation>
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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259 </citations>
31f5b5421a02 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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260 </tool>