annotate strip-it.xml @ 1:b8809b15e1a4 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:42:01 -0400
parents fc8d71a0fb9b
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fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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1 <tool id="ctb_stripit" name="Strip-it" version="1.0.2.1">
1
b8809b15e1a4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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2 <description>extracts scaffolds from molecules</description>
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fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="1000" shared_inputs="" merge_outputs="outfile"></parallelism-->
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4 <requirements>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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5 <requirement type="package" version="1.0.2">strip_it</requirement>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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6 </requirements>
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7 <command detect_errors="aggressive">
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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8 <![CDATA[
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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9 ln -s '$infile' '$infile.${infile.ext}' &&
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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10 strip-it
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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11 --input '$infile.${infile.ext}'
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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12 --output '$outfile'
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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13 --noLog
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14 $noHeader
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15 ]]>
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16 </command>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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17 <inputs>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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18 <param name="infile" type="data" format='sdf,mol,mol2,smi' label="Molecule file" />
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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19 <param argument='--noHeader' type='boolean' truevalue='--noHeader' falsevalue=''
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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20 label='Do not print a header in the output file' />
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21
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22 </inputs>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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23 <outputs>
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24 <data name="outfile" format="tabular" />
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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25 </outputs>
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26 <tests>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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27 <test>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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28 <param name="infile" ftype="sdf" value="CID_3037.sdf"/>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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29 <param name="noHeader" value="false"/>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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30 <output name="outfile" file="Strip-it_on_CID3037.tabular" />
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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31 </test>
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32 </tests>
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33 <help>
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34 <![CDATA[
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35
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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36
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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37 .. class:: infomark
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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38
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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39 **What this tool does**
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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40
1
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41 Strip-it is a program that extracts scaffolds from organic small molecules,
b8809b15e1a4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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42 based on predefined scaffold types. The scaffold types used by Strip-it include
0
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43
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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44 - `molecular frameworks`_ as originally described by Bemis and Murcko
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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45 - `molecular frameworks and the reduced molecular frameworks`_ as described by Ansgar Schuffenhauer and coworkers
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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46 - `scaffold topologies`_ as described by Sara Pollock and coworkers
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47
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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48 .. _molecular frameworks: http://www.ncbi.nlm.nih.gov/pubmed/8709122
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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49 .. _molecular frameworks and the reduced molecular frameworks: http://peter-ertl.com/reprints/Schuffenhauer-JCIM-47-47-2007.pdf
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50 .. _scaffold topologies: http://www.ncbi.nlm.nih.gov/pubmed/18605680
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51
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52 -----
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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53
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54 .. class:: infomark
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55
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56
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57 **Input**
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58
1
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59 | - `SDF format`_
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60 | - `SMILES format`_
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61 | - `MOL2 format`_
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62
1
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63 .. _SDF format: http://en.wikipedia.org/wiki/Chemical_table_file
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64 .. _SMILES format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
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65 .. _MOL2 format: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf
0
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66
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67
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68 -----
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69
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70 .. class:: infomark
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71
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72 **Output**
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73
1
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74 A tabular file with the name and SMILES of the molecule in the first two
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75 columns; subsequent columns show scaffolds extracted by different methods.
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76
0
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77 +-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
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78 | NAME | MOLECULE | RINGS_WITH_LINKERS_1 | RINGS_WITH_LINKERS_2 | MURCKO_1 | ... |
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79 +=============+================================+======================+========================+======================+=====+
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80 | Diclofenac | OC(=O)Cc1ccccc1Nc1c(Cl)cccc1Cl | c1ccc(cc1)Nc1ccccc1 | c1ccc(cc1)Nc1ccccc1 | C1CCC(CC1)CC1CCCCC1 | ... |
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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81 +-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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82 | Bupivacaine | CCCCN1CCCCC1C(=O)Nc1c(C)cccc1C | C1CCC(NC1)CNc1ccccc1 | O=C(C1CCCCN1)Nc1ccccc1 | C1CCC(CC1)CCC1CCCCC1 | ... |
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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83 +-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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84 | ... | ... | ... | ... | ... | ... |
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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85 +-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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86
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
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87 -----
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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88
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
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89 .. class:: infomark
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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90
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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91 **Cite**
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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92
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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93 `Silicos-it`_ - strip-it
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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94
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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95 .. _Silicos-it: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/strip-it/1.0.2/strip-it.html
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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96
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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97
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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98 ]]>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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99 </help>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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100 <citations>
1
b8809b15e1a4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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101 <citation type="bibtex">@misc{
b8809b15e1a4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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102 title={Strip-it},
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103 author={Silicos-it},
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104 year={2014},
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105
b8809b15e1a4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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106 }</citation>
0
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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107 </citations>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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108 </tool>