Mercurial > repos > bgruening > openbabel_filter
annotate ob_filter.xml @ 12:340f8d63c1f4 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
author | bgruening |
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date | Thu, 09 Apr 2020 10:09:51 -0400 |
parents | da03b00048b1 |
children | ff2dd4b7d918 |
rev | line source |
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da03b00048b1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
bgruening
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1 <tool id="openbabel_filter" name="Filter" version="@VERSION@.1"> |
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0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
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2 <description> a set of molecules from a file</description> |
0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism--> |
0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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4 <macros> |
0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
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5 <import>macros.xml</import> |
0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
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6 </macros> |
0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
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7 <expand macro="requirements"/> |
0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
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8 <command detect_errors="aggressive"> |
0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
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9 <![CDATA[ |
0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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10 python '$__tool_directory__/ob_filter.py' |
0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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11 -i '${infile}' |
0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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12 -o '${outfile}' |
12
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
bgruening
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13 -iformat "${infile.ext}" |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
bgruening
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14 -oformat "${infile.ext}" |
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da03b00048b1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
bgruening
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15 #if $filter_methods.filter_methods_opts == "__filter_by_name__": |
da03b00048b1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
bgruening
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16 --list_of_names '$name_file' |
da03b00048b1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
bgruening
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17 --filters '__filter_by_name__' |
da03b00048b1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
bgruening
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18 #else |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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19 --filters '{ |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
bgruening
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20 #if $filter_methods.filter_methods_opts == "ruleof5": |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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21 "hbd" : [0, 5], |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
bgruening
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22 "hba" : [0, 10], |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
bgruening
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23 "molwt" : [0, 500], |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
bgruening
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24 "logp" : [-5, 5], |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
bgruening
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25 #elif $filter_methods.filter_methods_opts == "LeadLike": |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
bgruening
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26 "rotbonds" : [0, 7], |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
bgruening
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27 "molwt" : [0, 350], |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
bgruening
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28 "logp" : [-5, 3.5], |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
bgruening
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29 #elif $filter_methods.filter_methods_opts == "DrugLike": |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
bgruening
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30 "hba" : [0, 10], |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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31 "rotbonds" : [0, 8], |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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32 "molwt" : [150, 500], |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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33 "logp" : [-5, 5], |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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34 "psa" : [0, 150], |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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35 #elif $filter_methods.filter_methods_opts == "FragmentLike": |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
bgruening
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36 "rotbonds" : [0, 5], |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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37 "molwt" : [0, 250], |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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38 "logp" : [-5, 2.5], |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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39 #else: |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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40 #for $filter in $filter_methods.filter_set: |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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41 #if $filter.filter_sel.filter_sel_opts == "field": |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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42 #set $filter_selected = $filter.filter_sel['field_name'] |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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43 "$filter_selected": [$filter.filter_sel['field_min'], $filter.filter_sel['field_max'] ], |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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44 #else: |
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da03b00048b1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
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45 #set $filter_selected = $filter.filter_sel.filter_sel_opts |
da03b00048b1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
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46 #set $filter_min = $filter_selected + "_min" |
da03b00048b1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
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47 #set $filter_max = $filter_selected + "_max" |
da03b00048b1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
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48 "$filter_selected" : [$filter.filter_sel[$filter_min], $filter.filter_sel[$filter_max] ], |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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49 #end if |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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50 #end for |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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51 #end if |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
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52 }' |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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53 #end if |
0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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54 ]]> |
0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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55 </command> |
0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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56 <inputs> |
0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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57 <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi" |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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58 label="Select input file (can be previously annotated with the 'Compute physico-chemical properties' tool)"/> |
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0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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59 <conditional name="filter_methods"> |
0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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60 <param name="filter_methods_opts" type="select" label="Select a pre-defined filtering set"> |
0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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61 <option value="user">User-defined properties</option> |
0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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62 <option value="ruleof5">Lipinski's Rule-of-Five</option> |
0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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63 <option value="LeadLike">Lead-like properties</option> |
0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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64 <option value="DrugLike">Drug-like properties</option> |
0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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65 <option value="FragmentLike">Fragment-like properties</option> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
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66 <option value="__filter_by_name__">Filter by molecule name</option> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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67 </param> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
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68 <when value="__filter_by_name__"> |
da03b00048b1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
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69 <param name="name_file" type="data" format="txt,tabular" |
da03b00048b1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
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70 label="File with molecule names that match the names in the SDF file" help="Every name one line."/> |
da03b00048b1
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
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71 </when> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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72 <when value="ruleof5" /> |
0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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73 <when value="LeadLike" /> |
0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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74 <when value="DrugLike" /> |
0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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75 <when value="FragmentLike" /> |
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76 <when value="user"> |
7
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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77 <repeat name="filter_set" title="Select custom filters"> |
0
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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78 <conditional name="filter_sel"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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79 <param name="filter_sel_opts" type="select" label="Select properties to filter"> |
7
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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80 <option value="hbd">Number of hydrogen-bond donor groups</option> |
0e382252d23d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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81 <option value="hba">Number of hydrogen-bond acceptor groups</option> |
0e382252d23d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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82 <option value="psa">Total polar surface area</option> |
0
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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83 <option value="rotbonds">Number of rotatable bonds</option> |
0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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84 <option value="molwt">Molecular weight</option> |
7
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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85 <option value="logp">Predicted value of logP</option> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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86 <option value="mr">Predicted value for the molecular refractivity</option> |
0
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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87 <option value="atoms">Number of atoms</option> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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88 <option value="field">Filter by a user-defined SDF property</option> |
0
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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89 <!-- Add later, we need to add a new smarts pattern to plugindefines.txt |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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90 <option value="hatoms">Number of heavy atoms</option>--> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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91 <!-- We skip that options, for further information please read: http://www.dalkescientific.com/writings/diary/archive/2011/06/04/dealing_with_sssr.html --> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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92 <!--<option value="rings">Number of rings</option>--> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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93 </param> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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94 <when value="hbd"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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95 <param name="hbd_min" type="integer" value="" label="Minimum number of hydrogen bond donors"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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96 <param name="hbd_max" type="integer" value="" label="Maximum number of hydrogen bond donors"/> |
0
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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97 </when> |
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98 <when value="hba"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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99 <param name="hba_min" type="integer" value="" label="Minimum number of hydrogen bond acceptors"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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100 <param name="hba_max" type="integer" value="" label="Maximum number of hydrogen bond acceptors"/> |
0
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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101 </when> |
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102 <when value="psa"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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103 <param name="psa_min" type="integer" value="" label="Minimum threshold for the total polar surface area"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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104 <param name="psa_max" type="integer" value="" label="Maximum threshold for the total polar surface area"/> |
0
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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105 </when> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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106 <when value="rotbonds"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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107 <param name="rotbonds_min" type="integer" value="" label="Minimum number of rotatable bonds"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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108 <param name="rotbonds_max" type="integer" value="" label="Maximum number of rotatable bonds"/> |
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109 </when> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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110 <when value="molwt"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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111 <param name="molwt_min" type="integer" value="" label="Minimum threshold value for the molecular weight"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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112 <param name="molwt_max" type="integer" value="" label="Maximum threshold value for the molecular weight"/> |
0
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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113 </when> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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114 <when value="logp"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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115 <param name="logp_min" type="float" value="" label="Minimum threshold value for log P"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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116 <param name="logp_max" type="float" value="" label="Maximum threshold value for log P"/> |
0
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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117 </when> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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118 <when value="mr"> |
7
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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119 <param name="mr_min" type="float" value="" label="Minimum threshold value for the molecular refractivity"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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120 <param name="mr_max" type="float" value="" label="Maximum threshold value for the molecular refractivity"/> |
0
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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121 </when> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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122 <when value="atoms"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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123 <param name="atoms_min" type="integer" value="" label="Minimum number of atoms"/> |
0d6e836460be
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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124 <param name="atoms_max" type="integer" value="" label="Maximum number of atoms"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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125 </when> |
12
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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126 <when value="field"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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127 <param name="field_name" type="text" value="" label="Name of the SDF property to filter by"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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128 <sanitizer invalid_char=""> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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129 <valid initial="string.ascii_letters,string.digits"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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130 <add value="_" /> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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131 <add value="." /> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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132 <add value=" " /> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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133 </valid> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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134 </sanitizer> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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135 </param> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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136 <param name="field_min" type="integer" value="" label="Minimum value"/> |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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137 <param name="field_max" type="integer" value="" label="Maximum value"/> |
340f8d63c1f4
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"
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138 </when> |
0
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139 <!--<when value="rings"> |
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140 <param name="rings_min" type="integer" value="" label="Minimum number of rings"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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141 <param name="rings_max" type="integer" value="" label="Maximum number of rings"/> |
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142 </when>--> |
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143 </conditional> |
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144 </repeat> |
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145 </when> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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146 </conditional> |
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147 </inputs> |
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148 <outputs> |
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149 <expand macro="output_like_input"/> |
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150 </outputs> |
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151 <tests> |
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152 <test> |
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153 <param name="infile" value="ligands_with_title.sdf" ftype="sdf" /> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
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154 <param name="filter_methods_opts" value="__filter_by_name__" /> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
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155 <param name="name_file" value="name_file.txt" /> |
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156 <output name="outfile" file="filterd_by_name.sdf" ftype="sdf" lines_diff="4" /> |
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157 </test> |
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158 <test> |
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159 <param name="infile" ftype="smi" value="CID_2244.smi"/> |
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160 <param name="filter_methods_opts" value="ruleof5" /> |
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161 <output name="outfile" ftype="smi" file="ob_filter_on_CID2244.smi" /> |
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162 </test> |
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163 <test> |
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164 <param name="infile" ftype="sdf" value="CID_2244.sdf"/> |
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165 <param name="filter_methods_opts" value="user" /> |
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166 <param name="filter_sel_opts" value="field" /> |
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167 <param name="field_name" value="PUBCHEM_EXACT_MASS"/> |
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168 <param name="field_min" value="100"/> |
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169 <param name="field_max" value="200"/> |
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170 <output name="outfile" ftype="sdf" file="ob_filter_on_CID2244.sdf" lines_diff="2"/> |
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171 </test> |
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172 <!-- |
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173 Limitation of the test framework: |
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174 https://trello.com/card/disambiguated-conditional-parameters-not-supported-in-unit-tests/506338ce32ae458f6d15e4b3/820 |
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175 <test> |
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176 <param name="infile" ftype="smi" value="CID_2244.smi"/> |
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177 <param name="filter_methods_opts" value="user" /> |
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178 <param name="filter_sel_opts" value="hba" /> |
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179 <param name="hbd_min" value="0" /> |
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180 <param name="hbd_max" value="5" /> |
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181 <output name="outfile" ftype="smi" file="ob_filter_on_CID2244_2.smi" /> |
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182 </test> |
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183 --> |
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184 </tests> |
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185 <help> |
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186 <![CDATA[ |
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187 |
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188 |
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189 .. class:: infomark |
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190 |
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191 **What this tool does** |
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192 |
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193 Filters a library of compounds based on user-defined physico-chemical parameters or predefined options (e.g. Ro5, lead-like properties, etc.). Multiple parameters can be selected for more specific queries. |
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194 |
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195 ----- |
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196 |
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197 .. class:: warningmark |
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198 |
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199 **Hint** |
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200 |
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201 | If your input file is in SDF format you can use the *Compute physico-chemical properties* tool to precalulate the properties and use the filter on that precomputed dataset. This should be faster and the file can be reused, although it is larger than a SMILES file. |
0
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202 | |
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203 | For exact matches use the target value for both minimum and maximum parameters (e.g. a selection of exactly 4 rotatable bonds can be performed by selecting 4 as minimum and maximum value). |
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204 | |
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205 | Selecting the same property multiple times with different parameters will result in querying the largest overlapping subset of values for the parameter (e.g. a selection of between 0 and 3 rotatable bonds plus a selection between 2 and 4 will result in a query for compounds between 2 and 3 rotatable bonds). |
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206 |
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207 ----- |
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208 |
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209 .. class:: infomark |
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210 |
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211 **Definition of the pre-defined filtering rules** |
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212 |
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213 **# Lipinski's Rule of Five:** |
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214 =< 5 Hydrogen-bond donor groups |
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215 |
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216 =< 10 Hydrogen-bond acceptor groups |
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217 |
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218 =< 500 Molecular weight |
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219 |
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220 =< 5 octanol/water partition coefficient (log P) |
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221 |
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222 **# Lead Like properties** (Teague, Davis, Leeson, Oprea, Angew Chem Int Ed Engl. 1999 Dec 16;38(24):3743-3748): |
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223 =< 7 rotatable bonds |
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224 |
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225 =< 350 Molecular weight |
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226 |
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227 =< 3.5 octanol/water partition coefficient (log P) |
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228 |
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229 **# Drug Like properties** (Lipinski, J Pharmacol Toxicol Methods. 2000 Jul-Aug;44(1):235-49): |
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230 =< 10 Hydrogen-bond acceptor groups |
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231 |
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232 =< 8 rotatable bonds |
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233 |
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234 150 =< Molecular weight =< 500 |
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235 |
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236 =< 150 Polar Surface Area |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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237 |
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238 =< 5 octanol/water partition coefficient (log P) |
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239 |
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240 **# Fragment Like properties** (Carr RA, Congreve M, Murray CW, Rees DC, Drug Discov Today. 2005 Jul 15;10(14):987): |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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241 =< 5 rotatable bonds |
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242 |
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243 =< 250 Molecular weight |
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244 |
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245 =< 2.5 octanol/water partition coefficient (log P) |
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246 |
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247 ----- |
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248 |
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249 .. class:: infomark |
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250 |
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251 **Input** |
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252 |
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253 | - `SD-Format`_ |
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254 | - `SMILES Format`_ |
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255 |
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256 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file |
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257 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification |
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258 |
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259 ----- |
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260 |
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261 .. class:: infomark |
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262 |
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263 **Output** |
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264 |
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265 | SDF formatted coordinates of the molecules, with selected properties stored as meta-data for each compound. |
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266 | |
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267 | SMILES, InChI or mol2 formatted files containing the 1D strings or 3D coordinates of each compound. |
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268 |
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269 |
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270 |
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271 ]]> |
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272 </help> |
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273 <expand macro="citations"> |
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274 <citation type="doi">10.1186/1752-153X-2-5</citation> |
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275 </expand> |
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276 </tool> |