Mercurial > repos > bgruening > rxdock_sort_filter

annotate sort_filter.xml @ 0:475cde209992 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5"
author bgruening
date Sat, 04 Apr 2020 15:08:15 -0400
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children 7be0793dd448
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475cde209992 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5"
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1 <tool id="rxdock_sort_filter" name="SDF sort and filter" version="0.1.0">
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2 <description>using the sdsort provided with rxDock</description>
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3 <macros>
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4 <import>rdock_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command><![CDATA[
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8
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9 sdsort -n $descending -s -f'$sort_field' -id'$name_field' '$input' |
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10 sdfilter -f'\$_COUNT <= $top' -s'$name_field' |
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11 sdsort -n $descending -f'$sort_field' > '$output'
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12
475cde209992 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5"
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13 ]]></command>
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475cde209992 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5"
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15 <inputs>
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16 <param type="data" name="input" format="sdf" label="Molecules" help="Molecules in SDF format"/>
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17 <param name="top" type="integer" value="1" label="Number of records to keep in output" help="Number of best scoring records to keep"/>
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18 <param name="sort_field" type="text" label="Field to sort on" optional="false" help="Name of the field to sort records by">
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19 <sanitizer>
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20 <valid initial="string.printable">
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21 <remove value="&apos;"/>
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22 </valid>
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23 <mapping initial="none"/>
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24 </sanitizer>
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25 </param>
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26 <param name="name_field" type="text" label="Grouping field name" optional="false" help="Name of the field to group records by (must be sequential)">
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27 <sanitizer>
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28 <valid initial="string.printable">
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29 <remove value="&apos;"/>
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30 </valid>
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31 <mapping initial="none"/>
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32 </sanitizer>
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33 </param>
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34 <param name="descending" type="boolean" label="Sort descending" truevalue="-r" falsevalue="" checked="true"
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35 help="Generate the name field (first line) for cases where this is empty"/>
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36 </inputs>
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37 <outputs>
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38 <data name="output" format="sdf" label="SDF sort+filter on ${on_string}"/>
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="input" value="poses.sdf"/>
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43 <param name="sort_field" value="TransFSScore"/>
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44 <param name="name_field" value="Name"/>
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45 <output name="output" file="poses-descending.sdf" ftype="sdf" />
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46 </test>
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47 <test>
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48 <param name="input" value="poses.sdf"/>
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49 <param name="sort_field" value="TransFSScore"/>
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50 <param name="name_field" value="Name"/>
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51 <param name="descending" value="False"/>
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52 <output name="output" file="poses-ascending.sdf" ftype="sdf" />
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53 </test>
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54 </tests>
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55 <help><![CDATA[
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56
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57 .. class:: infomark
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58
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59 This tool sorts and filters SD files using the sdsort and sdfilter tools from the rxDock suite.
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60 See https://www.rxdock.org for more details about rxDock and associated programs.
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61 The expected use is for filtering and sorting virtual screening results such as docking.
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62
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63 -----
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64
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65 .. class:: infomark
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66
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67 **Inputs**
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68 An SD-file, together with names of fields to sort and group records by, and the number of records to appear in the output.
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69 The sorting is performed on groups of molecules, with the group being identified by a field in the SDF (the name_field
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70 parameter). Records from a group MUST be sequential.
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71 The records within each group are sorted by the value of a field in the SDF (the sort_field parameter) and you can
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72 specify ascending or descending order (the descending parameter).
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73 Finally a number of top scoring (the top parameter, typically having a value of 1) are written to the output.
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74
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75 -----
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77 .. class:: infomark
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78
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79 **Outputs**
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80 An SD-file, containing molecules filtered by the field specified.
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81
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82 ]]></help>
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83 <expand macro="citations"/>
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84 </tool>