Mercurial > repos > bgruening > rdock_sort_filter
annotate sort_filter.xml @ 4:c88da0252e85 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"
author | bgruening |
---|---|
date | Mon, 04 May 2020 07:42:00 -0400 |
parents | a6ec6c55267e |
children | d1ca4b45f615 |
rev | line source |
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2
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
diff
changeset
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1 <tool id="rdock_sort_filter" name="SDF sort and filter" version="0.2.0"> |
0
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
changeset
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2 <description>using the sdsort provided with rDock</description> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
changeset
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3 <macros> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
changeset
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4 <import>rdock_macros.xml</import> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
changeset
|
5 </macros> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
changeset
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6 <expand macro="requirements"/> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
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7 <command><![CDATA[ |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
changeset
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8 |
2
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
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9 cat '$input' |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
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10 #if $filter |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
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11 | sdfilter -f'$filter' |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
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12 #end if |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
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13 #if $name_field |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
diff
changeset
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14 | sdsort -n $descending -s -f'$sort_field' -id'$name_field' |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
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15 | sdfilter -f'\$_COUNT <= $top' -s'$name_field' |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
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changeset
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16 #end if |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
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17 #if $global_sort and $sort_field |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
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changeset
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18 | sdsort -n $descending -f'$sort_field' |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
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changeset
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19 #end if |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
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changeset
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20 > '$output' |
0
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
changeset
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21 |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
changeset
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22 ]]></command> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
changeset
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23 |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
changeset
|
24 <inputs> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
changeset
|
25 <param type="data" name="input" format="sdf" label="Molecules" help="Molecules in SDF format"/> |
2
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
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26 |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
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changeset
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27 <param name="filter" type="text" label="Filter expression" optional="true" help="Perl expression for filter"> |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
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changeset
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28 <sanitizer> |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
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changeset
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29 <valid initial="string.printable"> |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
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changeset
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30 <remove value="'"/> |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
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31 <remove value="""/> |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
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32 <remove value="@"/> |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
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33 <remove value="#"/> |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
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34 <remove value="|"/> |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
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35 </valid> |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
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36 <mapping initial="none"/> |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
diff
changeset
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37 </sanitizer> |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
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changeset
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38 </param> |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
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39 |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
diff
changeset
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40 <param name="sort_field" type="text" label="Field to sort on" optional="true" help="Name of the field to sort records by"> |
0
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
changeset
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41 <sanitizer> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
changeset
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42 <valid initial="string.printable"> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
changeset
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43 <remove value="'"/> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
changeset
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44 </valid> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
changeset
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45 <mapping initial="none"/> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
changeset
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46 </sanitizer> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
changeset
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47 </param> |
2
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
diff
changeset
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48 <param name="descending" type="boolean" label="Sort descending" truevalue="-r" falsevalue="" checked="true" |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
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49 help="Sort ascending or descending"/> |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
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50 <param name="global_sort" type="boolean" label="Global sort" checked="true" |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
diff
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51 help="Sort all records in file after filtering (true) or just sort within the blocks identified by $name_field (false)"/> |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
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52 |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
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53 <param name="name_field" type="text" label="Grouping field name" optional="true" help="Name of the field to group records by (must be sequential)"> |
0
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
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54 <sanitizer> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
changeset
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55 <valid initial="string.printable"> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
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56 <remove value="'"/> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
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57 </valid> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
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58 <mapping initial="none"/> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
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59 </sanitizer> |
2
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
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60 </param> |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
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61 <param name="top" type="integer" value="1" label="Number of records to keep in output" optional="true" help="Number of best scoring records to keep"/> |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
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62 |
0
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
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63 </inputs> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
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64 <outputs> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
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65 <data name="output" format="sdf" label="SDF sort+filter on ${on_string}"/> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
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66 </outputs> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
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67 <tests> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
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68 <test> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
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69 <param name="input" value="poses.sdf"/> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
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70 <param name="sort_field" value="TransFSScore"/> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
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71 <param name="name_field" value="Name"/> |
2
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
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72 <param name="descending" value="True"/> |
a6ec6c55267e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
bgruening
parents:
0
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73 <output name="output" file="poses-descending.sdf" ftype="sdf"/> |
0
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
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74 </test> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
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75 <test> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
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76 <param name="input" value="poses.sdf"/> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
diff
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77 <param name="sort_field" value="TransFSScore"/> |
784a9f7f079e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 9ffbed897a816616ac05c479dcff75103cf9a7e8"
bgruening
parents:
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78 <param name="name_field" value="Name"/> |
784a9f7f079e
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79 <param name="descending" value="False"/> |
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80 <output name="output" file="poses-ascending.sdf" ftype="sdf"/> |
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81 </test> |
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82 <test> |
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83 <param name="input" value="poses.sdf"/> |
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84 <param name="filter" value="$TransFSScore > 0.2"/> |
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85 <param name="sort_field" value="TransFSScore"/> |
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86 <param name="name_field" value="Name"/> |
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87 <param name="descending" value="False"/> |
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88 <output name="output" file="poses-filt-0.2.sdf" ftype="sdf"/> |
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89 </test> |
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90 <test> |
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91 <param name="input" value="poses.sdf"/> |
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92 <param name="filter" value="$TransFSScore > 0.1 and $TransFSScore > 0.2"/> |
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93 <param name="sort_field" value="TransFSScore"/> |
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94 <param name="name_field" value="Name"/> |
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95 <param name="descending" value="False"/> |
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96 <output name="output" file="poses-filt-0.2.sdf" ftype="sdf"/> |
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97 </test> |
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98 <test> |
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99 <param name="input" value="poses.sdf"/> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
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100 <param name="sort_field" value="TransFSScore"/> |
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101 <param name="name_field" value="Name"/> |
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102 <param name="descending" value="True"/> |
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103 <param name="global_sort" value="False"/> |
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104 <output name="output" file="poses-desc-noglobal.sdf" ftype="sdf"/> |
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105 </test> |
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106 <test> |
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107 <param name="input" value="poses.sdf"/> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
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108 <param name="filter" value="$TransFSScore > 0.2"/> |
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109 <output name="output" file="poses-filt-only.sdf" ftype="sdf"/> |
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110 </test> |
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111 </tests> |
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112 <help><![CDATA[ |
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113 |
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114 .. class:: infomark |
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115 |
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116 This tool sorts and filters SD files using the sdsort and sdfilter tools from the rDock suite. |
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117 See http://rdock.sourceforge.net/ for more details about rDock and associated programs. |
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118 The expected use is for filtering and sorting virtual screening results such as docking. |
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119 |
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120 ----- |
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121 |
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122 .. class:: infomark |
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123 |
784a9f7f079e
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124 **Inputs** |
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125 An SD-file, together with names of fields to filter, sort and group records by, and the number of records to appear in the output. |
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126 |
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127 An optional filter can be specified that is first applied to the records. This filter (the 'filter' parameter) must be |
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128 specified as required by the 'sdfilter' application (see http://rdock.sourceforge.net/wp-content/uploads/2015/08/rDock_User_Guide.pdf) |
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129 which is a Perl expression. As an example, if your SDF has a field name 'SCORE' which has numeric values then a valid |
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130 filter expression would be '$SCORE > 90' (note the $ symbol). |
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131 If you require to use multiple filters then you can combine them in a single expression like this: |
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132 '$A < 5 and $B <7', or '$A < 5 or $B <7' |
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133 |
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134 The sorting is then performed on groups of molecules, with the groups being identified by a field in the SD-file (the 'name_field' |
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135 parameter). Records from a group MUST be sequential in the input file. If 'name_field' is not specified then this grouping |
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136 and sorting step is skipped. Sorting is performed by the rDock 'sdsort' application. |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
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137 The records within each group are sorted by the value of a field in the SD-file (the 'sort_field' parameter) and you can |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
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138 specify ascending or descending order (the 'descending' parameter). |
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139 Then a number of top scoring (the 'top' parameter, typically having a value of 1) are retained. |
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140 |
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141 Finally, if the 'global_sort' parameter is set to 'True' then the all the records remaining are sorted according to the |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db76c3bc4ced257e2f622fcf8fcc6d2e28de3577"
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142 'sort_field' and 'descending' parameters. Note: this step can use lots of memory if the files are very big. |
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143 |
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144 ----- |
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145 |
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146 .. class:: infomark |
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147 |
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148 **Outputs** |
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149 An SD-file, containing molecules filtered and sorted according to the parameters. |
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150 |
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151 ]]></help> |
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152 <expand macro="citations"/> |
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153 </tool> |