Mercurial > repos > fabio > btman
comparison query.xml @ 10:1af09c5ec0a1 draft
Uploaded 20180413
author | fabio |
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date | Fri, 13 Apr 2018 07:51:29 -0400 |
parents | 8d8a8fe0022e |
children | ba9d0fc8657f |
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9:c144495810c2 | 10:1af09c5ec0a1 |
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10 python '$__tool_directory__/query.py' | 10 python '$__tool_directory__/query.py' |
11 | 11 |
12 --tree 1 | 12 --tree 1 |
13 --search 'rrr' | 13 --search 'rrr' |
14 --sthreshold ${sthreshold} | 14 --sthreshold ${sthreshold} |
15 --sort ${sortcontrol} | |
15 --exact 0 | 16 --exact 0 |
16 | 17 |
17 #if $conditional_input.inputtype == '0': | 18 #if $conditional_input.inputtype == '0': |
18 #set file_paths = ','.join( [ str( $f ) for $f in $conditional_input.txtfiles ] ) | 19 #set file_paths = ','.join( [ str( $f ) for $f in $conditional_input.txtfiles ] ) |
19 #if $file_paths is not 'None': | 20 #if $file_paths is not 'None': |
40 <when value="1"> | 41 <when value="1"> |
41 <param name="sequences" type="text" area="True" size="5x25" label="Manually insert sequences" optional="false" help="Insert a list of (ID, TRANSCRIPT) couples in a tab delimited format, one for each line. The content of this text box will represent a query to the Sequence Bloom Tree that will return a collection containing a file for each ID. The content of these files as result of the tool will be a list of accession numbers." /> | 42 <param name="sequences" type="text" area="True" size="5x25" label="Manually insert sequences" optional="false" help="Insert a list of (ID, TRANSCRIPT) couples in a tab delimited format, one for each line. The content of this text box will represent a query to the Sequence Bloom Tree that will return a collection containing a file for each ID. The content of these files as result of the tool will be a list of accession numbers." /> |
42 </when> | 43 </when> |
43 </conditional> | 44 </conditional> |
44 <param name="sthreshold" size="3" type="float" value="0.7" min="0.0" max="1.0" label="Search threshold" help="This threshold controls the specificity. Lower values will produce more hits to the query. Higher values are more stringent and will produce fewer hits." /> | 45 <param name="sthreshold" size="3" type="float" value="0.7" min="0.0" max="1.0" label="Search threshold" help="This threshold controls the specificity. Lower values will produce more hits to the query. Higher values are more stringent and will produce fewer hits." /> |
46 <param name="sortcontrol" type="boolean" checked="true" truevalue="1" falsevalue="0" label="Sort the result by the number of hits per transcript." /> | |
45 </inputs> | 47 </inputs> |
46 <outputs> | 48 <outputs> |
47 <collection name="output_collect" type="list" label="BloomTree Manager - Query result collection"> | 49 <collection name="output_collect" type="list" label="BloomTree Manager - Query result collection"> |
48 <discover_datasets pattern="(?P<identifier_0>[^_]+)_(?P<ext>[^_]+)" directory="collection_content" ext="auto" /> | 50 <discover_datasets pattern="(?P<identifier_0>[^_]+)_(?P<ext>[^_]+)" directory="collection_content" ext="auto" /> |
49 </collection> | 51 </collection> |