Mercurial > repos > fabio > sbtas_se
comparison search.xml @ 0:00d6e82d74e9 draft
Uploaded 20180122
| author | fabio |
|---|---|
| date | Mon, 22 Jan 2018 16:41:50 -0500 |
| parents | |
| children | 4291c9d1ff07 |
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| -1:000000000000 | 0:00d6e82d74e9 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool name="Search" id="sbtas_se_search" version="1.0.0"> | |
| 3 <description>your sequences in the big SRA data lake</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2.7.10">python</requirement> | |
| 6 <requirement type="package" version="2.18.4">requests</requirement> | |
| 7 <requirement type="package" version="0.9.7">requests-futures</requirement> | |
| 8 </requirements> | |
| 9 <command detect_errors="exit_code"> | |
| 10 <![CDATA[ | |
| 11 python '$__tool_directory__/search.py' | |
| 12 | |
| 13 --treeid '0' | |
| 14 --search '0' | |
| 15 --sthreshold '${sthreshold}' | |
| 16 --exact '0' | |
| 17 | |
| 18 #if $conditional_input_zero.inputtype_zero == '0': | |
| 19 #set file_paths = ','.join( [ str( $f ) for $f in $conditional_input_zero.txtfiles ] ) | |
| 20 #if $file_paths is not 'None': | |
| 21 --files '${file_paths}' | |
| 22 #set file_names = ','.join( [ str( $f.name ) for $f in $conditional_input_zero.txtfiles ] ) | |
| 23 --names '${file_names}' | |
| 24 #end if | |
| 25 #elif $conditional_input_zero.inputtype_zero == '1': | |
| 26 --sequences '${conditional_input_zero.sequences}' | |
| 27 #end if | |
| 28 | |
| 29 --output '${output}' | |
| 30 ]]> | |
| 31 </command> | |
| 32 <inputs> | |
| 33 <conditional name="conditional_input_zero"> | |
| 34 <param name="inputtype_zero" type="select" label="Input mode" help="Select a mode based on how do you want to specify the input"> | |
| 35 <option value="0" selected="true">By file</option> | |
| 36 <option value="1">By manually inserted text</option> | |
| 37 </param> | |
| 38 <when value="0"> | |
| 39 <param format="txt" name="txtfiles" type="data" label="Select sequences" multiple="true" optional="true" help="Select one or more txt files containing a sequence. A single file can contain more sequences, one for each row. Every file will represent a query to the AllSome Sequence Bloom Tree Search Engine that will return a list of accession numbers. It is worth noting that the result could be empty." /> | |
| 40 </when> | |
| 41 <when value="1"> | |
| 42 <param name="sequences" type="text" area="True" size="5x25" label="Manually insert sequence" optional="true" help="Insert a list of sequences (one for each row) in this text field representing a query to the AllSome Sequence Bloom Tree Search Engine. It is worth noting that the result could be empty." /> | |
| 43 </when> | |
| 44 </conditional> | |
| 45 <param name="sthreshold" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Threshold applied to the search algorithm" /> | |
| 46 </inputs> | |
| 47 <outputs> | |
| 48 <data name="output" format="txt" label="${tool.name} on ${on_string}: AllSome Sequence Bloom Tree Search Result" /> | |
| 49 </outputs> | |
| 50 | |
| 51 <help><![CDATA[ | |
| 52 Authors: Fabio Cumbo, Robert S. Harris, Chen Sun | |
| 53 ]]></help> | |
| 54 | |
| 55 <citations> | |
| 56 <citation type="doi">10.1101/090464</citation> | |
| 57 </citations> | |
| 58 </tool> |