Mercurial > repos > fabio > srase
comparison search.xml @ 0:854be3d51221 draft
Uploaded 20171204
| author | fabio |
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| date | Mon, 04 Dec 2017 16:05:45 -0500 |
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| -1:000000000000 | 0:854be3d51221 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool name="Search" id="srase_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 #if $search_condition.sequences: | |
| 14 --sequences '${search_condition.sequences}' | |
| 15 #end if | |
| 16 --search ${search_condition.search} | |
| 17 | |
| 18 #if $search_condition.search is 0: | |
| 19 #set file_paths = ','.join( [ str( $f ) for $f in $search_condition.txtfiles ] ) | |
| 20 #if $file_paths is not 'None': | |
| 21 --files '${file_paths}' | |
| 22 #set file_names = ','.join( [ str( $f.name ) for $f in $search_condition.txtfiles ] ) | |
| 23 --names '${file_names}' | |
| 24 #end if | |
| 25 #elif $search_condition.search is 1: | |
| 26 #set file_paths = ','.join( [ str( $f ) for $f in $search_condition.fastafiles ] ) | |
| 27 #if $file_paths is not 'None': | |
| 28 --files '${file_paths}' | |
| 29 #set file_names = ','.join( [ str( $f.name ) for $f in $search_condition.fastafiles ] ) | |
| 30 --names '${file_names}' | |
| 31 #end if | |
| 32 --exact ${search_condition.exact} | |
| 33 #end if | |
| 34 | |
| 35 --sthreshold '${sthreshold}' | |
| 36 --output '${output}' | |
| 37 ]]> | |
| 38 </command> | |
| 39 <inputs> | |
| 40 <conditional name="search_condition"> | |
| 41 <param name="search" type="select" label="Search mode" help="Select a search mode between normal (slower but returns an optimal solution) and fast (faster but it is heuristic)"> | |
| 42 <option value="0" selected="true">Normal</option> | |
| 43 <option value="1">Fast</option> | |
| 44 </param> | |
| 45 <when value="0"> | |
| 46 <param format="txt" name="txtfiles" type="data" label="Select sequences" multiple="true" optional="true" help="Select one or more txt files containing a sequence. A single file can contain more sequences, one for each row. Every file will represent a query to the Sequence Read Archive Search Engine that will return a list of accession numbers in which your sequences occur on." /> | |
| 47 <param name="sequences" type="text" area="True" size="5x25" label="Manually insert sequence" optional="true" help="Optionally you can put a list of sequences (one for each row) in this text field." /> | |
| 48 </when> | |
| 49 <when value="1"> | |
| 50 <param format="fasta" name="fastafiles" type="data" label="Select fasta files" multiple="true" optional="false" help="Select one or more fasta files containing sequences. These files represent queries to the Sequence Read Archive Search Engine that will return a list of accession numbers in which your sequences occur on." /> | |
| 51 <param name="exact" type="boolean" truevalue="1" falsevalue="0" checked="False" label="Use exact algorithm" help="" /> | |
| 52 </when> | |
| 53 </conditional> | |
| 54 <param name="sthreshold" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Threshold applied to the search algorithm" /> | |
| 55 </inputs> | |
| 56 <outputs> | |
| 57 <data name="output" format="txt" label="${tool.name} on ${on_string}: SRA-SE Search Result" /> | |
| 58 </outputs> | |
| 59 | |
| 60 <help><![CDATA[ | |
| 61 Authors: Fabio Cumbo, Robert S. Harris, Chen Sun, Paul Medvedev, and Anton Nekrutenko | |
| 62 | |
| 63 Help section | |
| 64 ]]></help> | |
| 65 | |
| 66 <citations> | |
| 67 <citation type="doi">10.1101/090464</citation> | |
| 68 </citations> | |
| 69 </tool> |