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1 <?xml version="1.0"?>
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2 <tool name="Search" id="srase_search" version="1.0.0">
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3 <description>your sequences in the big SRA data lake</description>
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4 <requirements>
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5 <requirement type="package" version="2.7.10">python</requirement>
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6 <requirement type="package" version="2.18.4">requests</requirement>
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7 <requirement type="package" version="0.9.7">requests-futures</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 python '$__tool_directory__/search.py'
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12
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13 #if $search_condition.sequences:
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14 --sequences '${search_condition.sequences}'
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15 #end if
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16 --search ${search_condition.search}
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17
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18 #if $search_condition.search is 0:
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19 #set file_paths = ','.join( [ str( $f ) for $f in $search_condition.txtfiles ] )
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20 #if $file_paths is not 'None':
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21 --files '${file_paths}'
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22 #set file_names = ','.join( [ str( $f.name ) for $f in $search_condition.txtfiles ] )
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23 --names '${file_names}'
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24 #end if
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25 #elif $search_condition.search is 1:
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26 #set file_paths = ','.join( [ str( $f ) for $f in $search_condition.fastafiles ] )
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27 #if $file_paths is not 'None':
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28 --files '${file_paths}'
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29 #set file_names = ','.join( [ str( $f.name ) for $f in $search_condition.fastafiles ] )
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30 --names '${file_names}'
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31 #end if
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32 --exact ${search_condition.exact}
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33 #end if
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34
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35 --sthreshold '${sthreshold}'
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36 --output '${output}'
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37 ]]>
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38 </command>
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39 <inputs>
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40 <conditional name="search_condition">
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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)">
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42 <option value="0" selected="true">Normal</option>
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43 <option value="1">Fast</option>
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44 </param>
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45 <when value="0">
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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." />
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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." />
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48 </when>
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49 <when value="1">
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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." />
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51 <param name="exact" type="boolean" truevalue="1" falsevalue="0" checked="False" label="Use exact algorithm" help="" />
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52 </when>
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53 </conditional>
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54 <param name="sthreshold" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Threshold applied to the search algorithm" />
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55 </inputs>
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56 <outputs>
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57 <data name="output" format="txt" label="${tool.name} on ${on_string}: SRA-SE Search Result" />
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58 </outputs>
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59
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60 <help><![CDATA[
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61 Authors: Fabio Cumbo, Robert S. Harris, Chen Sun, Paul Medvedev, and Anton Nekrutenko
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62
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63 Help section
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64 ]]></help>
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65
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66 <citations>
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67 <citation type="doi">10.1101/090464</citation>
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68 </citations>
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69 </tool>
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