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1 <?xml version="1.0"?>
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2 <tool name="Search" id="sbtas_se_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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2
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13 --search 'rrr'
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14 --sthreshold ${sthreshold}
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15 --exact 0
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0
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16
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17 #if $conditional_input_zero.inputtype_zero == '0':
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18 #set file_paths = ','.join( [ str( $f ) for $f in $conditional_input_zero.txtfiles ] )
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19 #if $file_paths is not 'None':
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20 --files '${file_paths}'
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21 #set file_names = ','.join( [ str( $f.name ) for $f in $conditional_input_zero.txtfiles ] )
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22 --names '${file_names}'
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23 #end if
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24 #elif $conditional_input_zero.inputtype_zero == '1':
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25 --sequences '${conditional_input_zero.sequences}'
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26 #end if
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27
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28 --output '${output}'
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29 ]]>
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30 </command>
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31 <inputs>
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32 <conditional name="conditional_input_zero">
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33 <param name="inputtype_zero" type="select" label="Input mode" help="Select a mode based on how do you want to specify the input">
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34 <option value="0" selected="true">By file</option>
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35 <option value="1">By manually inserted text</option>
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36 </param>
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37 <when value="0">
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38 <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." />
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39 </when>
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40 <when value="1">
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41 <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." />
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42 </when>
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43 </conditional>
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44 <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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45 </inputs>
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46 <outputs>
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47 <data name="output" format="json" label="${tool.name} on ${on_string}: AllSome Sequence Bloom Tree Search Result" />
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0
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48 </outputs>
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49
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50 <help><![CDATA[
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51 Authors: Fabio Cumbo, Robert S. Harris, Chen Sun
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52 ]]></help>
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53
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54 <citations>
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55 <citation type="doi">10.1101/090464</citation>
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56 </citations>
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57 </tool>
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