|
0
|
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>
|
