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comparison query.xml @ 4:35593423c2e2 draft

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Uploaded 20180131
author fabio
date Wed, 31 Jan 2018 11:28:53 -0500
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3:d7b97b60d0ea 4:35593423c2e2
1 <?xml version="1.0"?>
2 <tool name="Query" id="sbtas_se_query" version="1.0.0">
3 <description>the AllSome Sequence Bloom Tree</description>
4 <requirements>
5 <requirement type="package" version="2.7.10">python</requirement>
6 <requirement type="package" version="2.18.4">requests</requirement>
7 </requirements>
8 <command detect_errors="exit_code">
9 <![CDATA[
10 python '$__tool_directory__/query.py'
11
12 --search 'rrr'
13 --sthreshold ${sthreshold}
14 --exact 0
15
16 #if $conditional_input.inputtype == '0':
17 #set file_paths = ','.join( [ str( $f ) for $f in $conditional_input.txtfiles ] )
18 #if $file_paths is not 'None':
19 --files '${file_paths}'
20 #set file_names = ','.join( [ str( $f.name ) for $f in $conditional_input.txtfiles ] )
21 --names '${file_names}'
22 #end if
23 #elif $conditional_input.inputtype == '1':
24 --sequences '${conditional_input.sequences}'
25 #end if
26
27 --outputdir 'collection_content'
28 ]]>
29 </command>
30 <inputs>
31 <conditional name="conditional_input">
32 <param name="inputtype" type="select" label="Input mode" help="Select a mode based on how do you want to specify the input">
33 <option value="0" selected="true">By file</option>
34 <option value="1">By manually inserted text</option>
35 </param>
36 <when value="0">
37 <param format="tabular" name="txtfiles" type="data" label="Select files" multiple="true" optional="true" help="Select one or more tabular files containing (ID, TRANSCRIPT) touples for each line. The content of these files will be merged and the result will represent a query to the AllSome Sequence Bloom Tree Search Engine that will return a collection containing a file for each id. The content of these files as result of the tool will be a list of accession numbers." />
38 </when>
39 <when value="1">
40 <param name="sequences" type="text" area="True" size="5x25" label="Manually insert sequences" optional="true" help="Insert a list of (ID, TRANSCRIPT) touples in a tab delimited format, one for each line. The content of this text box will represent a query to the AllSome Sequence Bloom Tree Search Engine that will return a collection containing a file for each id. The content of these files as result of the tool will be a list of accession numbers." />
41 </when>
42 </conditional>
43 <param name="sthreshold" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Search threshold" help="This threshold controls the specificity. Lower values will produce more hits to the query. Higher values are more stringent and will produce fewer hits." />
44 </inputs>
45 <outputs>
46 <collection name="output_collect" type="list" label="AllSome Sequence Bloom Tree Search Collection">
47 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;ext&gt;[^_]+)" directory="collection_content" ext="tabular" />
48 </collection>
49 </outputs>
50
51 <help><![CDATA[
52 The AllSome Sequence Bloom Tree Search Engine is a fast querying tool to identify all publicly available
53 sequenced samples which express a transcript of interest.
54
55 ----
56
57 **Example**
58
59 The input for this tool is a list of (ID, TRANSCRIPT) touples, one for each line,
60 in a tab delimited format::
61
62 seq_id_0 CCAACCAAAGGGAAAACTTTTTTCCGACTTTGGCCTAAAGGGTTTAACGGCCAAGTCAGAAGGGAAAAAGTTGCGCCA
63 seq_id_1 TTAATGACAGGGCCACATGATGTGAAAAAAAATCAGAAACCGAGTCAACGTGAGAAGATAGTACGTACTACCGCAAAT
64 ...
65 seq_id_n CAATTAATGATAAATATTTTATAAGGTGCGGAAATAAAGTGAGGAATATCTTTTAAATTCAAGTTCAATTCTGAAAGC
66
67 The output of the tool is a collection that contains a file for each ID with a list of
68 accession numbers representing the samples that express one particular transcript.
69
70 ----
71
72 .. class:: infomark
73
74 **Notes**
75
76 This Galaxy tool has been developed by Fabio Cumbo.
77
78 Please visit this GithHub_repository_ for more information about the AllSome Sequence Bloom Tree Search Engine
79
80 .. _GithHub_repository: https://github.com/fabio-cumbo/bloomtree-allsome-search-engine
81 ]]></help>
82
83 <citations>
84 <citation type="doi">10.1101/090464</citation>
85 </citations>
86 </tool>