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comparison query.xml @ 19:7f712cc0d3d5 draft

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Uploaded 20190304.2
author fabio
date Mon, 04 Mar 2019 08:31:28 -0500
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18:be864d79c9c7 19:7f712cc0d3d5
1 <?xml version="1.0"?>
2 <tool name="BloomTree Manager - Query" id="btman_query" version="1.0.0">
3 <description>a Sequence Bloom Tree</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code">
9 <![CDATA[
10 python '$__tool_directory__/query.py'
11
12 #set coll_paths = ','.join( [ str( $f ) for $f in $treecollection ] )
13 #if $coll_paths is not 'None':
14 --treep '${coll_paths}'
15 #set coll_names = ','.join( [ str( $f.name ) for $f in $treecollection ] )
16 --treen '${coll_names}'
17 #end if
18
19 #set file_paths = ','.join( [ str( $f ) for $f in $txtfiles ] )
20 #if $file_paths is not 'None':
21 --files '${file_paths}'
22 #set file_names = ','.join( [ str( $f.name ) for $f in $txtfiles ] )
23 --names '${file_names}'
24 #end if
25
26 --threshold ${threshold}
27 --sort ${sort}
28
29 --outputdir 'answer_collection'
30 --outfile '${resulttxt}'
31 ]]>
32 </command>
33 <inputs>
34 <param name="treecollection" type="data_collection" collection_type="list" label="Select a Sequence Bloom Tree" help="Select a collection generated by the Create tool of the BloomTree Manager suite." />
35 <param format="tabular" name="txtfiles" type="data" label="Select query files" multiple="true" optional="false" help="Select one or more tabular files containing (ID, TRANSCRIPT) couples for each line. The content of these files will be merged and the result will represent a query to the Sequence Bloom Tree 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." />
36 <param name="threshold" size="1" type="float" value="0.7" min="0.0" max="1.0" label="Search threshold" help="Fraction of query kmers that must be present in a leaf to be considered a match." />
37 <param name="sort" type="boolean" checked="true" truevalue="1" falsevalue="0" label="Sort matched leaves by the number of query kmers present, and report the number of kmers present (if not selected we just report the matched leaves without regard to which matches are better)." />
38 </inputs>
39 <outputs>
40 <collection name="output_collect" type="list:list" label="BloomTree Manager - Query result collection">
41 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)_(?P&lt;ext&gt;[^_]+)" directory="answer_collection" ext="auto" />
42 </collection>
43 <data format="txt" name="resulttxt" label="${tool.name} SBT: Result" from_work_dir="query.txt" />
44 </outputs>
45
46 <help><![CDATA[
47 This tool is part of the BloomTree Manager Framework that allow to rapidly identify all
48 sequenced samples which express a transcript of interest.
49
50 ----
51
52 The input for this tool is a list of (ID, TRANSCRIPT) couples, one for each line,
53 in a tab delimited format::
54
55 id0 CCAACCAAAGGGAAAACTTTTTTCCGACTTTGGCCTAAAGGGTTTAACGGCCAAGTCAGAAGGGAAAAAGTTGCGCCA
56 id1 TTAATGACAGGGCCACATGATGTGAAAAAAAATCAGAAACCGAGTCAACGTGAGAAGATAGTACGTACTACCGCAAAT
57 ...
58 idn CAATTAATGATAAATATTTTATAAGGTGCGGAAATAAAGTGAGGAATATCTTTTAAATTCAAGTTCAATTCTGAAAGC
59
60 The ID can contain alphanumeric characters in addition to spaces, dots, dashes, and round and square brackets.
61 Any additional character will be trimmed out.
62
63 The Sequence Bloom Tree identifier must be also specified. It is a string that identify an existing Sequence
64 Bloom Tree, which should be built with the Create tool of the BloomTree Manager Suite.
65
66 The output of the tool is a list of collections in which every collection contains a file for each ID with a list of
67 accession numbers representing the samples that express one particular transcript.
68
69 ----
70
71 .. class:: infomark
72
73 **Notes**
74
75 This Galaxy tool has been developed by Fabio Cumbo.
76
77 Please visit this GithHub_repository_ for more information about the BloomTree Manager
78
79 .. _GithHub_repository: https://github.com/fabio-cumbo/bloomtree-manager
80 ]]></help>
81
82 <expand macro="citations" />
83 </tool>