annotate query.xml @ 4:69a3505ac594 draft

Uploaded 20180405
author fabio
date Wed, 04 Apr 2018 18:54:40 -0400
parents a4abcc1e7459
children 8d8a8fe0022e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
1 <?xml version="1.0"?>
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
2 <tool name="BloomTree Manager - Query" id="btman_query" version="1.0.0">
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
3 <description>the Sequence Bloom Tree</description>
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
4 <requirements>
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
5 <requirement type="package" version="2.7.10">python</requirement>
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
6 <requirement type="package" version="2.18.4">requests</requirement>
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
7 </requirements>
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
8 <command detect_errors="exit_code">
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
9 <![CDATA[
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
10 python '$__tool_directory__/query.py'
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
11
4
69a3505ac594 Uploaded 20180405
fabio
parents: 2
diff changeset
12 --tree 1
0
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
13 --search 'rrr'
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
14 --sthreshold ${sthreshold}
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
15 --exact 0
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
16
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
17 #if $conditional_input.inputtype == '0':
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
18 #set file_paths = ','.join( [ str( $f ) for $f in $conditional_input.txtfiles ] )
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
19 #if $file_paths is not 'None':
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
20 --files '${file_paths}'
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
21 #set file_names = ','.join( [ str( $f.name ) for $f in $conditional_input.txtfiles ] )
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
22 --names '${file_names}'
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
23 #end if
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
24 #elif $conditional_input.inputtype == '1':
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
25 --sequences '${conditional_input.sequences}'
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
26 #end if
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
27
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
28 --outputdir 'collection_content'
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
29 --errorfile 'Error Log File'
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
30 ]]>
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
31 </command>
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
32 <inputs>
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
33 <conditional name="conditional_input">
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
34 <param name="inputtype" type="select" label="Input mode" help="Select a mode based on how do you want to specify the input">
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
35 <option value="0" selected="true">By file</option>
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
36 <option value="1">By manually inserted text</option>
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
37 </param>
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
38 <when value="0">
2
a4abcc1e7459 Uploaded 20180404
fabio
parents: 0
diff changeset
39 <param format="tabular" name="txtfiles" type="data" label="Select 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." />
0
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
40 </when>
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
41 <when value="1">
2
a4abcc1e7459 Uploaded 20180404
fabio
parents: 0
diff changeset
42 <param name="sequences" type="text" area="True" size="5x25" label="Manually insert sequences" optional="false" help="Insert a list of (ID, TRANSCRIPT) couples in a tab delimited format, one for each line. The content of this text box 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." />
0
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
43 </when>
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
44 </conditional>
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
45 <param name="sthreshold" size="3" type="float" value="0.7" 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." />
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
46 </inputs>
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
47 <outputs>
2
a4abcc1e7459 Uploaded 20180404
fabio
parents: 0
diff changeset
48 <collection name="output_collect" type="list" label="BloomTree Manager - Query result collection">
0
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
49 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;ext&gt;[^_]+)" directory="collection_content" ext="auto" />
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
50 </collection>
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
51 </outputs>
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
52
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
53 <help><![CDATA[
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
54 This Query tool is part of the BloomTree Manager Framework that allow to rapidly identify all publicly available
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
55 sequenced samples which express a transcript of interest.
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
56
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
57 ----
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
58
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
59 The input for this tool is a list of (ID, TRANSCRIPT) couples, one for each line,
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
60 in a tab delimited format::
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
61
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
62 id0 CCAACCAAAGGGAAAACTTTTTTCCGACTTTGGCCTAAAGGGTTTAACGGCCAAGTCAGAAGGGAAAAAGTTGCGCCA
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
63 id1 TTAATGACAGGGCCACATGATGTGAAAAAAAATCAGAAACCGAGTCAACGTGAGAAGATAGTACGTACTACCGCAAAT
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
64 ...
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
65 idn CAATTAATGATAAATATTTTATAAGGTGCGGAAATAAAGTGAGGAATATCTTTTAAATTCAAGTTCAATTCTGAAAGC
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
66
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
67 The ID can contain alphanumeric characters in addition to spaces, dots, dashes, and round and square brackets.
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
68 Any additional character will be trimmed out.
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
69
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
70 The output of the tool is a collection that contains a file for each ID with a list of
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
71 accession numbers representing the samples that express one particular transcript.
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
72
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
73 ----
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
74
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
75 .. class:: infomark
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
76
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
77 **Notes**
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
78
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
79 This Galaxy tool has been developed by Fabio Cumbo.
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
80
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
81 Please visit this GithHub_repository_ for more information about the BloomTree Manager
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
82
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
83 .. _GithHub_repository: https://github.com/fabio-cumbo/bloomtree-manager
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
84 ]]></help>
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
85
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
86 <citations>
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
87 <citation type="doi">10.1101/090464</citation>
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
88 </citations>
315246810bfa Uploaded 20180404
fabio
parents:
diff changeset
89 </tool>