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Uploaded 20190118
author fabio
date Fri, 18 Jan 2019 10:12:19 -0500
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15:9d2b9e65d73e 16:ba9d0fc8657f
1 <?xml version="1.0"?>
2 <tool name="BloomTree Manager - Create" id="btman_create" 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 '$__tool_directory__/create.py'
11
12 --explist '${explist}'
13
14 --qualitycontrol ${conditional_quality.quality_control}
15 #if $conditional_quality.quality_control == '0':
16 --qualitythreshold 0.0
17 #elif $conditional_quality.quality_control == '1':
18 --qualitythreshold ${conditional_quality.quality_threshold}
19 #end if
20
21 --klen ${kmer_len}
22 --minabundance ${min_abundance}
23
24 --outfile '${outfile}'
25 ]]>
26 </command>
27 <inputs>
28 <param format="tabular" name="explist" type="data" label="Select a file with the list of experiments" help="This should be a tabular file with two columns. Take a look at the tool documentation for a detailed explanation about the its content." />
29
30 <conditional name="conditional_quality">
31 <param name="quality_control" type="boolean" checked="false" truevalue="1" falsevalue="0" label="Apply a quality control procedure" />
32 <when value="1">
33 <param name="quality_threshold" size="1" type="float" value="0.8" min="0.0" max="1.0" label="Quality threshold" help="If the number of sequences flagged as poor quality on the total number of sequences in a file is less than this threshold, the sequence file will be excluded." />
34 </when>
35 </conditional>
36
37 <param name="kmer_len" type="integer" value="21" min="0" label="K-mer length" />
38 <param name="min_abundance" type="integer" value="2" min="0" label="Bloom filter minimum abundance" help="This value is the minimum abundance cutoff for the creation of the Bloom filters. It is worth noting that the same minimum abundance is used for each Bloom filter." />
39 </inputs>
40 <outputs>
41 <data format="txt" name="outfile" label="${tool.name} SBT: Result" from_work_dir="btman.create.txt" />
42 </outputs>
43
44 <help><![CDATA[
45 This tool is part of the BloomTree Manager Framework that allow to create a Sequence Bloom Tree starting
46 with a set of FASTA or FASTQ files. It allows also to control the quality of the input dataset and
47 exclude the files that do not reach a specified quality level.
48
49 -----
50
51 **Input file**
52
53 The input file for this tool must contain two columns with their values delimited by a tab.
54 The first column contains a list of SRA accessions, and the second column contains a unique identifier
55 for each set of SRA accessions.
56
57 The input file is structured like the example below::
58
59 SRR805782 blood
60 SRR837459 blood
61 SRR837458 blood
62 SRR837453 blood
63 SRR837456 blood
64 ...
65 SRR791048 breast
66 SRR553483 breast
67 SRR553482 breast
68 SRR791045 breast
69 ...
70 SRR950876 brain
71 SRR786621 brain
72
73 It is worth noting that for each cluster of accessions, every accession should be unique.
74 It is indeed possible to repeat an accession in multiple clusters.
75
76 The tool will create a Sequence Bloom Tree for each cluster of accessions.
77
78 -----
79
80 **Output**
81
82 The tool returns a single text file only. It contains the a tree identifier, one for
83 each cluster of accessions specified in the input file, that can be used with the
84 Query tool of the BloomTree Manager Suite to search for the presence of a set of
85 specific transcripts.
86
87 Take a look at the Query tool documentation for a detailed description about how
88 to query a Sequence Bloom Tree.
89
90 -----
91
92 .. class:: infomark
93
94 **Notes**
95
96 This Galaxy tool has been developed by Fabio Cumbo.
97
98 Please visit this GithHub_repository_ for more information about the BloomTree Manager
99
100 .. _GithHub_repository: https://github.com/fabio-cumbo/bloomtree-manager
101 ]]></help>
102
103 <expand macro="citations" />
104 </tool>