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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 - 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 #set formats = ''
13 #set filepaths = ''
14 #set filenames = ''
15 #set compressed = ''
16 #set minab = ''
17 #set qthres = ''
18 #for $i, $exp in enumerate( $experiments ):
19 #set formats += str( $exp.conditional_format.format ) + '|'
20 #if $exp.conditional_format.format == 'accessions':
21 #set filepaths += str( $exp.conditional_format.accession_numbers ) + '|'
22 #set filenames += str( $exp.conditional_format.accession_numbers.name ) + '|'
23 #set compressed += '0|'
24 #else:
25 #if $exp.conditional_format.format == 'fasta':
26 #set compressed += str( $exp.conditional_format.conditional_fasta_compressed.fasta_compressed ) + '|'
27 #if $exp.conditional_format.conditional_fasta_compressed.fasta_compressed == 0:
28 #set filepaths += ','.join( [ str( $f ) for $f in $exp.conditional_format.conditional_fasta_compressed.fastafiles ] ) + '|'
29 #set filenames += ','.join( [ str( $f.name ) for $f in $exp.conditional_format.conditional_fasta_compressed.fastafiles ] ) + '|'
30 #else:
31 #set filepaths += ','.join( [ str( $f ) for $f in $exp.conditional_format.conditional_fasta_compressed.fastagzfiles ] ) + '|'
32 #set filenames += ','.join( [ str( $f.name ) for $f in $exp.conditional_format.conditional_fasta_compressed.fastagzfiles ] ) + '|'
33 #end if
34 #elif $exp.conditional_format.format == 'fastq':
35 #set compressed += str( $exp.conditional_format.conditional_fastq_compressed.fastq_compressed ) + '|'
36 #if $exp.conditional_format.conditional_fastq_compressed.fastq_compressed == 0:
37 #set filepaths += ','.join( [ str( $f ) for $f in $exp.conditional_format.conditional_fastq_compressed.fastqfiles ] ) + '|'
38 #set filenames += ','.join( [ str( $f.name ) for $f in $exp.conditional_format.conditional_fastq_compressed.fastqfiles ] ) + '|'
39 #else:
40 #set filepaths += ','.join( [ str( $f ) for $f in $exp.conditional_format.conditional_fastq_compressed.fastqgzfiles ] ) + '|'
41 #set filenames += ','.join( [ str( $f.name ) for $f in $exp.conditional_format.conditional_fastq_compressed.fastqgzfiles ] ) + '|'
42 #end if
43 #end if
44 #end if
45 #set minab += str( $exp.min_abundance ) + '|'
46 #if $exp.conditional_quality.quality_control == '1':
47 #set qthres += str( $exp.conditional_quality.quality_threshold ) + '|'
48 #else:
49 #set qthres += '-1.0|'
50 #end if
51 #end for
52 #set klen = $kmer_len
53 #set bfsize = -1
54 #if $bloomsize_condition.bloomsize_control == '0':
55 #set bfsize = $bloomsize_condition.bloom_filter_size
56 #end if
57
58 --formats '${formats}'
59 --filepaths '${filepaths}'
60 --filenames '${filenames}'
61 --compressed '${compressed}'
62 --minabundances '${minab}'
63 --qualitythresholds '${qthres}'
64
65 --klen ${klen}
66 --bfsize ${bfsize}
67
68 --outfile '${resulttxt}'
69 --outdir 'sbt'
70 --tooldir '$__tool_directory__'
71 ]]>
72 </command>
73 <inputs>
74 <repeat name="experiments" title="Select a list of experiments" help="Select a set of experiments on which the Sequence Bloom Tree will be built." min="1">
75 <conditional name="conditional_format">
76 <param name="format" type="select" label="Select the experiment format" help="FASTA and FASTQ are the supported formats">
77 <option value="fasta">FASTA Experiments</option>
78 <option value="fastq">FASTQ Experiments</option>
79 <option value="accessions">SRA Accession Numbers</option>
80 </param>
81 <when value="fasta">
82 <conditional name="conditional_fasta_compressed">
83 <param name="fasta_compressed" type="boolean" checked="true" truevalue="1" falsevalue="0" label="Are your experiments compressed?" />
84 <when value="0">
85 <param format="fasta" name="fastafiles" multiple="true" type="data" label="Select one or more FASTA experiments" />
86 </when>
87 <when value="1">
88 <param format="fastagz" name="fastagzfiles" multiple="true" type="data" label="Select one or more FASTA .gz experiments" />
89 </when>
90 </conditional>
91 </when>
92 <when value="fastq">
93 <conditional name="conditional_fastq_compressed">
94 <param name="fastq_compressed" type="boolean" checked="true" truevalue="1" falsevalue="0" label="Are youe experiments compressed?" />
95 <when value="0">
96 <param format="fastq" name="fastqfiles" multiple="true" type="data" label="Select one or more FASTQ experiments" />
97 </when>
98 <when value="1">
99 <param format="fastqgz" name="fastqgzfiles" multiple="true" type="data" label="Select one or more FASTQ .gz experiments" />
100 </when>
101 </conditional>
102 </when>
103 <when value="accessions">
104 <param name="accession_numbers" type="data" format="tabular" label="Select a list of SRA Accession Numbers" help="Select a tabular file with a list of accession numbers in the first column." />
105 </when>
106 </conditional>
107
108 <param name="min_abundance" type="integer" value="2" min="0" label="Insert a Bloom filter minimum abundance" help="This value is the minimum abundance cutoff for the creation of the Bloom filter." />
109
110 <conditional name="conditional_quality">
111 <param name="quality_control" type="boolean" checked="false" truevalue="1" falsevalue="0" label="Apply a quality control procedure" />
112 <when value="1">
113 <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 whole experiment will be excluded." />
114 </when>
115 </conditional>
116 </repeat>
117
118 <param name="kmer_len" type="integer" value="21" min="0" label="K-mer length" />
119
120 <conditional name="bloomsize_condition">
121 <param name="bloomsize_control" type="boolean" checked="true" truevalue="1" falsevalue="0" label="Automatically estimate the Bloom filter size" />
122 <when value="0">
123 <param name="bloom_filter_size" size="1" type="integer" value="1" min="1" label="Bloom Filter size" help="Disable this field to let the tool estimate an appropriate Bloom filter size." />
124 </when>
125 </conditional>
126 </inputs>
127 <outputs>
128 <collection name="list_output" type="list" label="${tool.name} SBT Collection">
129 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*(?=\.)).(?P&lt;ext&gt;[^\.]*$)" ext="auto" directory="sbt" />
130 </collection>
131 <data format="txt" name="resulttxt" label="${tool.name} SBT: Result" from_work_dir="sbtres.txt" />
132 </outputs>
133
134 <help><![CDATA[
135 This tool allows to create Sequence Bloom Trees starting from a set of FASTA or FASTQ files.
136 It also allows to control the quality of the input dataset and exclude the files that do not reach a specified quality level.
137
138 -----
139
140 **Input file**
141
142 The input of this tool is a set of FASTA or FASTQ experiments, additionally to a set of SRA accession numbers.
143 For each of the selected experiments, the minimum abundance for the corresponding Bloom filter is required.
144 Additionally, a quality control procedure could be applied to guarantee that the quality of every experiment always exceed a
145 specified treshold. Otherwise, experiments with low quality level will be discarded.
146
147 The k-mer length must also be specified, additionally to the Bloom filter size. This last field is optional and it will be
148 automatically estimated if not provided.
149
150 -----
151
152 **Output**
153
154 This tool returns a collection containing the Sequence Bloom Tree nodes and a file representing the organization of the tree.
155
156 Take a look at the Query tool documentation for a detailed description about how
157 to query a Sequence Bloom Tree.
158
159 -----
160
161 .. class:: infomark
162
163 **Notes**
164
165 This Galaxy tool has been developed by Fabio Cumbo.
166
167 Please visit this GithHub_repository_ for more information about the BloomTree Manager
168
169 .. _GithHub_repository: https://github.com/fabio-cumbo/bloomtree-manager
170 ]]></help>
171
172 <expand macro="citations" />
173 </tool>