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planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
author frogs
date Thu, 28 Feb 2019 10:14:49 -0500
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1 <?xml version="1.0"?>
2 <!--
3 # Copyright (C) 2015 INRA
4 #
5 # This program is free software: you can redistribute it and/or modify
6 # it under the terms of the GNU General Public License as published by
7 # the Free Software Foundation, either version 3 of the License, or
8 # (at your option) any later version.
9 #
10 # This program is distributed in the hope that it will be useful,
11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 # GNU General Public License for more details.
14 #
15 # You should have received a copy of the GNU General Public License
16 # along with this program. If not, see <http://www.gnu.org/licenses/>.
17 -->
18 <tool id="FROGS_remove_chimera" name="FROGS Remove chimera" version="3.1">
19 <description>Remove PCR chimera in each sample.</description>
20 <requirements>
21 <requirement type="package" version="3.1.0">frogs</requirement>
22 </requirements>
23 <stdio>
24 <exit_code range="1:" />
25 <exit_code range=":-1" />
26 </stdio>
27 <command>
28 remove_chimera.py
29 --nb-cpus \${GALAXY_SLOTS:-1}
30 --input-fasta $sequence_file --non-chimera $non_chimera_fasta
31 --summary $summary_file
32 #if $abundance_type.abundance_type_selected == "biom"
33 --input-biom $abundance_biom
34 --out-abundance $out_abundance_biom
35 #else
36 --input-count $abundance_count
37 --out-abundance $out_abundance_count
38 #end if
39 </command>
40 <inputs>
41 <!-- Files -->
42 <param format="fasta" name="sequence_file" type="data" label="Sequences file" help="The sequences file (format: fasta)." optional="false" />
43 <conditional name="abundance_type">
44 <param name="abundance_type_selected" type="select" label="Abundance type" help="Select the type of file where the abundance of each sequence by sample is stored.">
45 <option value="biom" selected="true">BIOM file</option>
46 <option value="count">TSV file</option>
47 </param>
48 <when value="biom">
49 <param format="biom1" name="abundance_biom" type="data" label="Abundance file" help="It contains the count by sample for each sequence." optional="false" />
50 </when>
51 <when value="count">
52 <param format="tabular" name="abundance_count" type="data" label="Count file" help="It contains the count by sample for each sequence (see below)." optional="false" />
53 </when>
54 </conditional>
55 </inputs>
56 <outputs>
57 <data format="fasta" name="non_chimera_fasta" label="${tool.name}: non_chimera.fasta" from_work_dir="non_chimera.fasta"/>
58 <data format="biom1" name="out_abundance_biom" label="${tool.name}: non_chimera_abundance.biom" from_work_dir="non_chimera_abundance.biom">
59 <filter>abundance_type['abundance_type_selected'] == "biom"</filter>
60 </data>
61 <data format="tabular" name="out_abundance_count" label="${tool.name}: non_chimera_abundance.tsv" from_work_dir="non_chimera_abundance.tsv">
62 <filter>abundance_type['abundance_type_selected'] == "count"</filter>
63 </data>
64 <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html"/>
65 </outputs>
66 <tests>
67 <test>
68 <param name="sequence_file" value="references/02-clustering.fasta"/>
69 <conditional name="abundance_type">
70 <param name="abundance_type_selected" value="biom"/>
71 <param name="abundance_biom" value="references/02-clustering.biom" />
72 </conditional>
73 <output name="non_chimera_fasta" file="references/03-chimera.fasta"/>
74 </test>
75 </tests>
76 <help>
77
78 .. image:: static/images/frogs_images/FROGS_logo.png
79 :height: 144
80 :width: 110
81
82
83 .. class:: infomark page-header h2
84
85 What it does
86
87 Remove chimeric sequences by sample.
88
89
90 .. class:: infomark page-header h2
91
92 Context
93
94 Chimeras are sequences formed from two or more biological sequences joined together.
95
96 The majority of these anomalous sequences are formed from an incomplete extension during a PCR cycle. During subsequent cycles, a partially extended strand can bind to a template derived from a different but similar sequence.
97
98 This phenomena is particularly common in amplicon sequencing where closely related sequences are amplified.
99
100
101 .. class:: infomark page-header h2
102
103 Inputs/Outputs
104
105 .. class:: h3
106
107 Inputs
108
109 **Sequence file**:
110
111 The sequences (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
112
113 **Abundance file**:
114
115 The abundance of each cluster in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_).
116
117 OR
118
119 The abundance of each sequence in each sample (format `TSV &lt;https://en.wikipedia.org/wiki/Tab-separated_values&gt;`_). This type of file is produced by *FROGS pre-process*.
120
121 Example::
122
123 #id splA splB
124 seq1 1289 2901
125 seq2 3415 0
126
127 .. class:: h3
128
129 Outputs
130
131 **Sequence file** (non_chimera.fasta):
132
133 The sequence file with only non-chimera (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
134
135 **Abundance file** (non_chimera.biom or non_chimera.tsv):
136
137 The abundance file with only non-chimera (format the same of the abundance input).
138
139 **Summary file** (report.html):
140
141 This file presents the number of removed elements (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_).
142
143
144 .. class:: infomark page-header h2
145
146 How it works
147
148 .. csv-table::
149 :header: "Steps", "Description"
150 :widths: 10, 90
151 :class: table table-striped
152
153 "1", "Split input data by sample (classicaly the PCR is realised by sample)."
154 "2", "Find chimera in each sample (`vsearch &lt;https://github.com/torognes/vsearch&gt;`_)."
155 "3", "Remove the sequences identify as chimera in all samples where they are present."
156
157
158 ----
159
160 **Contact**
161
162 Contacts: frogs@inra.fr
163
164 Repository: https://github.com/geraldinepascal/FROGS
165 website: http://frogs.toulouse.inra.fr/
166
167 Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.*
168
169 </help>
170 <citations>
171 <citation type="doi">10.1093/bioinformatics/btx791</citation>
172 </citations>
173
174 </tool>