Mercurial > repos > frogs > frogs_3_1_0

comparison r_import_data.xml @ 0:59bc96331073 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:59bc96331073
1 <?xml version="1.0"?>
2 <!--
3 # Copyright (C) 2017 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 name="FROGSSTAT Phyloseq Import Data" id="FROGSSTAT_Phyloseq_Import_Data" version="3.1">
19 <description>from 3 files: biomfile, samplefile, treefile </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>r_import_data.py --biomfile $biomfile
28
29 --samplefile $samplefile
30 #if $treefile
31 --treefile $treefile
32 #end if
33 --ranks "$ranks"
34 #if $normalization
35 --normalization
36 #end if
37 --html $html
38 --rdata $data
39 </command>
40 <inputs>
41 <!-- Files -->
42 <param format="biom1" name="biomfile" type="data" label="Standard biom file" help="The file contains the OTU informations (format: biom1)." optional="false">
43 <validator type="empty_field" message="This parameter is required." />
44 </param>
45
46 <param format="tabular" name="samplefile" type="data" label="Sample tsv file" help="The file contains the samples informations (format: tabular)." optional="false">
47 <validator type="empty_field" message="This parameter is required." />
48 </param>
49
50 <param format="nhx" name="treefile" type="data" label="Tree file" help="The file contains the tree informations (format: Newick - nhx or nwk)." optional="true" />
51
52 <!-- Parameters -->
53 <param name="ranks" type="text" label="Names of taxonomics levels" help="The ordered taxonomic levels stored in BIOM. Each level is separated by one space." value="Kingdom Phylum Class Order Family Genus Species" size="80" optional="false"/>
54 <param name="normalization" type="boolean" label="Do you want to normalise your data ?" help="To normalise data before analysis." optional="false" />
55 </inputs>
56 <outputs>
57 <data format="rdata" name="data" label="${tool.name}: data.Rdata" from_work_dir="data.Rdata"/>
58 <data format="html" name="html" label="${tool.name}: summary.html" from_work_dir="summary.html"/>
59 </outputs>
60 <tests>
61 <test>
62 <param name="biomfile" value="input/chaillou.biom"/>
63 <param name="samplefile" value="input/sample_metadata.tsv"/>
64 <param name="treefile" value="input/tree.nwk"/>
65 <output name="data" value="references/14-phylo_import.Rdata" compare="sim_size" delta="10"/>
66 </test>
67 </tests>
68 <help>
69
70 .. image:: static/images/frogs_images/FROGS_logo.png
71 :height: 144
72 :width: 110
73
74 .. class:: infomark page-header h2
75
76 What it does
77
78 Launch Rmarkdown script to import data from 3 files: biomfile, samplefile, treefile into a `phyloseq &lt;https://joey711.github.io/phyloseq/&gt;`_ object.
79
80 .. class:: infomark page-header h2
81
82 Inputs/Outputs
83
84 .. class:: h3
85
86 Input
87
88 **OTU biom file**:
89
90 The OTU biom file (format `biom1 &lt;http://biom-format.org/documentation/format_versions/biom-1.0.html&gt;`_).
91 This file is the result of FROGS BIOM to std BIOM.
92 The example of biom file:
93
94 .. image:: static/images/frogs_images/biomfile.png
95 :height: 30
96 :width: 733
97
98 **Newick file** (tree.nwk):
99
100 Newick file (format `nxh &lt;https://en.wikipedia.org/wiki/Newick_format&gt;`_) is the result of FROGS Tree:
101
102 .. image:: static/images/frogs_images/nwk_treefile.png
103
104 **Sample file**:
105 The file contains the conditions of experiment with sample ID in the first column:
106
107 .. image:: static/images/frogs_images/phyloseq_samplefile.png
108 :height: 115
109 :width: 369
110
111 .. class:: h3
112
113 Output
114
115 **Html file** (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_): The summary of phyloseq object.
116
117 .. image:: static/images/frogs_images/phyloseq_import_data_html.png
118
119 **Data file** (format rdata): The informations of data in one phyloseq object.
120
121
122 .. class:: infomark page-header h2
123
124 **Contact**
125
126 Contacts: frogs@inra.fr
127
128 Repository: https://github.com/geraldinepascal/FROGS
129 website: http://frogs.toulouse.inra.fr/
130
131 Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.*
132
133 </help>
134 <citations>
135 <citation type="doi">10.1093/bioinformatics/btx791</citation>
136 </citations>
137
138 </tool>