Mercurial > repos > frogs > frogs_2_0_0
comparison r_import_data.xml @ 0:76c750c5f0d1 draft default tip
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
author | frogs |
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date | Thu, 25 Oct 2018 05:01:13 -0400 |
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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="1.0.0"> | |
19 <description>from 3 files: biomfile, samplefile, treefile </description> | |
20 <requirements> | |
21 <requirement type="package" version="2.0.1">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 #if $samplefile | |
29 --samplefile $samplefile | |
30 #end if | |
31 --treefile $treefile | |
32 --ranks "$ranks" | |
33 #if $normalization | |
34 --normalization | |
35 #end if | |
36 --html $html | |
37 --rdata $data | |
38 </command> | |
39 <inputs> | |
40 <!-- Files --> | |
41 <param format="biom1" name="biomfile" type="data" label="Standard biom file" help="The file contains the OTU informations (format: biom1)." optional="false"> | |
42 <validator type="empty_field" message="This parameter is required." /> | |
43 </param> | |
44 | |
45 <param format="tabular" name="samplefile" type="data" label="Sample tsv file" help="The file contains the samples informations (format: tabular)." optional="false"> | |
46 <validator type="empty_field" message="This parameter is required." /> | |
47 </param> | |
48 | |
49 <param format="nhx" name="treefile" type="data" label="Tree file" help="The file contains the tree informations (format: Newick - nhx or nwk)." optional="true" /> | |
50 | |
51 <!-- Parameters --> | |
52 <param name="ranks" type="text" label="Names of taxonomics levels" help="The ordered taxonomic levels stored in BIOM. Each level is separated by one space." value="Kingdom Phylum Class Order Family Genus Species" size="80" optional="false"/> | |
53 <param name="normalization" type="boolean" label="Do you want to normalise your data ?" help="To normalise data before analysis." optional="false" /> | |
54 </inputs> | |
55 <outputs> | |
56 <data format="rdata" name="data" label="${tool.name}: data.Rdata" from_work_dir="data.Rdata"/> | |
57 <data format="html" name="html" label="${tool.name}: summary.html" from_work_dir="summary.html"/> | |
58 </outputs> | |
59 <tests> | |
60 <test> | |
61 <param name="biomfile" value="references/chaillou.biom"/> | |
62 <param name="samplefile" value="references/sample_metadata.tsv"/> | |
63 <param name="treefile" value="references/tree.nwk"/> | |
64 <output name="data" value="references/11-phylo_import.Rdata"/> | |
65 </test> | |
66 </tests> | |
67 | |
68 <help> | |
69 | |
70 .. image:: static/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 <https://joey711.github.io/phyloseq/>`_ 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 <http://biom-format.org/documentation/format_versions/biom-1.0.html>`_). | |
91 This file is the result of FROGS BIOM to std BIOM. | |
92 The example of biom file: | |
93 | |
94 .. image:: static/images/biomfile.png | |
95 :height: 30 | |
96 :width: 733 | |
97 | |
98 **Newick file** (tree.nwk): | |
99 | |
100 Newick file (format `nxh <https://en.wikipedia.org/wiki/Newick_format>`_) is the result of FROGS Tree: | |
101 | |
102 .. image:: static/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/phyloseq_samplefile.png | |
108 :height: 115 | |
109 :width: 369 | |
110 | |
111 .. class:: h3 | |
112 | |
113 Output | |
114 | |
115 **Html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): The summary of phyloseq object. | |
116 | |
117 .. image:: static/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 | |
130 Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf | |
131 | |
132 Depending on the help provided you can cite us in acknowledgements, references or both. | |
133 | |
134 </help> | |
135 <citations> | |
136 <citation type="doi">10.7287/peerj.preprints.386v1</citation> | |
137 </citations> | |
138 </tool> |