Mercurial > repos > frogs > frogs_2_0_0

comparison clusters_stat.xml @ 0:76c750c5f0d1 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/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
author frogs
date Thu, 25 Oct 2018 05:01:13 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:76c750c5f0d1
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_clusters_stat" name="FROGS Clusters stat" version="1.4.0">
19 <description>Process some metrics on clusters.</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>
28 clusters_stat.py
29 --input-biom $biom
30 --output-file $summary_file
31 </command>
32 <inputs>
33 <param format="biom1" name="biom" type="data" label="Abundance file" help="Clusters abundance (format: BIOM)." optional="false" />
34 </inputs>
35 <outputs>
36 <data format="html" name="summary_file" label="${tool.name}: summary.html" from_work_dir="summary.html"/>
37 </outputs>
38 <tests>
39 <test>
40 <param name="biom" value="references/04-affiliation.biom"/>
41 <output name="summary_file" value="references/05-clustersStat.html" compare="sim_size" delta="0"/>
42 </test>
43 </tests>
44 <help>
45
46 .. image:: static/images/FROGS_logo.png
47 :height: 144
48 :width: 110
49
50
51 .. class:: infomark page-header h2
52
53 What it does
54
55 FROGS Clusters stat computes several metrics and generates a HTML file describing clusters based on abundances, samples, ...
56
57
58 .. class:: infomark page-header h2
59
60 Input/output
61
62 .. class:: h3
63
64 Input
65
66 **Abundance file**:
67
68 The abundance of each cluster in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_).
69
70 The FROGS's tools working on clusters and others metagenomic workflows produce files in BIOM format.
71
72 .. class:: h3
73
74 Output
75
76 **Summary file** (summary.html):
77
78 Clusters metrics (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_):
79
80 *Clusters distribution* : describes the sizes distribution of all clusters thank to boxplot and tables
81
82 .. image:: static/images/FROGS_cluster_stat_clusterDistrib1.png
83 :height: 426
84 :width: 520
85
86 .. image:: static/images/FROGS_cluster_stat_clusterDistrib2.png
87 :height: 300
88 :width: 460
89
90 *Sequences distributions* : describes the sequences distribution among clusters
91
92 .. image:: static/images/FROGS_cluster_stat_seq_dist.png
93 :height: 326
94 :width: 473
95
96 *Samples distribution* : describes clusters distribution among sample and give an `hierarchical clustering &lt;http://en.wikipedia.org/wiki/Hierarchical_clustering&gt;`_ on samples abundance profile (distance method = `braycurtis &lt;http://fr.wikipedia.org/wiki/Distance_de_Bray-Curtis&gt;`_, linkage method = average)
97
98 .. image:: static/images/FROGS_cluster_stat_sample_dist1.png
99 :height: 400
100 :width: 700
101
102 .. image:: static/images/FROGS_cluster_stat_sample_dist2.png
103 :height: 350
104 :width: 610
105
106 .. class:: infomark page-header h2
107
108 Advices
109
110 This is a very usefull tool to see the evolution of your OTU. Do not hesitate to run this tool after each FROGS step beginning at the clustering step.
111
112
113 ----
114
115 **Contact**
116
117 Contacts: frogs@inra.fr
118
119 Repository: https://github.com/geraldinepascal/FROGS
120
121 Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Hernadez-Raquet G., Pascal G., 2015. FROGS: Find Rapidly OTU with Galaxy Solution. In: The environmental genomic Conference, Montpellier, France,* http://bioinfo.genotoul.fr/fileadmin/user_upload/FROGS_2015_GE_Montpellier_poster.pdf
122
123 Depending on the help provided you can cite us in acknowledgements, references or both.
124 </help>
125 <citations>
126 <citation type="doi">10.7287/peerj.preprints.386v1</citation>
127 </citations>
128 </tool>