Mercurial > repos > frogs > frogs_3_1_0
comparison clusters_stat.xml @ 0:59bc96331073 draft default tip
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
author | frogs |
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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_clusters_stat" name="FROGS Clusters stat" version="3.1"> | |
19 <description>Process some metrics on clusters.</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 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/06-affiliation.biom"/> | |
41 <output name="summary_file" value="references/08-clustersStat.html" compare="sim_size" delta="0"/> | |
42 </test> | |
43 </tests> | |
44 <help> | |
45 | |
46 .. image:: static/images/frogs_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 <http://biom-format.org/>`_). | |
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 <https://en.wikipedia.org/wiki/HTML>`_): | |
79 | |
80 *Clusters distribution* : describes the sizes distribution of all clusters thank to boxplot and tables | |
81 | |
82 .. image:: static/images/frogs_images/FROGS_cluster_stat_clusterDistrib1.png | |
83 :height: 426 | |
84 :width: 520 | |
85 | |
86 .. image:: static/images/frogs_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_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 <http://en.wikipedia.org/wiki/Hierarchical_clustering>`_ on samples abundance profile (distance method = `braycurtis <http://fr.wikipedia.org/wiki/Distance_de_Bray-Curtis>`_, linkage method = average) | |
97 | |
98 .. image:: static/images/frogs_images/FROGS_cluster_stat_sample_dist1.png | |
99 :height: 400 | |
100 :width: 700 | |
101 | |
102 .. image:: static/images/frogs_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 website: http://frogs.toulouse.inra.fr/ | |
121 | |
122 Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.* | |
123 | |
124 </help> | |
125 <citations> | |
126 <citation type="doi">10.1093/bioinformatics/btx791</citation> | |
127 </citations> | |
128 </tool> |