Mercurial > repos > oinizan > frogs

annotate normalisation.xml @ 9:7bf54edaba24 draft

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/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
author oinizan
date Thu, 12 May 2022 10:44:30 +0000
parents 76dcbe930b1d
children ab9e3c8ab443
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
1 <?xml version="1.0"?>
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
2 <!--
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
3 # Copyright (C) 2015 INRA
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
4 #
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
5 # This program is free software: you can redistribute it and/or modify
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
6 # it under the terms of the GNU General Public License as published by
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
7 # the Free Software Foundation, either version 3 of the License, or
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
8 # (at your option) any later version.
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
9 #
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
10 # This program is distributed in the hope that it will be useful,
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
13 # GNU General Public License for more details.
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
14 #
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
15 # You should have received a copy of the GNU General Public License
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
16 # along with this program. If not, see <http://www.gnu.org/licenses/>.
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
17 -->
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
18 <tool id="FROGS_normalisation" name="FROGS Abundance normalisation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2
ea386220db3c "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 724acdef433b0c23e12c0c689da342bf5e753da2"
oinizan
parents: 0
diff changeset
19 <description>Normalise OTUs abundance.</description>
7
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
20
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
21 <macros>
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
22 <import>macros.xml</import>
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
23 </macros>
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
24 <expand macro="requirements"/>
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
25
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
26 <stdio>
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
27 <exit_code range="1:" />
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
28 <exit_code range=":-1" />
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
29 </stdio>
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
30 <command>
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
31 which normalisation.py;
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
32
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
33 normalisation.py
7
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
34 --input-biom '$input_biom'
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
35 --input-fasta '$input_fasta'
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
36 #if $sampling_method.sampling_by_min == "yes"
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
37 --sampling-by-min
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
38 #else
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
39 --num-reads $sampling_method.num_reads
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
40 #if $sampling_method.delete_samples
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
41 --delete-samples
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
42 #end if
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
43 #end if
7
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
44 --output-biom '$output_biom'
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
45 --output-fasta '$output_fasta'
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
46 --summary-file '$summary_file'
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
47 </command>
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
48 <inputs>
2
ea386220db3c "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 724acdef433b0c23e12c0c689da342bf5e753da2"
oinizan
parents: 0
diff changeset
49 <param format="fasta" name="input_fasta" type="data" label="Sequence file" help="Sequence file to normalise (format: fasta)." />
ea386220db3c "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 724acdef433b0c23e12c0c689da342bf5e753da2"
oinizan
parents: 0
diff changeset
50 <param format="biom1" name="input_biom" type="data" label="Abundance file" help="Abundance file to normalise (format: BIOM)." />
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
51 <conditional name="sampling_method">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
52 <param name="sampling_by_min" type="select" label="Sampling method" help='Sampling by the number of sequences of the smallest sample, or select a number manually' display='radio'>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
53 <option value="yes" selected="true">Sampling by the number of sequences of the smallest sample</option>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
54 <option value="no">Select a number of reads</option>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
55 </param>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
56 <when value="no">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
57 <param name="num_reads" type="integer" optional="true" min="1" value="" label="Number of reads" help="The final number of reads per sample." />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
58 <param name="delete_samples" type="boolean" label="Remove samples that have an initial number of reads below the number of reads to sample ?" />
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
59 </when>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
60 </conditional>
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
61 </inputs>
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
62 <outputs>
2
ea386220db3c "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 724acdef433b0c23e12c0c689da342bf5e753da2"
oinizan
parents: 0
diff changeset
63 <data format="fasta" name="output_fasta" label="${tool.name}: normalised_sequences.fasta" from_work_dir="normalised.fasta" />
ea386220db3c "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 724acdef433b0c23e12c0c689da342bf5e753da2"
oinizan
parents: 0
diff changeset
64 <data format="biom1" name="output_biom" label="${tool.name}: normalised_abundance.biom" from_work_dir="normalised.biom" />
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
65 <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html" />
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
66 </outputs>
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
67 <tests>
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
68 <test>
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
69 <param name="input_fasta" value="references/08-affiliation_postprocessed.fasta"/>
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
70 <param name="input_biom" value="references/08-affiliation_postprocessed.biom"/>
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
71 <conditional name="sampling_method">
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
72 <param name="sampling_by_min" value="true"/>
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
73 </conditional>
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
74 <output name="summary_file" file="references/09-normalisation.html" compare="sim_size" delta="0" />
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
75 <output name="summary_file" file="references/09-normalisation.html" compare="diff" lines_diff="4" />
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
76 <output name="output_fasta" file="references/09-normalisation.fasta" compare="diff" lines_diff="12" />
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
77 </test>
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
78 </tests>
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
79 <help>
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
80
7
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
81 @HELP_LOGO@
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
82
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
83 .. class:: infomark page-header h2
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
84
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
85 What it does
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
86
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
87 This tool keeps, in each sample, the same number of elements by random sampling.
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
88
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
89 .. class:: infomark page-header h2
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
90
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
91 Inputs/outputs
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
92
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
93 .. class:: h3
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
94
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
95 Inputs
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
96
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
97 **Sequence file**:
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
98
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
99 The sequences (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
100
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
101 **Abundance file**:
7
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
102
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
103 The abundance of each OTU in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_).
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
104
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
105 **Sampling method**:
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
106
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
107 Sequence normalisation method :
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
108
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
109 - **Sampling by the number of sequences of the smallest sample** : Automatically detects the number of reads of the smallest sample, and selects this number for all other samples.
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
110 - **Select number of reads** : Manually select a number of reads.
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
111
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
112 .. image:: static/images/icon_warning_sml.gif
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
113
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
114 If the **remove samples** option is enabled, samples whose total number of sequences is lower than the specified number will be removed inside the abundance table.
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
115 If the option is disabled, the samples will be kept in the analysis but with a number of sequences lower than the specified number (the total number of the sample).
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
116
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
117 .. class:: h3
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
118
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
119 Outputs
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
120
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
121 **Sequence file** (normalised_seed.fasta):
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
122
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
123 The normalised sequences file (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
124
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
125 **Abundance file** (normalised_abundance.biom):
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
126
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
127 The normalised abundance file. If option **remove samples** has been chosen, then the abundance table will no longer contain information about the removed samples. (format `BIOM &lt;http://biom-format.org/&gt;`_).
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
128
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
129 **Report file** (report.html):
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
130
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
131 Information about discarded data (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_).
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
132
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
133
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
134 .. class:: infomark page-header h2
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
135
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
136
7
76dcbe930b1d "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"
oinizan
parents: 6
diff changeset
137 @HELP_CONTACT@
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
138
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
139 </help>
9
7bf54edaba24 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
oinizan
parents: 7
diff changeset
140 <expand macro="citations" />
0
27f57425dc55 "planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"
oinizan
parents:
diff changeset
141 </tool>