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annotate normalisation.xml.bak @ 30:fce825ec2c84 draft default tip

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planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 01b92e7e17eb8bc125451bf41684f512cf16d3c5-dirty
author oinizan
date Fri, 02 May 2025 07:44:22 +0000
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30
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1 <?xml version="1.0"?>
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2 <!--
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3 # Copyright (C) 2015 INRA
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4 #
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5 # This program is free software: you can redistribute it and/or modify
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6 # it under the terms of the GNU General Public License as published by
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7 # the Free Software Foundation, either version 3 of the License, or
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8 # (at your option) any later version.
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9 #
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10 # This program is distributed in the hope that it will be useful,
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11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 # GNU General Public License for more details.
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14 #
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15 # You should have received a copy of the GNU General Public License
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16 # along with this program. If not, see <http://www.gnu.org/licenses/>.
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17 -->
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18 <tool id="FROGS_normalisation" name="FROGS Abundance normalisation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
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19 <description>Normalise ASV abundance. </description>
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21 <macros>
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22 <import>macros.xml</import>
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23 </macros>
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24 <expand macro="requirements"/>
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26 <command detect_errors="exit_code">
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27 [<![CDATA[
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28 normalisation.py
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29 --input-biom '$input_biom'
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30 --input-fasta '$input_fasta'
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31
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32 #if $sampling_method.sampling_by_min == "yes"
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33 --sampling-by-min
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34 #else
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35 --num-reads '$sampling_method.num_reads'
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36
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37 #if $sampling_method.delete_samples == "true"
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38 --delete-samples
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39 #end if
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40 #end if
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41
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42 --output-biom '$output_biom'
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43 --output-fasta '$output_fasta'
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44 --summary-file '$summary_file'
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45 ]]>
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46 </command>
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47 <inputs>
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48 <param format="fasta" argument="--input-fasta" type="data" label="Sequence file" help="Sequence file to normalise (format: fasta)." />
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49 <param format="biom1" argument="--input-biom" type="data" label="Abundance file" help="Abundance file to normalise (format: BIOM)." />
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50 <conditional name="sampling_method">
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51 <param argument="--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">
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52 <option value="yes" selected="true">Sampling by the number of sequences of the smallest sample</option>
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53 <option value="no">Select a number of sequences</option>
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54 </param>
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55 <when value="yes"/>
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56 <when value="no">
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57 <param argument="--num-reads" type="integer" optional="true" min="1" value="" label="Number of reads" help="The final number of reads per sample." />
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58 <param argument="--delete-samples" type="select" label="Remove samples that have an initial number of reads below the number of reads to sample ?" display="radio">
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59 <option value="false">No, subsampling threshold need to at most equal to the smallest sample</option>
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60 <option value="true">Yes, subsampling threshold may be greater than the smallest sample</option>
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61 </param>
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62 </when>
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63 </conditional>
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64 </inputs>
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65 <outputs>
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66 <data format="fasta" name="output_fasta" label="${tool.name}: normalised_sequences.fasta" from_work_dir="normalised.fasta" />
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67 <data format="biom1" name="output_biom" label="${tool.name}: normalised_abundance.biom" from_work_dir="normalised.biom" />
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68 <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html" />
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69 </outputs>
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70 <tests>
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71 <test>
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72 <param name="input_fasta" value="references/08-affiliation_postprocessed.fasta"/>
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73 <param name="input_biom" value="references/08-affiliation_postprocessed.biom"/>
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74 <conditional name="sampling_method">
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75 <param name="sampling_by_min" value="no"/>
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76 <param name="num_reads" value="100"/>
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77 </conditional>
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78 <output name="summary_file" file="references/09-normalisation.html" compare="sim_size" delta="0" />
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79 <output name="summary_file" file="references/09-normalisation.html" compare="diff" lines_diff="4" />
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80 <output name="output_fasta" file="references/09-normalisation.fasta" compare="diff" lines_diff="12" />
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81 </test>
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82 </tests>
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83 <help>
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84
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85 @HELP_LOGO@
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86
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87 .. class:: infomark page-header h2
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88
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89 What it does
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90
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91 This tool keeps, in each sample, the same number of elements by random sampling.
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92
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93 .. class:: infomark page-header h2
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94
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95 Inputs/outputs
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96
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97 .. class:: h3
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98
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99 Inputs
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100
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101 **Sequence file**:
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102
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103 The sequences (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
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104
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105 **Abundance file**:
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106
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107 The abundance of each ASV in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_).
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108
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109 **Sampling method**:
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110
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111 Sequence normalisation method :
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112
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113 - **Sampling by the number of sequences of the smallest sample** : Automatically detects the number of sequences of the smallest sample, and selects this number for all other samples.
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114 - **Select number of sequences** : Manually select a number of sequences.
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115
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116 With this number, a random draw of sequences is made and once normalisation is complete, each sample will contain the specified number of sequences.
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117
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118 .. class:: warningmark
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119
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120 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.
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121
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122 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).
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123
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124 .. class:: h3
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125
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126 Outputs
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127
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128 **Sequence file** (normalised_seed.fasta):
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129
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130 The normalised sequence file (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
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131
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132 **Abundance file** (normalised_abundance.biom):
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133
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134 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;`_).
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135
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136 **Report file** (report.html):
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137
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138 Information about discarded data (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_).
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139
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140
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141 .. class:: infomark page-header h2
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142
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143
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144 @HELP_CONTACT@
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145
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146 </help>
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147 <expand macro="citations" />
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148 </tool>