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annotate frogsfunc_pathways.xml @ 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
parents 646bee69560f
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1 <?xml version="1.0"?>
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2 <!--
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3 # Copyright (C) 2022 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="FROGSFUNC_step3_pathways" name="FROGSFUNC_3_pathways" version= "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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19 <description>Calculates pathway abundances in each sample. </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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25 <expand macro="requirements_frogsfunc" />
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26
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27 <command detect_errors="exit_code">
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28 [<![CDATA[
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29 frogsfunc_pathways.py
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30 --input-file $input_file
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31
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32 #if $normalisation
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33 --normalisation
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34 #end if
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36 --map $map_file.value
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37 --summary $summary_file
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38 ]]>
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39 </command>
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40 <inputs>
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41 <!-- Input files -->
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42 <param argument="--input-file" format="tsv" type="data" label="Function abundance file" help="TSV function abundances table from FROGSFUNC_2_functions tool, FROGSFUNC_2_functions_unstrat_EC.tsv for Metacyc database or FROGSFUNC_2_functions_unstrat_KO.tsv for Kegg database (unstratified table)." optional="false"/>
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44 <!-- References -->
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45 <param name="category" type="select" label="Taxonomic marker" help="Taxonomic marker of interest." multiple="false" display="radio">
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46 <options from_data_table="frogs_picrust2_pathways">
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47 <column name='name' index='2' />
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48 <column name='value' index='2' />
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49 <filter type="unique_value" column='2'/>
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50 <validator type="no_options" message="A built-in database is not available" />
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51 </options>
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52 </param>
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53 <param name="map_file" type='select' label="Pathway reference" help="For 16S marker, choose Metacyc or KEGG in accordance with your choice in the FROGSFUNC_1_placeseqs_copynumbers tool. For ITS or 18S marker, Metacyc is the only valid option." optional="false" multiple='false' display='radio'>
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54 <options from_data_table="frogs_picrust2_pathways">
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55 <column name='name' index='1'/>
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56 <column name='value' index='3'/>
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57 <filter type="param_value" ref="category" column="2" />
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58 <validator type="no_options" message="A built-in database is not available" />
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59 </options>
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60 </param>
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62 <!-- Parameters-->
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63 <param argument="--normalisation" label="Do you want to normalize the final output table ?" help='Values are divided by sum of columns, then multiplied by 10^6 (CPM values).' type="boolean" />
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64 </inputs>
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65 <outputs>
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66 <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html"/>
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67 <data format="tsv" name="abund" label="${tool.name}: frogsfunc_pathways_unstrat.tsv" from_work_dir="frogsfunc_pathways_unstrat.tsv"/>
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68 </outputs>
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70 <tests>
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71 <test>
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72 <param name="input_file" value="references/27-frogsfunc_functions_unstrat.tsv" />
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73 <param name="category" value="16S" />
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74 <param name="map_file" value="Metacyc" />
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76 <output name="abund" file="references/28-frogsfunc_pathways_unstrat.tsv" compare="diff" lines_diff="0" />
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77 <output name="summary_file" file="references/28-frogsfunc_pathways_report.html" compare="diff" lines_diff="0" />
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78 </test>
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79 </tests>
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81 <help>
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83 @HELP_LOGO@
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85 .. class:: infomark page-header h2
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87 What it does
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88
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89 **FROGSFUNC_3_pathways** is the last step of `PICRUSt2 &lt;https://github.com/picrust/picrust2&gt;`_. This script infers MetaCyc/KEGG pathway abundances based on **EC** or **KO** number abundances.
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90
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91 - Regroups EC or KO numbers to MetaCyc or KEGG reactions, depending of the unstrat abundances input file.
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92 - Infers which MetaCyc or KEGG pathways are present based on these reactions with `MinPath &lt;http://omics.informatics.indiana.edu/MinPath/&gt;`_.
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93 - Calculates and returns the abundance of pathways identified as present.
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95 .. class:: infomark page-header h2
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97 Inputs/Outputs
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99 .. class:: h3
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101 Input
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102
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103 **-Function prediction abundance file (EC or KO)-**:
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104
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105 TSV function abundances table from FROGSFUNC_2_functions tool, frogsfunc_functions_unstrat_EC.tsv or frogsfunc_functions_unstrat_KO.tsv (unstratified table).
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106
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107 **-Taxonomic marker-**:
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108
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109 Output table of predicted marker gene copy numbers per sequence from FROGSFUNC_1_placeseqs tool. (frogsfunc_marker.tsv)
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110
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111 **-Pathway reference-**:
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112
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113 Mapping of pathways to reactions.
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114
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115 - For 16S marker, choose Metacyc or KEGG in accordance with your choice in the FROGSFUNC_2_functions tool. If you want both, run this tool twice.
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116 - For ITS or 18S marker, Metacyc is the only valid option.
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118
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119 **-Do you want to normalize the final output table ?-**:
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120
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121 If this option is set, the pathway abundances file (frogsfunc_functions_unstrat.tsv) is normalized: values are divided by sum of columns, then multiplied by 10^6 (Count Per Million values).
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122
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123 .. class:: warningmark
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125 This normalization allows to compare the samples between them. But to perform more precise statistical analysis, some tools as **DESeq2 need the non-normalized abundance table** to perform the normalization by themselves. So be careful which table to use for further analysis.
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127 .. class:: h3
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129 Outputs
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130
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131 **-HTML report-**:
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133 The HTML file summarizes information about pathway abundances within each sample.
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135 .. image:: FROGS_frogsfunc_pathways_sunburst.png
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137
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138 **-Pathways abundances tables - unstratified-**:
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140 It is the pathways abundance predictions of metagenome, per sample. (frogsfunc_pathways_unstrat.tsv)
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142 - Classification column: the hierarchy classification of the pathway.
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143 - db_link column: the url on the link accession ID (observation_name) of the pathway.
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144 - observation_name: Accession identifier
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145 - last columns: Abundances of these pathway in each samples.
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150 @HELP_CONTACT@
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152 </help>
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154 <expand macro="citations" />
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156 </tool>