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annotate frogsfunc_pathways.xml @ 9:7bf54edaba24 draft

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planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty
author oinizan
date Thu, 12 May 2022 10:44:30 +0000
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9
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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_step4_pathways" name="FROGSFUNC_step4_pathways" version= "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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19 <description>Inference of pathway-level abundances. </description>
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20
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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 <stdio>
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28 <exit_code range="1:" />
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29 <exit_code range=":-1" />
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30 </stdio>
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31 <command >
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32 frogsfunc_pathways.py
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33 --input-file $input_file
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34 #if $normalisation
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35 --normalisation
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36 #end if
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37 --map $map_file.value
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38
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39 #if $category.value == "16S"
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40 #if $map_file.fields.name == "Kegg"
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41 --no-regroup
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42 #end if
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43 #end if
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44 --html $summary_file
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45 </command>
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46 <inputs>
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47 <!-- Input files -->
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48 <param argument="--input-file" format="tabular" name="input_file" type="data" label="Function abundance file" help="TSV function abundances table from FROGSFUNC_step3_function tool, frogsfunc_functions_unstrat.tsv (unstratified table)." optional="false"/>
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49
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50 <!-- References -->
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51 <param name="category" type="select" label="Taxonomic marker" help="Taxonomic marker of interest." multiple="false" display="radio">
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52 <options from_data_table="frogs_picrust2_pathway_map">
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53 <column name='name' index='2' />
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54 <column name='value' index='2' />
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55 <filter type="unique_value" column='2'/>
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56 <validator type="no_options" message="A built-in database is not available" />
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57 </options>
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58 </param>
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59 <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_step2_copynumbers tool. For ITS or 18S marker, Metacyc is the only valid option." optional="false" multiple='false' display='radio'>
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60 <options from_data_table="frogs_picrust2_pathway_map">
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61 <column name='name' index='1'/>
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62 <column name='value' index='3'/>
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63 <filter type="param_value" ref="category" column="2" />
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64 <validator type="no_options" message="A built-in database is not available" />
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65 </options>
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66 </param>
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67
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68 <!-- Parameters-->
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69 <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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70 </inputs>
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71 <outputs>
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72 <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html"/>
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73 <data format="tabular" name="abund" label="${tool.name}: frogsfunc_pathways_unstrat.tsv" from_work_dir="frogsfunc_pathways_unstrat.tsv"/>
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74 </outputs>
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75
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76 <tests>
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77 <test>
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78 <param name="input_file" value="input/frogsfunc_functions_unstrat.tsv" />
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79 <param name="category" value="16S" />
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80
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81 <output name="abund" file="references/28-frogsfunc_pathways_unstrat.tsv" compare="diff" lines_diff="0" />
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82 <output name="summary_file" file="references/28-frogsfunc_pathways_report.html" compare="diff" lines_diff="0" />
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83 </test>
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84 </tests>
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85
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86 <help>
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87
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88 @HELP_LOGO@
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89
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90 .. class:: infomark page-header h2
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91
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92 What it does
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93
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94 FROGSFUNC_step4_pathway is the last step of `PICRUSt2 &lt;https://github.com/picrust/picrust2&gt;`_. This script infers MetaCyc/KEGG pathway abundances based on EC/KO number abundances.
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96 - Regroups EC/KO numbers to MetaCyc/KEGG reactions.
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97 - Infers which MetaCyc/KEGG pathways are present based on these reactions with `MinPath &lt;http://omics.informatics.indiana.edu/MinPath/&gt;`_.
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98 - Calculates and returns the abundance of pathways identified as present.
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99
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100 .. class:: infomark page-header h2
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101
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102 Inputs/Outputs
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103
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104 .. class:: h3
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105
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106 Input
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107
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108 **Function prediction abundance file**:
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109
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110 TSV function abundances table from FROGSFUNC_step3_function tool, frogsfunc_functions_unstrat.tsv (unstratified table).
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111
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112 **Taxonomic marker:**
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113
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114 Output table of predicted marker gene copy numbers per sequence from FROGSFUNC_step2_copynumbers tool. (frogsfunc_copynumbers_marker.tsv)
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115
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116 **Pathway reference:**
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117
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118 Mapping of pathways to reactions.
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119
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120 - For 16S marker, choose Metacyc or KEGG in accordance with your choice in the FROGSFUNC_step2_copynumbers tool. If you want both, run this tool twice.
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121 - For ITS or 18S marker, Metacyc is the only valid option.
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122
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123
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124 **Do you want to normalize the final output table ?**:
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125
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126 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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127
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128 .. image:: icon_warning_sml.gif
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129
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130 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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131
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132 .. class:: h3
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133
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134 Outputs
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135
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136 **HTML report**:
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137
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138 The HTML file summarizes information about pathway abundances within each sample.
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139
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140 .. image:: FROGS_frogsfunc_pathways_sunburst.png
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141
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142
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143
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144
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145 **Pathways abundances tables - unstratified**:
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146
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147 It is the pathways abundance predictions of metagenome, per sample. (frogsfunc_pathways_unstrat.tsv)
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148
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149 - Classification column: the hierarchy classification of the pathway.
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150 - db_link column: the url on the link accession ID (observation_name) of the pathway.
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151 - observation_name: Accession identifier
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152 - last columns: Abundances of these pathway in each samples.
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153
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157 @HELP_CONTACT@
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158
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159 </help>
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160
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161 <expand macro="citations" />
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162
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163 </tool>