view frogsfunc_pathways.xml @ 30:fce825ec2c84 draft default tip

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 01b92e7e17eb8bc125451bf41684f512cf16d3c5-dirty

<?xml version="1.0"?>
<!--
# Copyright (C) 2022 INRA
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-->
<tool id="FROGSFUNC_step3_pathways" name="FROGSFUNC_3_pathways" version= "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
	<description>Calculates pathway abundances in each sample.  </description>

  <macros>
        <import>macros.xml</import>
  </macros>

  <expand macro="requirements_frogsfunc" />

  <command detect_errors="exit_code">
    [<![CDATA[    
       frogsfunc_pathways.py
          --input-file $input_file

          #if $normalisation
            --normalisation
          #end if

          --map $map_file.value
          --summary $summary_file
    ]]>
	</command> 
	<inputs>
        <!-- Input files -->       
        <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"/>

        <!-- References -->
        <param name="category" type="select" label="Taxonomic marker" help="Taxonomic marker of interest." multiple="false" display="radio">
            <options from_data_table="frogs_picrust2_pathways">
                <column name='name' index='2' />
                <column name='value' index='2' />
                <filter type="unique_value" column='2'/>
                    <validator type="no_options" message="A built-in database is not available" />
            </options>
        </param>
        <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'>
            <options from_data_table="frogs_picrust2_pathways">
                <column name='name' index='1'/>
                <column name='value' index='3'/>
                <filter type="param_value" ref="category" column="2" />               
                <validator type="no_options" message="A built-in database is not available" />
            </options>
        </param>

        <!-- Parameters-->
        <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" />
    </inputs>
	<outputs>
		<data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html"/>
		 <data format="tsv" name="abund" label="${tool.name}: frogsfunc_pathways_unstrat.tsv" from_work_dir="frogsfunc_pathways_unstrat.tsv"/>
	</outputs>

  <tests>
    <test>
      <param name="input_file" value="references/27-frogsfunc_functions_unstrat.tsv" />
      <param name="category" value="16S" />
      <param name="map_file" value="Metacyc" />

      <output name="abund" file="references/28-frogsfunc_pathways_unstrat.tsv" compare="diff" lines_diff="0" />
      <output name="summary_file" file="references/28-frogsfunc_pathways_report.html" compare="diff" lines_diff="0" />
    </test>
  </tests>

     <help>

@HELP_LOGO@

.. class:: infomark page-header h2
	     
What it does

**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.
	     
    - Regroups EC or KO numbers to MetaCyc or KEGG reactions, depending of the unstrat abundances input file.
    - Infers which MetaCyc or KEGG pathways are present based on these reactions with `MinPath &lt;http://omics.informatics.indiana.edu/MinPath/&gt;`_.
    - Calculates and returns the abundance of pathways identified as present.

.. class:: infomark page-header h2

Inputs/Outputs

.. class:: h3

Input

**-Function prediction abundance file (EC or KO)-**:

 TSV function abundances table from FROGSFUNC_2_functions tool, frogsfunc_functions_unstrat_EC.tsv or frogsfunc_functions_unstrat_KO.tsv (unstratified table).

**-Taxonomic marker-**:

 Output table of predicted marker gene copy numbers per sequence from FROGSFUNC_1_placeseqs tool. (frogsfunc_marker.tsv)

**-Pathway reference-**:

 Mapping of pathways to reactions.
 
 - 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.
 - For ITS or 18S marker, Metacyc is the only valid option.


**-Do you want to normalize the final output table ?-**:
 
 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).

.. class:: warningmark

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.

.. class:: h3

Outputs

**-HTML report-**:        
 
 The HTML file summarizes information about pathway abundances within each sample.
 
.. image:: FROGS_frogsfunc_pathways_sunburst.png


**-Pathways abundances tables - unstratified-**:

 It is the pathways abundance predictions of metagenome, per sample. (frogsfunc_pathways_unstrat.tsv)

 - Classification column: the hierarchy classification of the pathway.
 - db_link column: the url on the link accession ID (observation_name) of the pathway.
 - observation_name: Accession identifier
 - last columns: Abundances of these pathway in each samples.




@HELP_CONTACT@

  </help>

  <expand macro="citations" />
  
</tool>