view phyloseq_import_data.xml @ 2:094a2469204d draft

"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.3.1 commit 90093162b8cfb3e75908323761f4ef246222abea"

<?xml version="1.0"?>
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<tool name="FROGSSTAT Phyloseq Import Data" id="FROGSSTAT_Phyloseq_Import_Data" version="3.2.3.1">
    <description>from 3 files: biomfile, samplefile, treefile </description>
        <requirements>
            <requirement type="package" version="3.2.3">frogs</requirement>
            <requirement type="package" version="4.0.5">r-base</requirement>
            <requirement type="package" version="4.0">r-essentials</requirement>
            <requirement type="package" version="1.34.0">bioconductor-phyloseq</requirement>
        </requirements>
        <stdio>
            <exit_code range="1:" />
            <exit_code range=":-1" />
        </stdio>
    <command>
                phyloseq_import_data.py   --biomfile $biomfile
                                --samplefile $samplefile 
                                #if $treefile
                                  --treefile $treefile 
                                #end if
                                --ranks $ranks
                                #if $normalisation
                                    --normalisation
                                #end if
                                --html $html 
                                --rdata $data
    </command>
    <inputs>
        <!-- Files -->
        <param format="biom1" name="biomfile" type="data" label="Abundance biom file with taxonomical metadata" help="The file contains the  OTU informations (format: biom1)." optional="false">
            <validator type="empty_field" message="This parameter is required." />
        </param>
        
        <param format="tabular" name="samplefile" type="data" label="Sample tsv file" help="The file contains the samples informations (format: tabular)." optional="false">
            <validator type="empty_field" message="This parameter is required." />                
        </param>
        
        <param format="nhx" name="treefile" type="data" label="Tree file (optional)" help="The file contains the tree informations (format: Newick - nhx or nwk)." optional="true" />
        
        <!-- Parameters -->
        <param name="ranks" type="text" label="Names of taxonomics levels" help="The ordered taxonomic levels stored in BIOM. Each level is separated by one space."  value="Kingdom Phylum Class Order Family Genus Species" size="80" optional="false"/>
        <param name="normalisation" type="boolean" label="Do you want to normalise your data ?" help="To normalise data before statistical analysis (default : No)." optional="false" /> 
    </inputs>
    <outputs>
        <data format="rdata" name="data" label="${tool.name}: data.Rdata" from_work_dir="data.Rdata"/>
        <data format="html" name="html" label="${tool.name}: summary.nb.html" from_work_dir="summary.nb.html"/>
    </outputs>
    <tests>
        <test>
            <param name="biomfile" value="input/chaillou.biom"/>
            <param name="samplefile" value="input/sample_metadata.tsv"/>
            <param name="treefile" value="input/tree.nwk"/>
            <output name="data" value="references/16-phylo_import.Rdata" compare="sim_size" delta="10"/>
            <output name="html" value="references/16-phylo_import.nb.html" compare="diff" lines_diff="0"/>
        </test>
    </tests>
    <help>

.. image:: static/images/FROGS_logo.png 
   :height: 144
   :width: 110

.. class:: infomark page-header h2

What it does

Launch Rmarkdown script to import data from 3 files: biomfile, samplefile, treefile into a `phyloseq &lt;https://joey711.github.io/phyloseq/&gt;`_ object.

.. class:: infomark page-header h2

Inputs/Outputs

.. class:: h3

Input

**OTU biom file**:

The OTU biom file (format `biom1 &lt;http://biom-format.org/documentation/format_versions/biom-1.0.html&gt;`_).
The example of biom file: 

  .. image:: static/images/FROGS_Phyloseq_biomfile.png 
     :height: 30
     :width: 733 

**Newick file** (tree.nwk):

Newick file (format `nxh &lt;https://en.wikipedia.org/wiki/Newick_format&gt;`_) is the result of FROGS Tree:

  .. image:: static/images/FROGS_nwk_treefile.png

**Sample file**:
The file contains the conditions of experiment with sample ID in the first column:
  
  .. image:: static/images/FROGS_Phyloseq_samplefile.png 
     :height: 115
     :width: 369
      
.. class:: h3

Output

**Html file** (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_): The summary of phyloseq object.
  
  .. image:: static/images/FROGS_Phyloseq_import_data_html.png 
 
**Data file** (format rdata): The informations of data in one phyloseq object.


.. class:: infomark page-header h2

**Contact**

Contacts: [e-mail]

Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers

Website: http://frogs.toulouse.inrae.fr/

Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. &lt;https://doi.org/10.1093/bioinformatics/btx791&gt;`_

    </help>
</tool>