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planemo upload for repository https://github.com/workflow4metabolomics/nmr_annotation commit 3791815505685d0038e392a702860843fe1d443e

<tool id="NmrAnnotation" name="NMR_Annotation" version="3.0.0">

    <description> Annotation of complex mixture NMR spectra and metabolite proportion estimation </description>

    <requirements>
        <requirement type="package" version="1.1_4">r-batch</requirement>
        <requirement type="package" version="1.0.1">r-asics</requirement>
    </requirements>

    <stdio>
        <exit_code range="1:" level="fatal" />
    </stdio>

    <command><![CDATA[
        ## Wrapper
        Rscript '$__tool_directory__/asics_wrapper.R' standards '$__tool_directory__/Library.Rdata'

        ## Bruker files
        zipfile '$zip_file'

        ## Exclusion zone
        zone_exclusion_choices.choice ${zone_exclusion_choices.choice}
        #if str($zone_exclusion_choices.choice) == 'yes':
            #for $i in $zone_exclusion_choices.conditions:
                zone_exclusion_left ${i.zone_exclusion_left}
                zone_exclusion_right ${i.zone_exclusion_right}
            #end for
        #end if

        ## Maximal shift (spectrum alignement)
        shift $shift

        ## Graphical zone
        zone_graphical_choices.choice ${zone_graphical_choices.choice}
        #if str($zone_graphical_choices.choice) == 'yes':
            #for $i in $zone_graphical_choices.conditions:
                zone_graphical_left ${i.zone_graphical_left}
                zone_graphical_right ${i.zone_graphical_right}
            #end for
        #end if

        ## Outputs
        logOut '$logOut'
        proportionEstimation '$proportionEstimation'
        graphOut '$graphOut'
    ]]></command>

    <inputs>
        <param name="zip_file" type="data" format="no_unzip.zip, zip" label="Zip file" />

    <conditional name="zone_exclusion_choices">
        <param name="choice" type="select" label="Exclusion zone(s)" help="Choose if you want to exclude particular zone(s)" >
            <option value="yes" > yes </option>
            <option value="no" selected="true"> no </option>
        </param>
        <when value="yes">
            <repeat name="conditions" title="exclusion zones">
                <param name="zone_exclusion_left" label="Left exclusion zone border" type="float" value="10.0" />
                <param name="zone_exclusion_right" label="Right exclusion zone border" type="float" value="10.0" />
            </repeat>
        </when>
        <when value="no" />
    </conditional>

    <param name="shift" type="float" value="0.01" help="Maximal allowed shift for spectra alignment. Default value is 0.01 ppm" />

    <conditional name="zone_graphical_choices">
        <param name="choice" type="select" label="Graphical zone(s)" help="Choose if you want to display particular zone(s)" >
            <option value="yes" > yes </option>
            <option value="no" selected="true"> no </option>
        </param>
        <when value="yes">
            <repeat name="conditions" title="grapical zones">
                <param name="zone_graphical_left" label="Left graphical zone border" type="float" value="10.0" />
                <param name="zone_graphical_right" label="Right graphical zone border" type="float" value="10.0" />
            </repeat>
        </when>
        <when value="no" />
    </conditional>
    </inputs>

    <outputs>
        <data format="txt" name="logOut" label="${tool.name}_log" />
        <data format="tabular" name="proportionEstimation" label="${tool.name}_proportionEstimation" />
        <data format="pdf" name="graphOut" label="${tool.name}_graph" />
    </outputs>

    <tests>
        <test>
            <param name="zip_file" value="ADG_007.zip" ftype="zip" />
            <output name="proportionEstimation" value="MTBLS1_177_NMR_Annotation_proportionEstimation.tabular" />
            <output name="graphOut"  value="MTBLS1_177_NMR_Annotation.pdf" compare="sim_size" delta="300" />
        </test>
    </tests>

    <help><![CDATA[

.. class:: infomark

**Authors** Marie Tremblay-Franco ([e-mail]), Patrick Tardivel ([e-mail]), Rémi Servien ([e-mail]) and Gaelle Lefort ([e-mail])

.. class:: infomark

**Please cite**

Tardivel P., Servien R. and Concordet D. Non asymptotic active set properties of lasso-type estimators in small-dimension (submitted)
Tardivel P., Servien R., Canlet C., Tremblay-Franco M., Debrauwer L. and Concordet D. ASICS: an automatic method for identification and quantification of metabolites in NMR 1D 1H spectra (in preparation)

---------------------------------------------------

==============
NMR Annotation
==============

-----------
Description
-----------

ASICS, based on a strong statistical theory, handles automatically the metabolite identification and quantification

-----------------
Workflow position
-----------------

**Upstream tools**

========================= ================= ======= =========
Name                      output file       format  parameter
========================= ================= ======= =========
NA                        NA                NA      NA
========================= ================= ======= =========


**Downstream tools**

========================= ================= ======= =========
Name                      output file       format  parameter
========================= ================= ======= =========
NA                        NA                NA      NA
========================= ================= ======= =========



-----------
Input files
-----------

+---------------------------+------------+
| Parameter : num + label   |   Format   |
+===========================+============+
| 1 : Choose your inputs    |   zip      |
+---------------------------+------------+

**Choose your inputs**

You have two methods for your inputs:

| Zip file : You can put a zip file containing one condition (sample): myinputs.zip.

.. image:: ./static/images/Mth_Architecture_Repertoire_Bruker.png

----------
Parameters
----------

Exclusion zone(s)
| Spectral regions to exclude, water, solvent or contaminant resonances
| If YES: parameters **Lower exclusion zone** and **Upper exclusion zone** are visible,
| If NO: no zone to exclude
| Default value is NO
|

Left exclusion zone
| Upper boundary of exclusion zone


Right exclusion zone
| Lower boundary of exclusion zone

| *Notes:*
| - these parameters can be used several times using the "Add new exclusion zones" button


Shift
| Maximum variation of the chemical shift (due to experimental conditions) of a peak of a fixed metabolite allowed in the warping function


Graphical zone(s)
| Spectral regions to display
| If YES: parameters **Lower graphical zone** and **Upper graphical zone** are visible,
| If NO: no zone to display
| Default value is NO


------------
Output files
------------

proportionEstimation.tsv
| tabular output
| Array with p rows (corresponding to the identified metabolites) and 1 column containing the estimated relative intensities


spectra.pdf
| pdf output
| Graphical chart of real and estimated spectrum (whole spectral width and zooms depending on exclusion zone(s))



---------------------------------------------------

-------
Example
-------

.. image:: ./static/images/NmrAnnotation_ASICS.png


   ]]></help>

   <citations>
       <citation type="doi">10.1007/s11306-017-1244-5</citation>
       <citation type="doi">10.1093/bioinformatics/btu813</citation>
   </citations>

</tool>