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asics_xml.xml
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<tool id="NmrAnnotation" name="NMR_Annotation" version="3.0.0+galaxy1">
<description> Annotation of complex mixture NMR spectra and metabolite proportion estimation </description>
<requirements>
<requirement type="package" version="3.0.0">libgfortran</requirement>
<requirement type="package" version="1.1_4">r-batch</requirement>
<requirement type="package" version="1.0.1">r-asics</requirement>
</requirements>
<required_files>
<include path="asics_wrapper.R" />
<include path="DrawSpec.R" />
<include path="Library.Rdata" />
</required_files>
<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 ([email protected]), Patrick Tardivel ([email protected]), Rémi Servien ([email protected]) and Gaelle Lefort ([email protected])
.. 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>