diff asics_xml.xml @ 1:b55559a2854f draft

planemo upload for repository https://github.com/workflow4metabolomics/nmr_annotation commit 1f3516e77a7c7a08ed16a66c913df456ba720553

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/asics_xml.xml	Wed Mar 28 09:48:25 2018 -0400
@@ -0,0 +1,226 @@
+<tool id="NmrAnnotation" name="NMR_Annotation" version="1.0.0">
+
+    <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>