--- a/macros.xml	Tue Feb 13 04:47:50 2018 -0500
+++ b/macros.xml	Tue Sep 18 16:07:36 2018 -0400
@@ -1,141 +1,52 @@
 <?xml version="1.0"?>
 <macros>
-    <xml name="requirements">
-        <requirements>
-            <requirement type="package" version="0.4_1">r-snow</requirement>
-            <requirement type="package" version="1.46.0">bioconductor-xcms</requirement>
-            <requirement type="package" version="1.1_4">r-batch</requirement>
-        </requirements>
-    </xml>
-    <xml name="requirements_light">
-        <requirements>
-            <requirement type="package" version="1.46.0">bioconductor-xcms</requirement>
-        </requirements>
-    </xml>
     <xml name="stdio">
         <stdio>
             <exit_code range="1" level="fatal" />
         </stdio>
     </xml>
 
-    <token name="@COMMAND_XCMS_SCRIPT@">
-        LC_ALL=C Rscript $__tool_directory__/xcms.r
-    </token>
+    <!-- COMMAND -->
+    <token name="@COMMAND_RSCRIPT@">LC_ALL=C Rscript $__tool_directory__/</token>
 
     <token name="@COMMAND_LOG_EXIT@">
         ;
         return=\$?;
-        mv log.txt '$log';
-        cat '$log';
+        cat 'log.txt';
         sh -c "exit \$return"
     </token>
 
-    <!-- zipfile load for planemo test -->
-
-    <token name="@COMMAND_FILE_LOAD@">
-        #if $file_load_section.file_load_conditional.file_load_select == "yes":
-            #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"):
-                #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
-                #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )
-
-                singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
-            #else
-                zipfile '$file_load_section.file_load_conditional.input'
-            #end if
-        #end if
-    </token>
-
-    <xml name="input_file_load">
-        <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
-            <conditional name="file_load_conditional">
-                <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." >
-                    <option value="no" >no need</option>
-                    <option value="yes" >yes</option>
-                </param>
-                <when value="no">
-                </when>
-                <when value="yes">
-                    <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />
-                </when>
-            </conditional>
-        </section>
+    <!-- INPUT_VALIDATORS -->
+    <xml name="input_validator_range_integer">
+        <validator type="regex" message="The format is 'min,max'" >[0-9]+ *, *[0-9]+</validator>
     </xml>
 
-    <xml name="test_file_load_zip">
-        <section name="file_load_section">
-            <conditional name="file_load_conditional">
-                <param name="file_load_select" value="yes" />
-                <param name="input" value="faahKO_reduce.zip" ftype="zip" />
-            </conditional>
-        </section>
+    <xml name="input_validator_range_float">
+        <validator type="regex" message="The format is 'min,max'" >[0-9]+\.?[0-9]* *, *[0-9]+\.?[0-9]*</validator>
     </xml>
 
-    <xml name="test_file_load_single">
-        <section name="file_load_section">
-            <conditional name="file_load_conditional">
-                <param name="file_load_select" value="yes" />
-                <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
-            </conditional>
-        </section>
+    <xml name="input_validator_list_integer">
+        <validator type="regex" message="The format is '1,2,4,6'" >[0-9, ]+</validator>
     </xml>
 
-    <token name="@COMMAND_PEAKLIST@">
-        #if $peaklist.peaklistBool
-            variableMetadataOutput '$variableMetadata'
-            dataMatrixOutput '$dataMatrix'
-            convertRTMinute $peaklist.convertRTMinute
-            numDigitsMZ $peaklist.numDigitsMZ
-            numDigitsRT $peaklist.numDigitsRT
-            intval $peaklist.intval
-        #end if
-    </token>
+
+    <token name="@INPUT_IMAGE_LABEL@">RData file</token>
+    <token name="@INPUT_IMAGE_HELP@">It contains a xcms3::XCMSnExp object (named xdata)</token>
 
-    <xml name="input_peaklist">
-        <conditional name="peaklist">
-            <param name="peaklistBool" type="boolean" label="Get a Peak List" />
-            <when value="true">
-              <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
-              <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
-              <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
-              <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below">
-                  <option value="into" selected="true">into</option>
-                  <option value="maxo">maxo</option>
-                  <option value="intb">intb</option>
-              </param>
-            </when>
-            <when value="false" />
-        </conditional>
-    </xml>
 
-    <xml name="output_peaklist"  token_function="">
-        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv">
-            <filter>(peaklist['peaklistBool'])</filter>
-        </data>
-        <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" >
-            <filter>(peaklist['peaklistBool'])</filter>
-        </data>
-    </xml>
-
-    <token name="@HELP_AUTHORS@">
-.. class:: infomark
-
-**Authors**  Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu
+    <!-- MISC -->
+    <token name="@HELP_AUTHORS_WRAPPERS@">
 
 .. class:: infomark
 
-**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M]
+**Galaxy integration** ABiMS TEAM - SU/CNRS - Station biologique de Roscoff and Yann Guitton - LABERCA
+Part of Workflow4Metabolomics.org [W4M]
 
  | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
 
----------------------------------------------------
-
     </token>
 
-
-    <xml name="citation">
-        <citations>
-            <citation type="doi">10.1021/ac051437y</citation>
+    <xml name="citation_w4m">
             <citation type="doi">10.1093/bioinformatics/btu813</citation>
-        </citations>
     </xml>
 </macros>