diff macros.xml @ 30:4d6f4cd7c3ef draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e

--- a/macros.xml	Tue Feb 13 04:44:03 2018 -0500
+++ b/macros.xml	Thu Mar 01 04:16:45 2018 -0500
@@ -1,15 +1,12 @@
 <?xml version="1.0"?>
 <macros>
+    <token name="@WRAPPER_VERSION@">3.0.0</token>
     <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="@WRAPPER_VERSION@">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>
+            <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
+            <yield />
         </requirements>
     </xml>
     <xml name="stdio">
@@ -18,15 +15,12 @@
         </stdio>
     </xml>
 
-    <token name="@COMMAND_XCMS_SCRIPT@">
-        LC_ALL=C Rscript $__tool_directory__/xcms.r
-    </token>
+    <token name="@COMMAND_XCMS_SCRIPT@">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>
 
@@ -70,6 +64,15 @@
         </section>
     </xml>
 
+    <xml name="test_file_load_zip_sacuri">
+        <section name="file_load_section">
+            <conditional name="file_load_conditional">
+                <param name="file_load_select" value="yes" />
+                <param name="input" value="sacuri_dir_root.zip" ftype="zip" />
+            </conditional>
+        </section>
+    </xml>
+
     <xml name="test_file_load_single">
         <section name="file_load_section">
             <conditional name="file_load_conditional">
@@ -81,8 +84,6 @@
 
     <token name="@COMMAND_PEAKLIST@">
         #if $peaklist.peaklistBool
-            variableMetadataOutput '$variableMetadata'
-            dataMatrixOutput '$dataMatrix'
             convertRTMinute $peaklist.convertRTMinute
             numDigitsMZ $peaklist.numDigitsMZ
             numDigitsRT $peaklist.numDigitsRT
@@ -108,10 +109,10 @@
     </xml>
 
     <xml name="output_peaklist"  token_function="">
-        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv">
+        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" >
             <filter>(peaklist['peaklistBool'])</filter>
         </data>
-        <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" >
+        <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" from_work_dir="dataMatrix.tsv" >
             <filter>(peaklist['peaklistBool'])</filter>
         </data>
     </xml>
@@ -131,6 +132,39 @@
 
     </token>
 
+    <token name="@HELP_XCMS_MANUAL@">
+
+For details and explanations for all the parameters and the workflow of xcms_ package, see its manual_ and this example_
+
+.. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
+.. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf
+.. _example: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html
+
+    </token>
+
+    <token name="@HELP_PEAKLIST@">
+
+Get a Peak List
+---------------
+
+If 'true', the module generates two additional files corresponding to the peak list:
+- the variable metadata file (corresponding to information about extracted ions such as mass or retention time)
+- the data matrix (corresponding to related intensities)
+
+**decimal places for [mass or retention time] values in identifiers**
+
+    | Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time.
+    | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively.
+    | Theses parameters do not affect decimal places in columns other than the identifier one.
+
+**Reported intensity values**
+
+    | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter:
+    | - into: integrated area of original (raw) peak
+    | - maxo: maximum intensity of original (raw) peak
+    | - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’)
+
+    </token>
 
     <xml name="citation">
         <citations>