diff macros.xml @ 8:198b035d4848 draft

planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
author lecorguille
date Fri, 07 Apr 2017 07:42:38 -0400
parents c23aa0cbc550
children a3024f51082d
line wrap: on
line diff
--- a/macros.xml	Wed Feb 01 12:24:21 2017 -0500
+++ b/macros.xml	Fri Apr 07 07:42:38 2017 -0400
@@ -2,12 +2,11 @@
 <macros>
     <xml name="requirements">
         <requirements>
-	    <requirement type="package" version="0.4_1">r-snow</requirement>
+            <requirement type="package" version="0.4_1">r-snow</requirement>
             <requirement type="package" version="1.26.0">bioconductor-camera</requirement>
             <requirement type="package" version="2.26.0">bioconductor-multtest</requirement>
-	    <requirement type="package" version="1.1_4">r-batch</requirement>
-            <requirement type="package" version="1.6.27">libpng</requirement>
-            <requirement type="package" version="1.3.20">graphicsmagick</requirement>
+            <requirement type="package" version="1.1_4">r-batch</requirement>
+            <requirement type="package" version="1.3.23">graphicsmagick</requirement>
         </requirements>
     </xml>
     <xml name="stdio">
@@ -19,33 +18,137 @@
     <token name="@COMMAND_CAMERA_SCRIPT@">
         LANG=C Rscript $__tool_directory__/CAMERA.r
     </token>
-    
-    <!-- zipfile load for planemo test -->
-    <token name="@COMMAND_ZIPFILE_LOAD@">
-        #if $zipfile_load_conditional.zipfile_load_select == "yes":
-            #if $zipfile_load_conditional.zip_file:
-                zipfile $zipfile_load_conditional.zip_file
+
+    <!-- raw file 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    
+        #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>
+    </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>
+
+    <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>
+
+    <!-- peaklist export option management -->
+    <token name="@COMMAND_PEAKLIST@">
+        convertRTMinute $export.convertRTMinute
+        numDigitsMZ $export.numDigitsMZ
+        numDigitsRT $export.numDigitsRT
+        intval $export.intval
     </token>
-    <xml name="zipfile_load">
-        <conditional name="zipfile_load_conditional">
-            <param name="zipfile_load_select" type="select" label="Resubmit your zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." >
-                <option value="no" >no need</option>
-                <option value="yes" selected="peakgroups">yes</option>
+
+    <xml name="input_peaklist">
+        <section name="export" title="Export options">
+            <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="General used intensity value" 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 value="no">
-            </when>
-            <when value="yes">
-                <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
-            </when>
+        </section>
+    </xml>
+
+    <xml name="test_peaklist">
+        <section name="export">
+            <param name="convertRTMinute" value="True"/>
+            <param name="numDigitsMZ" value="4" />
+            <param name="numDigitsRT" value="1" />
+            <param name="intval" value="into"/>
+        </section>
+    </xml>
+
+    <!-- annotate_diffreport <test> commun part -->
+    <xml name="test_annotate_diffreport">
+        <section name="groupfwhm">
+            <param name="sigma" value="6"/>
+            <param name="perfwhm" value="0.6"/>
+        </section>
+        <section name="findisotopes">
+            <param name="maxcharge" value="3"/>
+            <param name="maxiso" value="4"/>
+            <param name="minfrac" value="0.5"/>
+        </section>
+        <section name="findgeneral">
+            <param name="ppm" value="5"/>
+            <param name="mzabs" value="0.015"/>
+            <param name="max_peaks" value="100"/>
+        </section>
+        <section name="diffreport">
+        <conditional name="options">
+            <param name="option" value="show"/>
+            <param name="eicmax" value="200"/>
+            <param name="eicwidth" value="200"/>
+            <param name="value" value="into"/>
+            <param name="h" value="480"/>
+            <param name="w" value="640"/>
+            <param name="mzdec" value="2"/>
+            <param name="sortpval" value="False"/>
+        </conditional>
+        </section>
+        <expand macro="test_peaklist"/>
+    </xml>
+
+    <xml name="test_annotate_quick_false">
+        <param name="quick" value="FALSE"/>
+        <section name="groupcorr">
+            <param name="cor_eic_th" value="0.75"/>
+            <param name="graphMethod" value="hcs"/>
+            <param name="pval" value="0.05"/>
+            <param name="calcCiS" value="True"/>
+            <param name="calcIso" value="False"/>
+            <param name="calcCaS" value="False"/>
+        </section>
+    </xml>
+
+    <xml name="test_annotate_quick_true">
+        <conditional name="quick_block">
+            <param name="quick" value="TRUE"/>
         </conditional>
     </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 
+**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
 
 .. class:: infomark