Mercurial > repos > tomnl > flag_remove_peaks

diff flag-remove-peaks.xml @ 8:0ccb8c91be19 draft

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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit fdaf9fc69c205ed76ef7cd82f4fa1624cf40419b-dirty
author tomnl
date Wed, 09 May 2018 09:28:12 -0400
parents 9c4fabc5f7f9
children 2cba35789adf
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--- a/flag-remove-peaks.xml	Fri May 04 10:21:13 2018 -0400
+++ b/flag-remove-peaks.xml	Wed May 09 09:28:12 2018 -0400
@@ -1,7 +1,8 @@
-<tool id="flag_remove_peaks" name="flag_remove_peaks" version="0.1.3">
+<tool id="flag_remove_peaks" name="flag_remove_peaks" version="0.1.4">
     <requirements>
         <requirement type="package" >r</requirement>
 	    <requirement type="package" >r-optparse</requirement>
+    <requirement type="package" version="1.5.4" >bioconductor-mspurity</requirement>
         <requirement type="package" version="0.0.3" >r-xcmswrapper</requirement>
     </requirements>
     <description>Tool to flag and remove XCMS grouped peaks from the xcmsSet object based on various thresholds
@@ -43,6 +44,9 @@
                     $advanced.temp_save.value
 
                 #end if
+                #if $choose_samp.choose_samp=='yes'
+                        --samplelist=$choose_samp.samplelist
+                #end if
     ]]></command>
     <inputs>
         <param type="data" name="xset_path"
@@ -132,9 +136,22 @@
                  (--grp_rm_ids)"/>
                 <param name="xset_name" type="text" label="xset_name" value="xset"
                     help="Name of the xcmsSet object within the RData file (--xset_name)"/>
+	      </when>
+	</conditional>
+	    	<conditional name="choose_samp">
+            		<param name="choose_samp" type="select" label="Samplelist">
+            		    <option value="yes" >Use samplelist</option>
+            		    <option value="" selected="true">Don't use samplelist</option>
+            		</param>
+            		<when value="">
+            		</when>
+            		<when value="yes">
+            		    <param name="samplelist" type="data" label="samplelist" format="tsv,tabular"
+            		        help="A samplelist can be provided to find an appriopiate blank class (requires a column 'blank' where 'yes' indicates
+            	              the class should be used as the blank (--samplelist)"/>
 
-            </when>
-        </conditional>
+            		</when>
+	        </conditional>
     </inputs>
     <outputs>
 	    <data name="peaklist_filtered" format="tabular" label="peaklist_filtered"
@@ -255,4 +272,4 @@
 
 The output file is an xcmsSet.RData file.
     ]]></help>
-</tool>
\ No newline at end of file
+</tool>