--- a/flag-remove-peaks.xml	Tue Jun 12 12:20:38 2018 -0400
+++ b/flag-remove-peaks.xml	Thu Jun 14 09:19:47 2018 -0400
@@ -1,19 +1,21 @@
 <tool id="flag_remove_peaks" name="flag_remove_peaks" version="0.1.6">
-    <requirements>
-	<requirement type="package" >r-optparse</requirement>
-        <requirement type="package" version="1.7.2" >bioconductor-mspurity</requirement>
-        <requirement type="package" version="0.2.5" >r-xcmswrapper</requirement>
-    </requirements>
     <description>Tool to flag and remove XCMS grouped peaks from the xcmsSet object based on various thresholds
         (e.g. RSD of intensity and retention time).
     </description>
 
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
     <stdio>
         <exit_code range="1:" />
     </stdio>
     <command interpreter="Rscript"><![CDATA[
         flag-remove-peaks.R
                 --xset_path=$xset_path
+                --out_dir=.
 
                 #if $sample_flag.sample_flag=='update'
                     --rsd_i_sample=$sample_flag.rsd_i_sample
@@ -48,7 +50,7 @@
                 #end if
     ]]></command>
     <inputs>
-        <param type="data" name="xset_path"
+        <param type="data" name="xset_path" format='rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata'
                 help="The path to the xcmsSet object saved as an RData file"/>
         <conditional name="sample_flag">
             <param name="sample_flag" type="select" label="Change biological sample flag parameters?">
@@ -153,16 +155,19 @@
 	        </conditional>
     </inputs>
     <outputs>
-	    <data name="peaklist_filtered" format="tabular" label="peaklist_filtered"
-              from_work_dir="peaklist_filtered.txt" visible="true"/>
-        <data name="removed_peaks" format="tabular" label="removed_peaks"
-              from_work_dir="removed_peaks.txt" visible="true"/>
+       <data name="peaklist_filtered" format="tsv" label="${tool.name} on ${on_string}: peaklist_filtered (tsv)"
+              from_work_dir="peaklist_filtered.tsv" />
+        <data name="removed_peaks" format="tsv" label="${tool.name} on ${on_string}: removed_peaks (tsv)"
+              from_work_dir="removed_peaks.tsv" />
         <data name="xset_filtered" format="rdata" label="xset_filtered"
-              from_work_dir="xset_filtered.RData" visible="true"/>
+              from_work_dir="xset_filtered.RData"/>
     </outputs>
     <tests>
         <test>
             <param name="blank_flag.blank_flag" value="update" />
+            <param name="xset_path" value="xset_flag_filter_input.RData"/>
+
+            <param name="blank_flag.blank_flag" value="update" />
             <conditional name="blank_flag">
                 <param name="blank_flag"  value="update"/>
                 <param name="blank_class" value="KO" />
@@ -170,11 +175,9 @@
             <conditional name="peak_removal">
                 <param name="peak_removal"  value="remove"/>
             </conditional>
-            <param name="xset_path" value="xset.RData" type="rdata"  />
-            <output name="peaklist_filtered" type="tabular" file="peaklist_filtered.tabular">
-            </output>
-            <output name="removed_peaks" type="tabular" file="removed_peaks.tabular">
-            </output>
+            <output name="peaklist_filtered" file="peaklist_filtered.tsv"/>
+
+
 
 
         </test>
@@ -272,4 +275,6 @@
 
 The output file is an xcmsSet.RData file.
     ]]></help>
+
+<expand macro="citations" />
 </tool>