--- a/alevin.xml	Wed Oct 02 04:31:23 2019 -0400
+++ b/alevin.xml	Tue Oct 15 12:02:30 2019 -0400
@@ -80,6 +80,7 @@
         #if $optional.keepCBFraction:
             --keepCBFraction '${optional.keepCBFraction}'
         #end if
+        ${optional.noDedup}
         ${optional.dumpBfh}
         ${optional.dumpFeatures}
         ${optional.dumpUmiGraph}
@@ -90,6 +91,14 @@
         #if $optional.maxNumBarcodes:
             --maxNumBarcodes '${optional.maxNumBarcodes}'
         #end if
+
+        #if $optional.dumpMtx != "--dumpMtx":
+            && python '$__tool_directory__/vpolo_convert.py' -m
+        #end if
+        #if $optional.dumpUmiGraph:
+            && python '$__tool_directory__/vpolo_convert.py' -u
+            && sh '$__tool_directory__/umiout.sh'
+        #end if
         ]]>
     </command>
     <inputs>
@@ -122,7 +131,7 @@
         <param name="allout" type="boolean" label="Retrieve all output files" truevalue="Yes" falsevalue="No" checked="false" help="If not selected, all log, info.txt, and json files output by Alevin will not be retrieved"/>
         <section name="optional" title="Optional commands" expanded="false">
             <param name="whitelist" type="data" format="tsv,tabular" optional="true" label="Whitelist file" help="Explicitly specify whitelist CP for cell detection and CB sequence correction. If not specified, putative CBs generated."/>
-            <param name="noDedup" type="boolean" truevalue="Yes" falsevalue="No" checked="false" help="Causes pipeline to only perform CB correction, then maps the read-sequences to the transcriptome generating the interim data-structure of CB-EqClass-UMI-count. Used in parallel with --dumpBarcodeEq or --dumpBfh for the purposes of obtaining raw information or debugging."/>
+            <param name="noDedup" type="boolean" truevalue="--noDedup" falsevalue="" checked="false" help="Causes pipeline to only perform CB correction, then maps the read-sequences to the transcriptome generating the interim data-structure of CB-EqClass-UMI-count. Used in parallel with --dumpBarcodeEq or --dumpBfh for the purposes of obtaining raw information or debugging."/>
             <param name="mrna" type="data" format="tsv" optional="true" help="Single column tsv of mitochondrial genes which are to be used as a feature for CB whitelising naive Bayes classification."/>
             <param name="rrna" type="data" format="tsv" optional="true" help="Single column tsv of ribosomal genes which are to be used as a feature for CB whitelising naive Bayes classification."/>
             <param name="dumpBfh" type="boolean" truevalue="--dumpBfh" falsevalue="" checked="false" help="Dumps the full CB-EqClass-UMI-count data-structure for the purposed of allowing raw data analysis and debugging."/>
@@ -139,10 +148,12 @@
         </section>
     </inputs>
     <outputs>
-        <data name="quants_mat.gz" label="quants_mat.gz" format="txt" from_work_dir="output/alevin/quants_mat.gz">
-            <filter>optional["dumpMtx"] != "Yes"</filter>
+        <data name="quants_mat.tsv" label="quants_mat.tsv" format="txt" from_work_dir="quants_mat.tsv">
+            <filter>not optional["dumpMtx"]</filter>
         </data>
-        <data name="quants_mat.mtx.gz" label="quants_mat.mtx.gz" format="mtx" from_work_dir="output/alevin/quants_mat.mtx.gz"/>
+        <data name="quants_mat.mtx.gz" label="quants_mat.mtx.gz" format="mtx" from_work_dir="output/alevin/quants_mat.mtx.gz">
+            <filter>optional["dumpMtx"]</filter>
+        </data>
         <data name="quants_mat_cols.txt" label="quants_mat_cols.txt" format="txt" from_work_dir="output/alevin/quants_mat_cols.txt"/>
         <data name="quants_mat_rows.txt" label="quants_mat_rows.txt" format="txt" from_work_dir="output/alevin/quants_mat_rows.txt"/>
         <data name="quants_tier_mat.gz" label="quants_tier_mat.gz" format="mtx" from_work_dir="output/alevin/quants_tier_mat.gz"/>
@@ -152,7 +163,7 @@
         <data name="featureDump.txt" label="featureDump.txt" format="txt" from_work_dir="output/alevin/featureDump.txt"/>
         <data name="whitelist.txt" label="whitelist.txt" format="txt" from_work_dir="output/alevin/whitelist.txt"/>
         <data name="bfh.txt" label="bfh.txt" format="txt" from_work_dir="output/alevin/bfh.txt">
-            <filter>optional["dumpBfh"] == "Yes"</filter>
+            <filter>optional["dumpBfh"]</filter>
         </data>
         <data name="quants_mean_mat.gz" label="quants_mean_mat.gz" format="mtx" from_work_dir="output/alevin/quants_mean_mat.gz">
             <filter>optional["numCellBootstraps"]</filter>
@@ -179,9 +190,13 @@
         <data name="salmon_quant.log" format="txt" label="salmon_quant.log" from_work_dir="output/logs/salmon_quant.log">
             <filter>allout</filter>
         </data>
+        <collection name="umigraphs" type="list" label="Umi graph PDFs">
+            <filter>optional["dumpUmiGraph"]</filter>
+            <discover_datasets pattern="__name_and_ext__" ext="pdf" directory="fixed"/>
+        </collection>
     </outputs>
     <tests>
-        <test expect_num_outputs="11">
+        <test expect_num_outputs="10">
             <conditional name="refTranscriptSource">
                 <param name="TranscriptSource" value="history"/>
                 <section name="s_index">