--- a/make.sra.xml	Tue Sep 05 16:25:24 2017 -0400
+++ b/make.sra.xml	Wed Feb 14 09:47:57 2018 -0500
@@ -7,40 +7,42 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$project" project.dat &&
-        ln -s "$sff" sff.dat &&
-        ln -s "$oligos" oligos.dat &&
-        ln -s "$mimark" mimark.dat &&
-        ln -s "$fastq" fastq.dat &&
+## create symlinks to input datasets
+ln -s '$project' project.dat &&
+ln -s '$sff' sff.dat &&
+ln -s '$oligos' oligos.dat &&
+ln -s '$mimark' mimark.dat &&
+ln -s '$fastq' fastq.dat &&
 
-        echo 'make.sra(
-            project=project.dat,
-            sff=sff.dat,
-            oligos=oligos.dat,
-            mimark=mimark.dat,
-            #if $fastq:
-                fastq=fastq.dat,
-            #end if
-            bdiffs=$bdiffs,
-            pdiffs=$pdiffs,
-            tdiffs=$tdiffs,
-            ldiffs=$ldiffs,
-            sdiffs=$sdiffs,
-            checkorient=$checkorient,
-            orientation=$orientation,
-            platform=$platform,
-            instrument=$instrument,
-            libstrategy=$libstrategy,
-            libselection=$libselection,
-            libsource=$libsource,
-            datatype=$datatype
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'make.sra(
+    project=project.dat,
+    sff=sff.dat,
+    oligos=oligos.dat,
+    mimark=mimark.dat,
+    #if $fastq:
+        fastq=fastq.dat,
+    #end if
+    bdiffs=$bdiffs,
+    pdiffs=$pdiffs,
+    tdiffs=$tdiffs,
+    ldiffs=$ldiffs,
+    sdiffs=$sdiffs,
+    checkorient=$checkorient,
+    orientation=$orientation,
+    platform=$platform,
+    instrument=$instrument,
+    libstrategy=$libstrategy,
+    libselection=$libselection,
+    libsource=$libsource,
+    datatype=$datatype,
+    trim=$trim,
+    includescrap=$includescrap
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="project" type="data" format="tabular" label="Project file"/>
@@ -158,6 +160,8 @@
             <option value="GENOTYPE">GENOTYPE</option>
             <option value="OTHER">OTHER</option>
         </param>
+        <param name="trim" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Trim sequences and quality scores?" help="will trim to the clipQualLeft and clipQualRight values in sff file"/>
+        <param name="includescrap" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Include scrapped sequences in your submission?"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -191,8 +195,7 @@
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -202,8 +205,7 @@
 
 .. _make.sra: https://www.mothur.org/wiki/Make.sra
 
-]]>
-    </help>
+    ]]></help>
     <citations>
         <citation type="doi">10.1128/AEM.01541-09</citation>
     </citations>