--- a/compare2sequences.xml	Wed Nov 04 15:30:22 2015 -0500
+++ b/compare2sequences.xml	Wed Nov 04 16:46:58 2015 -0500
@@ -12,45 +12,14 @@
 ## code chunk: Load all required libraries quietly
 library(CRISPRseek, quietly=TRUE, warn.conflicts=FALSE,verbose = FALSE)
 
-compare2Sequences("${s1.inputfile}", "${s2.inputfile}", inputNames=c("Seq1", "Seq2"), REpatternFile = system.file('extdata', 'NEBenzymes.fa', package = 'CRISPRseek'), max.mismatch="${maxmismatch}", searchDirection="${a.searchDirection}", findPairedgRNAOnly=${a.fg.fpg_only}, min.gap = "${a.fg.mingap}", max.gap = "${a.fg.maxgap}", gRNA.name.prefix = "gRNA", PAM.size = "${a.PAMsize}", gRNA.size = "${a.gRNAsize}", PAM = "${a.PAM}", PAM.pattern = "${a.PAMPattern}", outputDir, weights="${a.weights}" )
+compare2Sequences("${inputfile1}", "${inputfile2}", inputNames=c("Seq1", "Seq2"), REpatternFile = system.file('extdata', 'NEBenzymes.fa', package = 'CRISPRseek'), max.mismatch="${maxmismatch}", searchDirection="both", findPairedgRNAOnly=${a.fg.fpg_only}, min.gap = "${a.fg.mingap}", max.gap = "${a.fg.maxgap}", gRNA.name.prefix = "gRNA", PAM.size = "${a.PAMsize}", gRNA.size = "${a.gRNAsize}", PAM = "${a.PAM}", PAM.pattern = "${a.PAMPattern}", outputDir="./", weights="${a.weights}" )
 
      ]]></configfile>
     </configfiles>
   <inputs>
-     <conditional name="s1">
-       <param name="input_source" type="select" label="Select Input File Path" help="Sequence input file path that contains sequences to be searched for potential gRNAs">
-           <option value="history">History</option>
-           <option value="FullPath">Free Text</option>
-           <option value="Fasta">Fasta</option>
-       </param>
-       <when value="FullPath">
-          <param name="inputfile" type="text" area="true" size="2x60" label="Input File Path" help="Full path in the cluster"/>
-       </when>
-       <when value="Fasta">
-          <param name="inputfile" type="text" area="true" size="2x60" label="Input Fasta Sequence/s" help="Free text fasta sequences"/>
-       </when>
-       <when value="history">
-       <param format="fastq,fa,fasta" name="inputfile" type="data" label="Input File Path" />
-       </when>
-    </conditional>
-     <conditional name="s2">
-       <param name="input_source" type="select" label="Select Input File Path" help="Sequence input file path that contains sequences to be searched for potential gRNAs">
-           <option value="history">History</option>
-           <option value="FullPath">Free Text</option>
-           <option value="Fasta">Fasta</option>
-       </param>
-       <when value="FullPath">
-          <param name="inputfile" type="text" area="true" size="2x60" label="Input File Path" help="Full path in the cluster"/>
-       </when>
-       <when value="Fasta">
-          <param name="inputfile" type="text" area="true" size="2x60" label="Input Fasta Sequence/s" help="Free text fasta sequences"/>
-       </when>
-       <when value="history">
-       <param format="fastq,fa,fasta" name="inputfile" type="data" label="Input File Path" />
-       </when>
-    </conditional>
+    <param format="fastq,fa,fasta" name="inputfile1" type="data" label="Input File Path" />
+    <param format="fastq,fa,fasta" name="inputfile2" type="data" label="Input File Path" />
     <param name="maxmismatch" type="text" label="Max Mismatch" value="3" help="Maximum mismatch allowed in off target search, default 3. Warning: will be considerably slower if set > 3"/>
-    <param name="outputdir" type="text"  area="true" size="2x60" label="Output Directory" help="Output directory in the cluster"/>
     <conditional name="a">
        <param name="advanced" type="select" label="Advanced Options">
            <option value="No" selected="True">No</option>

--- a/tool_dependencies.xml	Wed Nov 04 15:30:22 2015 -0500
+++ b/tool_dependencies.xml	Wed Nov 04 16:46:58 2015 -0500
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-        <package name="CRISPRseek" version="1.11.0">
-                <repository changeset_revision="7342c81ca1f7" name="package_r_crisprseek_1_11_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <package name="crisprseek" version="1.11.0">
+           <repository changeset_revision="7342c81ca1f7" name="package_r_crisprseek_1_11_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
         </package>
         <package name="R" version="3.2.1">
-        <repository changeset_revision="fae49a02a848" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
+           <repository changeset_revision="fae49a02a848" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        </package>
 </tool_dependency>