--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CRISPRSeek/compare2sequences.xml	Tue Nov 03 10:12:14 2015 -0500
@@ -0,0 +1,147 @@
+<tool id="compare2sequences" name="compare2sequences" version="1.0.0">
+  <description>CRISPRSeek compare2sequences</description>
+    <macros>
+        <import>crisprseek_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code">
+        Rscript "${compare2sequences}"
+    </command>
+    <configfiles>
+        <configfile name="compare2sequences"><![CDATA[
+## code chunk: Load all required libraries quietly
+library(CRISPRseek, quietly=TRUE, warn.conflicts=FALSE,verbose = FALSE)
+
+compare2Sequences("${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}" )
+
+     ]]></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 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>
+           <option value="Yes">Yes</option>
+       </param>
+       <when value="Yes">
+          <param name="searchDirection" type="select" label="Search Direction">
+             <option value="both" selected="True">both</option>
+             <option value="1to2">1to2</option>
+             <option value="2to1">2to1</option>
+          </param>
+         <conditional name="fg">
+           <param name="fpg_only" type="select" label="Find Paired gRNA Only" help="Choose whether to only search for paired gRNAs in such an orientation that the first one is on minus strand called reverse gRNA and the second one is on plus strand called forward gRNA. TRUE or FALSE, default FALSE">
+              <option value="FALSE" selected="True">No</option>
+              <option value="TRUE">Yes</option>
+           </param>
+           <when value="True">
+              <param name="mingap" type="text" label="Min Gap" value="0" />
+              <param name="maxgap" type="text" label="Max Gap" value="20" />
+           </when>
+         </conditional>
+         <param name="PAMsize" type="text" label="PAM Size" value="3" help="PAM length, default 3"/>
+         <param name="PAM" type="text" label="PAM" value="NGG" help="PAM sequence after the gRNA, default NGG"/>
+         <param name="PAMPattern" type="text" label="PAM Pattern" value="N[A_p_G]G_d_"  help="Regular expression of protospacer-adjacent motif (PAM), default N[A|G]G$. Please use _p_ for | and _d_ for $ symbols"/>
+         <param name="gRNAsize" type="text" label="gRNA Size" value="20" help="The size of the gRNA, default 20"/>
+         <param name="weights" type="text" area="true" size="5x60" value="0, 0, 0.014, 0, 0, 0.395, 0.317, 0, 0.389, 0.079, 0.445, 0.508, 0.613, 0.851, 0.732, 0.828, 0.615, 0.804, 0.685, 0.583" label="Off Target Weights" help="a numeric vector size of gRNA length, default 0, 0, 0.014, 0, 0, 0.395, 0.317, 0, 0.389, 0.079, 0.445, 0.508, 0.613, 0.851, 0.732, 0.828, 0.615, 0.804, 0.685, 0.583 which is used in Hsu et al., 2013 cited in the reference section"/>
+       </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="gz" name="output"/>
+  </outputs>
+  <help>
+
+**What it does**
+
+The package includes functions to find potential guide RNAs for input target se-
+quences, optionally filter guide RNAs without restriction enzyme cut site, or with-
+out paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank se-
+quence and indicate whether the target and off-targets are located in exon region or not. Poten-
+tial guide RNAs are annotated with total score of the top5 and topN off-targets, de-
+tailed topN mismatch sites, restriction enzyme cut sites, and paired guide RNAs.
+
+**Description**
+
+Generate all possible guide RNAs (gRNAs) for two input sequences, or two sets of sequences and generate scores for potential off-targets in the other sequence.
+
+**Usage**
+
+   compare2Sequences(inputFile1Path, inputFile2Path, inputNames=c("Seq1", "Seq2"), format = "fasta", findgRNAsWithREcutOnly = FALSE, searchDirection=c("both","1to2", "2to1"), REpatternFile=system.file("extdata", "NEBenzymes.fa", package = "CRISPRseek"), minREpatternSize = 6, overlap.gRNA.positions = c(17, 18), findPairedgRNAOnly = FALSE, min.gap = 0, max.gap = 20, gRNA.name.prefix = "gRNA", PAM.size = 3, gRNA.size = 20, PAM = "NGG", PAM.pattern = "N[A|G]G$", max.mismatch = 3, outputDir, weights = c(0, 0, 0.014, 0, 0, 0.395, 0.317, 0, 0.389, 0.079, 0.445, 0.508, 0.613, 0.851, 0.732, 0.828, 0.615, 0.804, 0.685, 0.583), overwrite = FALSE)
+
+**Author(s)**
+
+Lihua Julie Zhu and Michael Brodsky Maintainer: julie.zhu@umassmed.edu
+
+Alper Kucukural, Galaxy Maintainer: alper.kucukural@umassmed.edu
+
+**Citation**
+
+(from within R, enter citation("CRISPRseek")):
+
+Zhu LJ, Holmes BR, Aronin N and Brodsky MH (2014). “CRISPRseek: A Bioconductor Package to Identify Target-Specific Guide RNAs for CRISPR-Cas9 Genome-Editing Systems.” PLoS one, 9(9). http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4172692/.
+
+**References**
+
+Patrick D Hsu, David A Scott, Joshua A Weinstein, F Ann Ran, Silvana Konermann, Vineeta Agar-
+wala, Yinqing Li, Eli J Fine, Xuebing Wu, Ophir Shalem, Thomas J Cradick, Luciano A Marraffini,
+Gang Bao, Feng Zhang (2013) DNA targeting specificity of rNA-guided Cas9 nucleases. Nature
+Biotechnology 31:827-83
+
+Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM.CAS9
+transcriptional activators for target specificity screening and paired nickases for cooperative genome
+engineering. Nat Biotechnol. 2013. 31(9):833-8 Patrick D Hsu, David A Scott, Joshua A Wein-
+stein, F Ann Ran, Silvana Konermann, Vineeta Agarwala, Yinqing Li, Eli J Fine, Xuebing Wu,
+Ophir Shalem, Thomas J Cradick, Luciano A Marraffini, Gang Bao, Feng Zhang. DNA targeting
+specificity of rNA-guided Cas9 nucleases. Nat Biotechnol. 2013. 31:827-834
+
+**Reference Manual and Materials**
+
+http://www.bioconductor.org/packages/release/bioc/vignettes/CRISPRseek/inst/doc/CRISPRseek.pdf
+
+http://www.bioconductor.org/packages/release/bioc/manuals/CRISPRseek/man/CRISPRseek.pdf
+
+http://www.bioconductor.org/packages/release/bioc/vignettes/CRISPRseek/inst/doc/CRISPRseek.R
+
+
+
+
+
+  </help>
+  <expand macro="citations" />
+
+</tool>
+