--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE	Wed Jan 30 06:26:32 2019 -0500
@@ -0,0 +1,186 @@
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--- a/bin/sRNAPipe.pl	Wed Jan 30 02:41:24 2019 -0500
+++ b/bin/sRNAPipe.pl	Wed Jan 30 06:26:32 2019 -0500
@@ -278,7 +278,7 @@
 
 Usage:
 
-sRNAPipe --fastq <fastq file 1> --fastq_n <name 1> [--fastq <fastq file 2> --fastq_n <name 2> --fastq <fastq file 3> -- fastq_n <name 3> ...] --ref <reference genome> [--build_index] --transcripts <transcripts> [--build_transcripts] --TE <transposable elements> [--build_TE] --miRNAs <miRNAs> [--build_miRNAs] --snRNAs <snRNAs> [--build_snRNAs] --rRNAs <rRNAs> [--build_rRNAs] --tRNAs <tRNAs> [--buid_tRNAs] [options]
+sRNAPipe.pl --fastq <fastq file 1> --fastq_n <name 1> [--fastq <fastq file 2> --fastq_n <name 2> --fastq <fastq file 3> -- fastq_n <name 3> ...] --ref <reference genome> [--build_index] --transcripts <transcripts> [--build_transcripts] --TE <transposable elements> [--build_TE] --miRNAs <miRNAs> [--build_miRNAs] --snRNAs <snRNAs> [--build_snRNAs] --rRNAs <rRNAs> [--build_rRNAs] --tRNAs <tRNAs> [--buid_tRNAs] [options]
 
 Arguments:
 --fastq <fastq file>\t\tFastq file to process

--- a/sRNAPipe.xml	Wed Jan 30 02:41:24 2019 -0500
+++ b/sRNAPipe.xml	Wed Jan 30 06:26:32 2019 -0500
@@ -252,20 +252,6 @@
  	"https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf"
     </help>
     <citations>
-        <citation type="doi">10.1038/nature12962</citation>
-        <citation type="doi">10.1038/nature11233</citation>
-        <citation type="doi">10.1186/gb4172</citation>
-        <citation type="doi">10.1038/nature04916</citation>
-        <citation type="doi">10.1016/j.cell.2007.01.043</citation>
-        <citation type="doi">10.1016/j.celrep.2015.02.062</citation>
-        <citation type="doi">10.1093/bioinformatics/btp324</citation>
-        <citation type="doi">10.1093/bioinformatics/btp352</citation>
-        <citation type="doi">10.1002/0471250953.bi1112s47</citation>
-        <citation type="doi">10.1093/bioinformatics/btu379</citation>
-        <citation type="doi">10.1002/embr.201337898</citation>
-        <citation type="doi">10.1038/ncomms13739</citation>
-        <citation type="doi">10.1093/nar/gkt310</citation>
-        <citation type="doi">10.1186/s13072-015-0041-5</citation>
-        <citation type="doi">10.1093/bioinformatics/btu647</citation>
+        <citation type="doi">10.1186/s13100-018-0130-7</citation>
     </citations>
 </tool>