diff README.md @ 0:6895de35a263 draft

planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Thu Oct 19 18:16:51 2017 -0400
@@ -0,0 +1,54 @@
+
+# GalaxySeqSero
+#This Project has been modified by the CFSAN FDA office to work in Galaxy it also has a batch functionality as well add by the Galaxy rapper code.
+
+All below dependencies are the same for Seqsero.
+ Add this project to the galaxy tools directory and then added to tool_conf.xml
+
+Adding custom tools to Galaxy
+
+https://galaxyproject.org/admin/tools/add-tool-tutorial/
+
+
+# SeqSero 1.1
+Salmonella serotyping from genome sequencing data
+
+
+# Introduction 
+SeqSero is a pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies. A web app is available at www.denglab.info/SeqSero 
+
+# Dependencies 
+SeqSero depends on:
+
+1. Python 2.7 and [Biopython 1.65](http://biopython.org/wiki/Download); 
+
+2. [Burrows-Wheeler Aligner](http://sourceforge.net/projects/bio-bwa/files/); 
+
+3. [Samtools](http://sourceforge.net/projects/samtools/files/samtools/);
+
+4. [NCBI BLAST](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download);
+
+5. [SRA Toolkit](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software);
+
+6. [isPcr](http://hgwdev.cse.ucsc.edu/~kent/exe/linux/) written by Jim Kent. 
+
+# Executing the code 
+    Usage: SeqSero.py 
+
+    -m <int> (input data type, '1' for interleaved paired-end reads , '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly) 
+
+    -i <file> (/path/to/input/file) 
+
+    -b <string> (algorithms for bwa mapping; 'mem' for mem, 'sam' for samse/sampe; default=sam; optional) 
+
+# Output 
+Upon executing the command, a directory named 'SeqSero_result_<time_you_run_SeqSero>' will be created. Your result will be stored in 'Seqsero_result.txt' in that directory
+
+# Citation
+Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.  
+Salmonella serotype determination utilizing high-throughput genome sequencing data.  
+**J Clin Microbiol.** 2015 May;53(5):1685-92.[PMID:25762776](http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15)
+=======
+# GalaxySeqSero
+GalaxySeqSero
+>>>>>>> 99716906dbfd51e33c03185441d7af761d5f74b2