# HG changeset patch
# User estrain
# Date 1512651583 18000
# Node ID 2f81c626194a7407ecbd7f466d61c4ff54390332
# Parent  19ed3e4528c845b33df7dde71e89669c7538f8d8
Uploaded

diff -r 19ed3e4528c8 -r 2f81c626194a SeqSero/seqsero.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SeqSero/seqsero.xml	Thu Dec 07 07:59:43 2017 -0500
@@ -0,0 +1,79 @@
+<tool id="seqsero_v1" name="seqsero_v1" version="1.0">
+    <requirements>
+      <requirement type="package" version="2.7">python</requirement>
+      <requirement type="package">biopython</requirement>
+      <requirement type="package">blast</requirement>
+      <requirement type="package">samtools</requirement>
+      <requirement type="package">sra-tools</requirement>
+      <requirement type="package">bwa</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+      #if $jobtype.select == "asm"
+        ln -s $jobtype.draft sample.fasta;  
+      #else if $jobtype.select == "se"
+        ln -s $jobtype.fastq1 sample_1.fastq;  
+      #else if $jobtype.select == "pe"
+        ln -s $jobtype.fastq1 sample_1.fastq;  
+        ln -s $jobtype.fastq2 sample_2.fastq;  
+      #end if
+
+      $__tool_directory__/SeqSero.py
+      #if $jobtype.select == "asm"
+        -m 4
+        -i sample.fasta
+      #else if $jobtype.select == "se"
+        -m 3
+        -i sample_1.fastq
+      #else if $jobtype.select == "pe"
+        -m 2
+        -i sample_1.fastq sample_2.fastq
+      #end if
+      -b $maptype.select 
+      ; cat  SeqSero_result*/Seqsero_result.txt > results.txt; 
+
+    ]]></command>
+    <inputs>
+      <conditional name="jobtype">
+        <param name="select" type="select" label="Assembly or FASTQ Reads?">
+          <option value="asm">Genome Assembly</option>
+          <option value="se">Single-End Reads</option>
+          <option value="pe">Paired-End Reads</option>
+        </param>
+        <when value="asm">
+          <param name="draft" type="data" format="fasta" label="FASTA" />
+        </when>
+        <when value="se">
+          <param name="fastq1" type="data" format="fastq" label="FASTQ" />
+        </when>
+        <when value="pe">
+          <param name="fastq1" type="data" format="fastq" label="FASTQ" />
+          <param name="fastq2" type="data" format="fastq" label="FASTQ" />
+        </when>
+      </conditional>
+
+      <conditional name="maptype">
+        <param name="select" type="select" label="Algorithms for BWA mapping?">
+          <option value="sam">sam</option>
+          <option value="mem">mem</option>
+        </param>
+      </conditional>
+
+    </inputs>
+    <outputs>
+      <data format="txt" label="SeqSero Results" name="results" from_work_dir="results.txt"/>
+    </outputs>
+    <help><![CDATA[
+
+    ]]></help>
+    <citations>
+       <citation type="bibtex">
+        @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
+        title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
+        journal={J Clin Microbiol}, publisher={ASM},
+        author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
+        year={2015}, month={Max},
+        url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
+       }</citation>
+    </citations>
+
+</tool>