--- a/SeqSero/seqsero.xml	Wed Dec 06 15:59:29 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,79 +0,0 @@
-<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 ample_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>