# HG changeset patch
# User estrain
# Date 1512557410 18000
# Node ID 18fa9b4a6309bf4a9bf2f38c6ddbc84d701a031b
# Parent  1eb237c630cbd24848296b237cd3e8e762335e73
Deleted selected files

diff -r 1eb237c630cb -r 18fa9b4a6309 btyper-2.0.3/btyper.xml
--- a/btyper-2.0.3/btyper.xml	Wed Dec 06 05:47:40 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
-<tool id="btyper" name="BTyper" version="2.0.3">
-    <requirements>
-      <requirement type="package" version="2.7">python</requirement>
-      <requirement type="package">biopython</requirement>
-      <requirement type="package">blast</requirement>
-    </requirements>
-    <command detect_errors="exit_code"><![CDATA[
-
-      $__tool_directory__/btyper
-      -t seq     
-      #if $jobtype.select == "seq"
-        -i $jobtype.asm  
-      #else if $jobtype.select == "draft"
-        -i $jobtype.draft --draft_genome
-      #end if
-
-      -o "./"; cat btyper_final_results/*.txt > results.txt; 
-
-    ]]></command>
-    <inputs>
-      <conditional name="jobtype">
-        <param name="select" type="select" label="Assembly or FASTQ Reads?">
-          <option value="draft">Draft Genome</option>
-          <option value="seq">Complete Genome</option>
-        </param>
-        <when value="seq">
-          <param name="asm" type="data" format="fasta" label="FASTA" />
-        </when>
-        <when value="draft">
-          <param name="draft" type="data" format="fasta" label="FASTA" />
-        </when>
-      </conditional>
-
-    </inputs>
-    <outputs>
-      <data format="tabular" label="BTyper Results" name="results" from_work_dir="*.txt"/>
-    </outputs>
-    <help><![CDATA[
-        TODO: Fill in help.
-    ]]></help>
-      BTyper is a that employs a combination of (i) virulence gene-based typing, (ii) multi-locus sequence typing (MLST), (iii) panC clade typing, and (iv) rpoB allelic typing to rapidly classify B. cereus group isolates using nucleotide sequencing data. 
-
-      The Draft Genome option concatenates contigs in a single fasta file and produces a single report. The Complete Genome option assumes a single chromosome, and plasmids if present, and the report contains a section for each fasta header in the input file.
-    <citations>
-       <citation type="bibtex">
-        @misc{carrol_kovac_miller_wiedman_2017,
-        title={Rapid, high-throughput identification of anthrax-causing and emetic Bacillus cereus group genome assemblies using BTyper, a computational tool for virulence-based classification of Bacillus cereus group isolates using nucleotide sequencing data.},
-        url={http://aem.asm.org/content/early/2017/06/12/AEM.01096-17},
-        journal={Applied and Environmental Microbiology}, publisher={ASM},
-        author={Carroll, Laura M., Jasna Kovac, Rachel A. Miller, Martin Wiedmann},
-        year={2017}, month={Jun}} ,
-       }</citation>
-    </citations>
-
-
-
-</tool>