changeset 8:e05db4173fc7 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/btyper-2.0.3/btyper.xml	Tue Dec 05 22:25:21 2017 -0500
@@ -0,0 +1,61 @@
+<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[
+      btyper
+      -t $jobtype.select     
+      #if $jobtype.select == "seq"
+        -i $jobtype.asm  
+      #else if $jobtype.select == "se"
+        -i $jobtype.fastq1 
+      #else if $jobtype.select == "pe"
+        -i $jobtype.fastq1 $jobtype.fastq2 
+      #end if
+
+      -o "./" 
+
+    ]]></command>
+    <inputs>
+      <conditional name="jobtype">
+        <param name="select" type="select" label="Assembly or FASTQ Reads?">
+          <option value="seq">Assembly (fasta)</option>
+          <option value="se">Single-end FASTQ</option>
+          <option value="pe">Paired-end FASTQ</option>
+        </param>
+        <when value="seq">
+          <param name="asm" type="data" format="fasta" label="FASTA" />
+        </when>
+        <when value="se">
+          <param name="fastq1" type="data" format="fastq" label="FASTQ file" help="FASTQ" />
+        </when>
+        <when value="pe">
+          <param name="fastq1" type="data" format="fastq" label="Forward FASTQ file" help="FASTQ" />
+          <param name="fastq2" type="data" format="fastq" label="Reverse FASTQ file" help="FASTQ" />
+        </when>
+      </conditional>
+
+    </inputs>
+    <outputs>
+      <data format="tabular" label="BTyper Results" name="results" from_work_dir="*.txt"/>
+    </outputs>
+    <help><![CDATA[
+        TODO: Fill in help.
+    ]]></help>
+
+    <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>