--- a/ecoli_serotyping/ecoli_serotyping/ectyper.xml	Tue Jan 09 11:34:51 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,103 +0,0 @@
-<tool id="ectyper" name="ectyper" version="2.0">
-    <requirements>
-      <requirement type="package" version="3.6.3">python</requirement>
-      <requirement type="package">ectyper</requirement>
-      <requirement type="package">biopython</requirement>
-      <requirement type="package">blast</requirement>
-      <requirement type="package">samtools</requirement>
-      <requirement type="package">bcftools</requirement>
-      <requirement type="package">bowtie</requirement>
-      <requirement type="package">spades</requirement>
-      <requirement type="package">seqtk</requirement>
-      <requirement type="package">pandas</requirement>
-      <requirement type="package">mash</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
-
-      python $__tool_directory__/bin/ectyper
-      #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  ectyper_result*/ectyper_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="ectyper Results" name="results" from_work_dir="results.txt"/>
-    </outputs>
-    <tests>
-       <test>
-         <output name="results" file="results.txt"/>
-       </test>
-    </tests>
-    <help><![CDATA[
-    
-**Usage: ectyper**
-
-**INPUT**
-
-A fasta assembly
-
-**PERCENTIDENTITY**
-
-Percentage of identity wanted to use against the database. From 0 to 100, default is 90%.
-
-**PERCENTLENGTH**
-
-Percentage of length wanted to use against the database. From 0 to 100, default is 50%.
-
-**verify**
-
-Enable E. Coli. verification
-
-**species**
-
-Enable species identification when non-ecoli genome is found Note: refseq downloading is required when running this option for the first time.
-
-**OUTPUT**
-Directory location of output files.
-    ]]></help>
-</tool>