--- a/mitokmer.1.xml	Sun Apr 28 00:42:24 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,82 +0,0 @@
-<tool id="mitokmer_v1" name="mitokmer 1" version="1.0">
-    <description>Eukaryotic abundance prediction by mitochondrial content</description>
-    <requirements>
-      <requirement type="package" version="2.7">python</requirement>
-    </requirements>
-    <command detect_errors="exit_code"><![CDATA[
-
-        rm $__tool_directory__/R*.fastq;
-        #if $reads.reads_select == "paired"
-        #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
-        #set $forward = $reads.forward
-        #set $reverse = $reads.reverse
-        #else
-        #set $name = $reads.allreads.name.split('.')[0].replace(' ','_')
-        #set $forward = $reads.allreads
-        #set $reverse = $reads.allreads
-        #end if
-        echo $name;
-        echo "-=-=-";
-        #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz')
-        #set $fwd = "R1.fastq.gz"
-        #set $rev = "R2.fastq.gz"
-        #else if $forward.is_of_type('fastq', 'fastqsanger')
-        #set $fwd = "R1.fastq"
-        #set $rev = "R2.fastq"
-        #else if $forward.is_of_type('fasta.gz')
-        #set $fwd = "R1.fasta.gz"
-        #set $rev = "R2.fasta.gz"
-        #else
-        #set $fwd = "R1.fasta"
-        #set $rev = "R2.fasta"
-        #end if
-        ln -s $forward $__tool_directory__/$fwd;
-        ln -s $reverse $__tool_directory__/$rev;
-        #if $reads.reads_select == "single"
-        #set $rev = "none"
-        #end if
-        python $__tool_directory__/kmer_read_m3.py
-        -w $__tool_directory__
-        -d $__tool_directory__/output
-        -i $__tool_directory__/$fwd $__tool_directory__/$rev
-    ]]></command>
-    <inputs>
-
-        <conditional name="reads">
-            <param name="reads_select" type="select" label="One FASTQ dataset from your history, or two datasets from your history">
-                <option value="single">One FASTQ dataset from your history</option>
-                <option value="paired">Two FASTQ datasets from your history</option>
-            </param>
-            <when value="single">
-                <param label="all reads" type="data" name="allreads" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz"/>
-            </when>
-            <when value="paired">
-                <param label="Forward reads" type="data" name="forward" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
-                <param label="Reverse reads" type="data" name="reverse" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
-            </when>
-        </conditional>
-
-    </inputs>
-    <outputs>
-      <data format="tabular" label="mitokmer Results" name="results" from_work_dir="output/mitokmer_result.csv"/>
-    </outputs>
-    <tests>
-        <test>
-         <param name="reads_select" value="single" />
-         <param name="allreads" value="1a.fasta" format="fasta"/>
-         <output name="output1" file="mitokmer_result.csv"/>
-        </test>
-    </tests>
-
-    <help><![CDATA[
-
-**Usage: mitokmer.py**
-
-    ]]></help>
-    <citations>
-       <citation type="bibtex">
-        meh
-       }</citation>
-    </citations>
-
-</tool>
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