diff mykrobe_genotype.xml @ 0:d783eb846f59 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mykrobe_genotype.xml	Sat Jan 13 09:02:58 2018 -0500
@@ -0,0 +1,64 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="mykrobe_genotype" name="mkyrobe genotype" version="0.5.6" >
+  <description>Antibiotic resistance predictions</description>
+  <macros>
+    <import>macro.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code">
+<![CDATA[
+        @select_inputs@
+
+        mykrobe genotype 
+        '$name'
+        '$probe_set'
+
+        #if $kmer:
+          --kmer $kmer
+        #end if
+
+        #if $expected_depth:
+          --expected_depth $expected_depth
+        #end if
+
+
+        -q
+        -t "\${GALAXY_SLOTS:-1}"
+
+        -1
+        #if $type == 'fastq':
+          *.fastq
+        #elif $type == 'bam':
+          *.bam
+        #else
+          *.fasta  
+        #end if
+         > $json
+]]>
+  </command>
+  <inputs>
+    <expand macro="inputs" />
+    <param name="probe_set" type="data" format="fasta" label="Probe Set"/>
+    <param name="kmer" argument="--kmer" optional="True" type="integer" min="0" label="Kmer length" value="21" help="default = 21"/>
+    <param name="expected_depth" argument="--expected_depth" optional="True" type="integer" min="0" label="Expected Depth"  help=""/>
+  </inputs>
+  <outputs>
+    <data name="json" format="json" label="JSON prediction"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="type" value="single"/>
+      <param name="fastq_input1" value="reads.fastq"/>
+      <param name="probe_set" value="tb-bradley-probe-set-feb-09-2017.fasta.gz"/>
+      <output name="json">
+        <assert_contents>
+          <has_text_matching expression="ref-S315T"/>
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+  <help>
+@ATTRIBUTION@
+  </help>
+  <expand macro="citation" />
+</tool>