# HG changeset patch
# User artbio
# Date 1517439320 18000
# Node ID 304adcfe366000dc903e0ab583ce50d90bf62662
# Parent  5f4fbba31b6a38df6bac1f192b8dae49ac7a27a6
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 9700ca1c08ed2cfbca33630892569f3b8acec6fe

diff -r 5f4fbba31b6a -r 304adcfe3660 sRbowtie.xml
--- a/sRbowtie.xml	Wed Oct 11 06:01:15 2017 -0400
+++ b/sRbowtie.xml	Wed Jan 31 17:55:20 2018 -0500
@@ -1,7 +1,7 @@
-<tool id="bowtieForSmallRNA" name="sR_bowtie" version="2.0.1">
+<tool id="bowtieForSmallRNA" name="sR_bowtie" version="2.0.2">
     <description>for small RNA short reads</description>
     <requirements>
-        <requirement type="package" version="1.1.2=py27_2">bowtie</requirement>
+        <requirement type="package" version="1.1.2=py27_0">bowtie</requirement>
         <requirement type="package" version="1.2">samtools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
@@ -14,7 +14,7 @@
         #end if
         #if $input.extension == "fasta":
             #set format = "-f"
-        #elif $input.extension == "fastq":
+        #elif $input.extension == "fastq" or $input.extension == "fastqsanger":
             #set format = "-q"
         #end if
 
@@ -153,6 +153,15 @@
         <test>
             <param name="genomeSource" value="history" />
             <param ftype="fasta" name="ownFile" value="297_reference.fa" />
+            <param name="method" value="unique" />
+            <param ftype="fastqsanger" name="input" value="input.fastqsanger" />
+            <param name="v_mismatches" value="1" />
+            <param name="output_format" value="bam" />
+            <output file="output2.bam" ftype="bam" compare="sim_size" delta="1000" name="output" />
+        </test>
+        <test>
+            <param name="genomeSource" value="history" />
+            <param ftype="fasta" name="ownFile" value="297_reference.fa" />
             <param name="method" value="multiple" />
             <param ftype="fasta" name="input" value="input.fa" />
             <param name="v_mismatches" value="1" />
diff -r 5f4fbba31b6a -r 304adcfe3660 test-data/input.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.fastqsanger	Wed Jan 31 17:55:20 2018 -0500
@@ -0,0 +1,20 @@
+@HTW-1
+CATTCTGCGAAGAAGC
++
+HHHHHHHHHHHHHHHH
+@HTW-2
+GGAGAGACGACGTCAATTACT
++
+HHHHHHHHHHHHHHHHHHHHH
+@HTW-3
+AATTTCGAAACTACACCTGGAAGGTAACCA
++
+HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
+@HTW-4
+ATCGGATTTTCTTATTTATATTCAGGGTATTAAAGAATCTAT
++
+HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
+@HTW-5
+TAAGATACTGATAAGGAAACTACCAATA
++
+HHHHHHHHHHHHHHHHHHHHHHHHHHHH