# HG changeset patch
# User bgruening
# Date 1501097128 14400
# Node ID be1a3cc2cf45cd6df65e7f91ff75951dc4c3a043
# Parent  c6cef240817ec49a27b96a7e6b24ea4f4e8601fb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit b193689f9f30ce65a77be2d2c00929e3335a7d82

diff -r c6cef240817e -r be1a3cc2cf45 segemehl.xml
--- a/segemehl.xml	Wed Jul 26 10:14:42 2017 -0400
+++ b/segemehl.xml	Wed Jul 26 15:25:28 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="segemehl" name="segemehl" version="0.2.0.2">
+<tool id="segemehl" name="segemehl" version="0.2.0.3">
   <description>short read mapping with gaps</description>
   <requirements>
     <requirement type="package" version="0.2.0">segemehl</requirement>
@@ -72,12 +72,12 @@
         #if $maxout:
             --maxout $maxout
         #end if
-        #if str( $splitreads.splits ) == "--split":
+        #if str( $splitreads.splits ) == "splits":
             --splits
-            --minsplicecover $minsplicecover
-            --minfragscore $minfragscore
-            --minfraglen $minfraglen
-            --splicescorescale $splicescorescale
+            --minsplicecover $splitreads.minsplicecover
+            --minfragscore $splitreads.minfragscore
+            --minfraglen $splitreads.minfraglen
+            --splicescorescale $splitreads.splicescorescale
         #end if
         -M $maxinterval
         -E $evalue
@@ -131,9 +131,9 @@
     <conditional name="splitreads">
       <param name="splits" type="select" label="Detect split/spliced reads" help="(--splits)">
         <option value="nosplit">No splits</option>
-        <option value="--splits">Split reads</option>
+        <option value="splits">Split reads</option>
       </param>
-      <when value="--splits">
+      <when value="splits">
         <param name="minsplicecover" type="integer" value="80" label="Min coverage for spliced transcripts" help="(--minsplicecover)" />
         <param name="minfragscore" type="integer" value="18" label="Min coverage for spliced transcripts" help="(--minfragscore)" />
         <param name="minfraglen" type="integer" value="20" label="Min length of a spliced fragment" help="(--minfraglen)" />
@@ -172,9 +172,18 @@
       <param name="own_reference_genome" value="chr1.fa" />
       <param name="library" value="single" />
       <param name="input_query" value="test.fastq" />   
-      <param name="splits" value="true" />
+      <param name="splits" value="nosplit" />
       <output name="segemehl_out" file="testmap.sam" lines_diff="2" />
     </test>
+    <test>
+      <param name="genomeSource" value="history" />
+      <param name="own_reference_genome" value="chr1.fa" />
+      <param name="library" value="single" />
+      <param name="input_query" value="test.fastq" />   
+      <param name="splits" value="splits" />
+	  <param name="minsplicecover" value="40" />
+      <output name="segemehl_out" file="testmap2.sam" lines_diff="2" />
+    </test>
   </tests>
   <help>
     <![CDATA[
diff -r c6cef240817e -r be1a3cc2cf45 test-data/testmap2.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/testmap2.sam	Wed Jul 26 15:25:28 2017 -0400
@@ -0,0 +1,9 @@
+@HD	VN:1.0
+@SQ	SN:TestChromosomeForGalaxy	LN:3459
+@PG	ID:segemehl	VN:0.2.0-$Rev: 418 $ ($Date: 2015-01-05 05:17:35 -0500 (Mon, 05 Jan 2015) $)	CL:segemehl.x -t 2 -d test-data/chr1.fa -i test-data/chr1.idx -q test-data/test.fastq -m 12 -A 85 -H 1 -M 100 -E 5.0 -D 1 -s --splits --minsplicecover 40 -o testout2.sam
+10.516 HWI-EAS100R:1:1:550:1622/1	0	TestChromosomeForGalaxy	182	255	70M	*	0	0	CATGTACTGTTAAAGCGTGCGTTTATTTCAAACATTAATGAAATTTGCAGAACCCAAACTAAAGAGAGAG	3MIa!,$)8EA)!1>tMJ{:2WrL`s|`gg{]'0+Op!6RxNw;V)XKV#Go5}b!`_V]A?!F>{LM(z	NM:i:0	MD:Z:70	NH:i:1	XI:i:0	XA:Z:Q
+10.2869 HWI-EAS100R:1:1:1698:585/1	0	TestChromosomeForGalaxy	661	255	70M	*	0	0	AACCATGCATAAAAGGGGTTCGCCGTTCTCGGAGAGCCACAGAGCCCGGGCCACAGGCAGCTCCTTGCCA	Q-a;@)*!F]Za^4!P*B?&!!No!^76b+X[6eOgr1$3:-Ywg;!Vzj!`=+e>YV|ok_z!D<2+jx	NM:i:0	MD:Z:70	NH:i:1	XI:i:0	XA:Z:Q
+10.2085 HWI-EAS100R:1:1:32:109/2	0	TestChromosomeForGalaxy	1021	255	70M	*	0	0	GGGAATTCACCTCAAGAACATCCAAAGTGTGAAGGTGAAGTCCCCCGGACCCCACTGCGCCCAAACCGAA	V:e@~!I\GQ>>]?)-qpe!nVI4IJ+4!wE{YoSsVrr~P;PnY/.!a;~!S"n+J#St-g!lQdGA9;	NM:i:0	MD:Z:70	NH:i:1	XI:i:0	XA:Z:Q
+10.2869 HWI-EAS100R:1:1:1698:585/2	0	TestChromosomeForGalaxy	1321	255	43M	*	0	0	CGACTGGAGCTGTTGGTCAGAAATACTGGCGTCTGCCCCCTAA	btOb!D1"=hSm"'G_#I{b!!l#6JQ&iq4A`F%Uug!x!'h	NM:i:0	MD:Z:43	NH:i:1	XI:i:0	XL:i:2	XA:Z:Q	XX:i:1	XY:i:43	XQ:i:0	XC:Z:TestChromosomeForGalaxy	XV:i:2123	XT:i:32
+10.2869 HWI-EAS100R:1:1:1698:585/2	0	TestChromosomeForGalaxy	2123	255	27M	*	0	0	TGGCAAATCCAACTGACCAGAAGGAAG	7o<%qCKQEtM)!bP>!."DvsX9T}=	NM:i:0	MD:Z:27	NH:i:1	XI:i:0	XL:i:2	XA:Z:Q	XX:i:44	XY:i:70	XQ:i:1	XP:Z:TestChromosomeForGalaxy	XU:i:1363	XS:i:64
+10.516 HWI-EAS100R:1:1:550:1623/1	0	TestChromosomeForGalaxy	182	255	70M	*	0	0	CATGTACTGTTAAAGCGTGCGTTTATTTCAAACATTAATGAAATTTGCAGAACCCAAACTAAAGAGAGAG	3MIa!,$)8EA)!1>tMJ{:2WrL`s|`gg{]'0+Op!6RxNw;V)XKV#Go5}b!`_V]A?!F>{LM(z	NM:i:0	MD:Z:70	NH:i:1	XI:i:0	XA:Z:Q