# HG changeset patch
# User iuc
# Date 1488399432 18000
# Node ID 0a5c7992b1ac5c0d2ed36e49f0d3daffa1f9ecf5
# Parent  f048033da666e589279c4ef6740d09144f87d840
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty

diff -r f048033da666 -r 0a5c7992b1ac abyss-pe.xml
--- a/abyss-pe.xml	Fri Jun 19 09:26:16 2015 -0400
+++ b/abyss-pe.xml	Wed Mar 01 15:17:12 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="abyss-pe" name="ABySS" version="1.9.0.0">
+<tool id="abyss-pe" name="ABySS" version="2.0.1.0">
     <description>de novo sequence assembler</description>
     <macros>
         <xml name="reads_conditional">
@@ -22,7 +22,7 @@
         </xml>
     </macros>
     <requirements>
-        <requirement type="package" version="1.9.0">abyss</requirement>
+        <requirement type="package" version="2.0.1">abyss</requirement>
     </requirements>
     <stdio>
         <!-- Anything other than zero is an error -->
@@ -33,107 +33,114 @@
     </stdio>
     <version_command>ABYSS --version | head -n 1</version_command>
     <command>
-abyss-pe name=abyss j=\${GALAXY_SLOTS:-1} k=$k
-#if str($K)
-  K=$K
-#end if
-#if str($q)
-  q=$q
-#end if
-#if str($Q)
-  Q=$Q
-#end if
-#if str($e)
-  e=$e
-#end if
-#if str($E)
-  E=$E
-#end if
-#if str($t)
-  t=$t
-#end if
-#if str($c)
-  c=$c
-#end if
-#if str($b)
-  b=$b
-#end if
-#if $SS
-  SS=--SS
-#end if
-#if str($m)
-  m=$m
-#end if
-#if str($p)
-  p=$p
-#end if
-#if str($a)
-  a=$a
-#end if
-#if str($l)
-  l=$l
-#end if
-#if str($s)
-  s=$s
-#end if
-#if str($n)
-  n=$n
-#end if
-#if str($d)
-  d=$d
-#end if
-#if str($S)
-  S=$S
-#end if
-#if str($N)
-  N=$N
-#end if
-#if $lib_repeat
-  lib='
-  #for $i in range(len($lib_repeat))
-    lib$i
-  #end for
-  '
-  #for $i, $v in enumerate($lib_repeat)
-    #if $v.reads.reads_selector == 'paired'
-      lib${i}='${v.reads.reads1} ${v.reads.reads2}'
-    #elif $v.reads.reads_selector == 'paired_collection'
-      lib${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}'
-    #else
-      lib${i}='${v.reads.reads_il}'
-    #end if
-  #end for
-#end if
-#if str($se_reads) != 'None'
-  se='
-  #for $v in $se_reads
-    $v
-  #end for
-  '
-#end if
-#if $mp_repeat
-  mp='
-  #for $i in range(len($mp_repeat))
-    mp$i
-  #end for
-  '
-  #for $i, $v in enumerate($mp_repeat)
-    #if $v.reads.reads_selector == 'paired'
-      mp${i}='${v.reads.reads1} ${v.reads.reads2}'
-    #elif $v.reads.reads_selector == 'paired_collection'
-      mp${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}'
-    #else
-      mp${i}='${v.reads.reads_il}'
-    #end if
-  #end for
-#end if
-#if str($long_seqs) != 'None'
-  long='
-  #for $v in $long_seqs
-    $v
-  #end for
-  '
-#end if
+        abyss-pe
+            name=abyss
+            j=\${GALAXY_SLOTS:-1}
+            k=$k
+
+            #if str($K)
+              K=$K
+            #end if
+            #if str($q)
+              q=$q
+            #end if
+            #if str($Q)
+              Q=$Q
+            #end if
+            #if str($e)
+              e=$e
+            #end if
+            #if str($E)
+              E=$E
+            #end if
+            #if str($t)
+              t=$t
+            #end if
+            #if str($c)
+              c=$c
+            #end if
+            #if str($b)
+              b=$b
+            #end if
+            #if $SS
+              SS=--SS
+            #end if
+            #if str($m)
+              m=$m
+            #end if
+            #if str($p)
+              p=$p
+            #end if
+            #if str($a)
+              a=$a
+            #end if
+            #if str($l)
+              l=$l
+            #end if
+            #if str($s)
+              s=$s
+            #end if
+            #if str($n)
+              n=$n
+            #end if
+            #if str($d)
+              d=$d
+            #end if
+            #if str($S)
+              S=$S
+            #end if
+            #if str($N)
+              N=$N
+            #end if
+            #if $lib_repeat
+              lib='
+              #for $i in range(len($lib_repeat))
+                lib$i
+              #end for
+              '
+              #for $i, $v in enumerate($lib_repeat)
+                #if $v.reads.reads_selector == 'paired'
+                  lib${i}='${v.reads.reads1} ${v.reads.reads2}'
+                #elif $v.reads.reads_selector == 'paired_collection'
+                  lib${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}'
+                #else
+                  lib${i}='${v.reads.reads_il}'
+                #end if
+              #end for
+            #end if
+            #if str($se_reads) != 'None'
+              se='
+              #for $v in $se_reads
+                $v
+              #end for
+              '
+            #end if
+            #if $mp_repeat
+              mp='
+              #for $i in range(len($mp_repeat))
+                mp$i
+              #end for
+              '
+              #for $i, $v in enumerate($mp_repeat)
+                #if $v.reads.reads_selector == 'paired'
+                  mp${i}='${v.reads.reads1} ${v.reads.reads2}'
+                #elif $v.reads.reads_selector == 'paired_collection'
+                  mp${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}'
+                #else
+                  mp${i}='${v.reads.reads_il}'
+                #end if
+              #end for
+            #end if
+            #if str($long_seqs) != 'None'
+              long='
+              #for $i in range(len($long_seqs))
+                long$i
+              #end for
+              '
+              #for $i, $v in enumerate($long_seqs)
+                long${i}='$v'
+              #end for
+            #end if
     </command>
 
     <inputs>
@@ -174,6 +181,9 @@
         <data name="scaffolds" format="fasta" label="${tool.name} on ${on_string}: scaffolds" from_work_dir="abyss-scaffolds.fa">
             <filter>lib_repeat or mp_repeat</filter>
         </data>
+        <data name="long_scaffolds" format="fasta" label="${tool.name} on ${on_string}: scaffolds" from_work_dir="abyss-long-scaffs.fa">
+            <filter>long_seqs</filter>
+        </data>
         <data name="bubbles" format="fasta" label="${tool.name} on ${on_string}: bubbles" from_work_dir="abyss-bubbles.fa" />
         <data name="indels" format="fasta" label="${tool.name} on ${on_string}: indels" from_work_dir="abyss-indel.fa" />
         <data name="coverage_histogram_outfile" format="tabular" label="${tool.name} on ${on_string}: coverage histogram" from_work_dir="coverage.hist" />
@@ -207,6 +217,17 @@
             <output name="coverage_histogram_outfile" file="coverage2.hist" />
             <output name="stats" file="abyss-stats2.tab" />
         </test>
+        <test>
+            <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq,assembly_sample-R2.fastq" />
+            <param name="long_seqs" ftype="fastqsanger" value="assembly_sample-R2.fastq" />
+            <param name="k" value="50" />
+            <output name="unitigs" file="abyss-unitigs3.fa" />
+            <output name="long_scaffolds" file="abyss-long-scaffolds3.fa" />
+            <output name="bubbles" file="empty_file.fasta" />
+            <output name="indels" file="empty_file.fasta" />
+            <output name="coverage_histogram_outfile" file="coverage3.hist" />
+            <output name="stats" file="abyss-stats3.tab" />
+        </test>
     </tests>
     <help>
 **What it does**
@@ -229,10 +250,10 @@
 
 **License and citation**
 
-This Galaxy tool is Copyright © 2015 `The Genome Analysis Centre (TGAC)`_ and is released under the `MIT license`_.
+This Galaxy tool is Copyright © 2015-2016 `Earlham Institute`_ and is released under the `MIT license`_.
 
-.. _The Genome Analysis Centre (TGAC): http://www.tgac.ac.uk/
-.. _MIT license: http://opensource.org/licenses/MIT
+.. _Earlham Institute: http://www.earlham.ac.uk/
+.. _MIT license: https://opensource.org/licenses/MIT
 
 You can use this tool only if you agree to the license terms of: `ABySS`_.
 
diff -r f048033da666 -r 0a5c7992b1ac test-data/abyss-long-scaffolds3.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abyss-long-scaffolds3.fa	Wed Mar 01 15:17:12 2017 -0500
@@ -0,0 +1,2 @@
+>0 556 6128
+GAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGC
diff -r f048033da666 -r 0a5c7992b1ac test-data/abyss-stats3.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abyss-stats3.tab	Wed Mar 01 15:17:12 2017 -0500
@@ -0,0 +1,3 @@
+n	n:500	L50	min	N80	N50	N20	E-size	max	sum	name
+1	1	1	556	556	556	556	556	556	556	abyss-unitigs.fa
+1	1	1	556	556	556	556	556	556	556	abyss-long-scaffs.fa
diff -r f048033da666 -r 0a5c7992b1ac test-data/abyss-unitigs3.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abyss-unitigs3.fa	Wed Mar 01 15:17:12 2017 -0500
@@ -0,0 +1,2 @@
+>0 556 6128
+GAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGC
diff -r f048033da666 -r 0a5c7992b1ac test-data/coverage3.hist
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/coverage3.hist	Wed Mar 01 15:17:12 2017 -0500
@@ -0,0 +1,27 @@
+1	4
+2	8
+3	6
+4	13
+5	20
+6	36
+7	70
+8	56
+9	60
+10	66
+11	56
+12	32
+13	27
+14	44
+15	24
+16	25
+17	39
+18	28
+19	23
+20	11
+21	12
+22	5
+23	5
+24	2
+25	2
+26	2
+27	16
diff -r f048033da666 -r 0a5c7992b1ac tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Jun 19 09:26:16 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="abyss" version="1.9.0">
-        <repository changeset_revision="ded58f1da91c" name="package_abyss_1_9_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>