Merge pull request #984 from nsoranzo/abyss

Update ABySS to 2.0.1 (Conda-only)
galaxyproject · Oct 12, 2016 · 586fd63 · 586fd63
2 parents 1bb8f1f + f40d091
commit 586fd63
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Showing 6 changed files with 47 additions and 8 deletions.
diff --git a/tools/abyss/abyss-pe.xml b/tools/abyss/abyss-pe.xml
@@ -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 -->
@@ -217,6 +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**

diff --git a/tools/abyss/test-data/abyss-long-scaffolds3.fa b/tools/abyss/test-data/abyss-long-scaffolds3.fa
@@ -0,0 +1,2 @@
+>0 556 6128
+GAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGC
diff --git a/tools/abyss/test-data/abyss-stats3.tab b/tools/abyss/test-data/abyss-stats3.tab
@@ -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 --git a/tools/abyss/test-data/abyss-unitigs3.fa b/tools/abyss/test-data/abyss-unitigs3.fa
@@ -0,0 +1,2 @@
+>0 556 6128
+GAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGC
diff --git a/tools/abyss/test-data/coverage3.hist b/tools/abyss/test-data/coverage3.hist
@@ -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 --git a/tools/abyss/tool_dependencies.xml b/tools/abyss/tool_dependencies.xml
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		>0 556 6128
		GAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGC
-Original file line number
+Diff line change
@@ -0,0 +1,27 @@
+	4
+	8
+	6
+	13
+	20
+	36
+	70
+	56
+	60
+	66
+	56
+	32
+	27
+	44
+	24
+	25
+	39
+	28
+	23
+	11
+	12
+	5
+	5
+	2
+	2
+	2
+	16