[hg] galaxy 3816: sff_converter tool functional test

25 May 2010

details:   http://www.bx.psu.edu/hg/galaxy/rev/8833ebe82ed1
changeset: 3816:8833ebe82ed1
user:      rc
date:      Mon May 24 15:08:57 2010 -0400
description:
sff_converter tool functional test

diffstat:

 test-data/2.sff                   |    0 
 test-data/sff_converter_fasta.dat |    6 ++
 test-data/sff_converter_fastq.dat |   12 +++++
 test-data/sff_converter_qual.dat  |    6 ++
 test-data/sff_converter_xml_1.dat |   18 ++++++++
 test-data/sff_converter_xml_2.dat |   18 ++++++++
 tools/filters/sff_extractor.xml   |   83 +++++++++++++++++++++++--------------
 7 files changed, 111 insertions(+), 32 deletions(-)

diffs (176 lines):

diff -r cbacbb736899 -r 8833ebe82ed1 test-data/2.sff
Binary file test-data/2.sff has changed
diff -r cbacbb736899 -r 8833ebe82ed1 test-data/sff_converter_fasta.dat

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sff_converter_fasta.dat	Mon May 24 15:08:57 2010 -0400
@@ -0,0 +1,6 @@
+>GGOQ6K301BJT46
+gactACACGTAGTATAAGCTAAATGTTGGAGAGGATGCTGTAATCAACGTTTTGTGTCTCCTTACAGGACACCAGCTGATTTGGAGGTCATCCAATATAAACCTGGCTGGAACTTGCTATGGTTAGGAGAGCTATGAATGGAAGAGATAATTCCATTATTTAATAAGGCTACAGACAAATTAGGACAAGAAGCAGCTATTAGATTATTTAGTGCTAGCACACCTAAATAGAGAGAGATAAATTCATTAGACTTTTTGCTAttttattgacttttggagagacagtatttaaagtaccaaatcccagaggttgcctatgttggtggtgttgcaagctctattattggcgattgcaatctaccttatccataagttctgcttagagattatttgttattaattttcatctacatcaataaatataggacagtaaggattttgtacaaaatagacaatgggataggtaccagaagaggacagaggaattactggtattttgatatagactacactaacgtacgtacgtaggaattttaaccgggg
+>GGOQ6K301AWPXS
+gactACGTACACACTGGAATAAAATGGAGTTTTCATACTAGAGATTATTATATGGGCTATGTAAAAGAACTAGTAGCAGGATCTAGCACACCAGACAGCCTAAGACTGTATATTTTATATAAGCAACCCGTTATGGCATGGGAAATATCGCCCAGGGTTAAAAAATTTTAACAAGGAATGGCCTTTTTGTAAATATGTGGATAAAAAACAGGGTTCATGTGGGATGATATTGAAAAACAAAAGATTTGCGTAGGAGGAGAAATATCACCAGGATGGGGACCTGGAATGGTTGGCATAGCAAATAAAAGCCTTTAGTTGTGGGGAGAGAAAAATCGAGGCAACTCCTGTTATGATTATAAGAGAAGAGATAGATCCCAAAAAATGGTGTGGAGATTGTTGGAATTTAATGTGTCTTAGAAACTCACCTCCAGGAACGTTGTCAAAGACTCGCTATGTTGGCATGTGGACGGaaagactaaatgttggagaggatgctgtatcaacgttttgttgtcgtccttacacggacaccagctgtagttgtctgtagnttttaccggg
+>GGOQ6K301A8J46
+gactACTATACGAGTCTGCCAATCTTCTTCACTCATCCCCTTCAGGAAGAGTGCAGGGTTCTGGGACTCTCCGTATGTGCCTCCTAGGTACAAGAAAATATCCCCTCTCTTCATCCTTTAATAACACTGATCCTTGTCCCCAATACTCTACTCTCATTGGTCCTTTCCAATTTTTGTCTTTTTTGATCTTTATAGTAAATCCACTGACCTTGCAATTTGCTTGGAATTTGAGAAAAATAATCCTGTATTCTTAATGATTCTTGTTGTGTTAATAATTCATATGGGGGCCATTCCCCCTATTCTACCCCTTTGTTTAAAATTAAGGCAATGCAGAGCGAGAGCCAAAGCATTGTCTAAAGATGTTGTTTCAGGCAAAAACTTCTGAATCCAACACTTTAAAGTATTATTggcattttcaaccaaagcttgagtattgagggttgcctggtattccaaatttatgttttattccctatgtaattgtagtaaaccttcctattttttgattttctaaaatttggtccctattgttctgtttgctagttctgtaactattatgagtccaacctgtttagg
diff -r cbacbb736899 -r 8833ebe82ed1 test-data/sff_converter_fastq.dat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sff_converter_fastq.dat	Mon May 24 15:08:57 2010 -0400
@@ -0,0 +1,12 @@
+@GGOQ6K301BJT46
+gactACACGTAGTATAAGCTAAATGTTGGAGAGGATGCTGTAATCAACGTTTTGTGTCTCCTTACAGGACACCAGCTGATTTGGAGGTCATCCAATATAAACCTGGCTGGAACTTGCTATGGTTAGGAGAGCTATGAATGGAAGAGATAATTCCATTATTTAATAAGGCTACAGACAAATTAGGACAAGAAGCAGCTATTAGATTATTTAGTGCTAGCACACCTAAATAGAGAGAGATAAATTCATTAGACTTTTTGCTAttttattgacttttggagagacagtatttaaagtaccaaatcccagaggttgcctatgttggtggtgttgcaagctctattattggcgattgcaatctaccttatccataagttctgcttagagattatttgttattaattttcatctacatcaataaatataggacagtaaggattttgtacaaaatagacaatgggataggtaccagaagaggacagaggaattactggtattttgatatagactacactaacgtacgtacgtaggaattttaaccgggg
++
+FFFFFFFFFFFFFFFIIIIIHHHHHFFBBBFEDDFFFFFHHGFFFFFFF????FFFFFFDDFFFFF<==<ADDDDDDAC8::DCDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFFFFFFFFFFFFFFFFFFFFFA@@FFFFFFDD?????AAAAAB=??ADAACFFFFFDDDFFFFFFFFFDDDD544??8888000<2449=:<<?@841114?>AAAA?:::A???DBBA:::A?A//...::33,,,,------,,,,;;:89=9:9733...2223//9<688<444<AA::::8::BBAA@@>>>43434<4444449??@AA@BBBA:8:<A998<?4448<<<<244<3338<<>:884433822255,,,3--3,,,,,,,,,3774,,,33043///0,,,,,,,,,,,,111,,,,,),0....0),,,.,,,,,,,143.,,,.---86---20787777870206433,,,,,0,,,,,,,0..,,,...3,,,,-44444489965225666----
+@GGOQ6K301AWPXS
+gactACGTACACACTGGAATAAAATGGAGTTTTCATACTAGAGATTATTATATGGGCTATGTAAAAGAACTAGTAGCAGGATCTAGCACACCAGACAGCCTAAGACTGTATATTTTATATAAGCAACCCGTTATGGCATGGGAAATATCGCCCAGGGTTAAAAAATTTTAACAAGGAATGGCCTTTTTGTAAATATGTGGATAAAAAACAGGGTTCATGTGGGATGATATTGAAAAACAAAAGATTTGCGTAGGAGGAGAAATATCACCAGGATGGGGACCTGGAATGGTTGGCATAGCAAATAAAAGCCTTTAGTTGTGGGGAGAGAAAAATCGAGGCAACTCCTGTTATGATTATAAGAGAAGAGATAGATCCCAAAAAATGGTGTGGAGATTGTTGGAATTTAATGTGTCTTAGAAACTCACCTCCAGGAACGTTGTCAAAGACTCGCTATGTTGGCATGTGGACGGaaagactaaatgttggagaggatgctgtatcaacgttttgttgtcgtccttacacggacaccagctgtagttgtctgtagnttttaccggg
++
+FFFFFFFFFFFFFDDDFFD@3333BAA?95558HFFFFFHIIIIIIIHIIIHH?;;A???940000836?AAABDFFFFFFFFFFFFA@@FFFFFFFFFF===?<?????88111119??????ADCCCCAAAAAAAAB555:::?>CFD==;A<9966,,,,,,,,,,,,=887766=;;22-----<466694?ABAAAD666666D7FFFFFFFFFF666FFFF?;;:A;<<75B....D7333<@A@?888<AA==;;<7@><;;<688<00009<>???<<<===<<897==73...3----:99666:>7996/////-<<11202>??AA=:55448BBB===AAADDDDDAA>>===DB@>9723000,,,,,,300004;;><<:99666666.,,,,/7600,,,9922/33000020.00011742---223380220786646770---0331.00..,,,,,,0,,,,,,,..0144330,,,0.0,,,,,,,,,,,)),,,,,,1..,,,,,,,...,,,,,,.,,,,,,,,,,,,!//,--226::
+@GGOQ6K301A8J46
+gactACTATACGAGTCTGCCAATCTTCTTCACTCATCCCCTTCAGGAAGAGTGCAGGGTTCTGGGACTCTCCGTATGTGCCTCCTAGGTACAAGAAAATATCCCCTCTCTTCATCCTTTAATAACACTGATCCTTGTCCCCAATACTCTACTCTCATTGGTCCTTTCCAATTTTTGTCTTTTTTGATCTTTATAGTAAATCCACTGACCTTGCAATTTGCTTGGAATTTGAGAAAAATAATCCTGTATTCTTAATGATTCTTGTTGTGTTAATAATTCATATGGGGGCCATTCCCCCTATTCTACCCCTTTGTTTAAAATTAAGGCAATGCAGAGCGAGAGCCAAAGCATTGTCTAAAGATGTTGTTTCAGGCAAAAACTTCTGAATCCAACACTTTAAAGTATTATTggcattttcaaccaaagcttgagtattgagggttgcctggtattccaaatttatgttttattccctatgtaattgtagtaaaccttcctattttttgattttctaaaatttggtccctattgttctgtttgctagttctgtaactattatgagtccaacctgtttagg
++
+FFFFFFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIFFFFIIIIIIIIIIIIFHFFFFFFFF:::DFFFFFFFFFFFFFDDDFFFFAAABBDD=3333=7B::99?7BBBBBA?4400088/0008??BDDDDFFFFDDBBFFFFFFFFFFFFFFFFFFFFFF???DDB@--,,,=/7,,,,,-::==68<BAFFFFFFFDDDFFFFFFFFFDDD???FFFFDBA>999?94/////>34=;;?>?ABBB5666=BBBB?><=<<986....255---3==8,,,,,--357,,,,-8766=<=2444000977757664400554444<<?@@BDDDDDAAA???AAAAA555:???D<??>DD===DD88833553B443238<76654222....,07/166622///345429:<8888022263,,,.1300,,,00,0034413..,,,,-330-,000207..2220202.344.0.0.00027:----8://22--00,,,,,),,,,,,,00-000.0..00,,,0,,,.0430,,,.2022611...143,,,,,,,,,,000000
diff -r cbacbb736899 -r 8833ebe82ed1 test-data/sff_converter_qual.dat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sff_converter_qual.dat	Mon May 24 15:08:57 2010 -0400
@@ -0,0 +1,6 @@
+>GGOQ6K301BJT46
+37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 40 40 40 40 40 39 39 39 39 39 37 37 33 33 33 37 36 35 35 37 37 37 37 37 39 39 38 37 37 37 37 37 37 37 30 30 30 30 37 37 37 37 37 37 35 35 37 37 37 37 37 27 28 28 27 32 35 35 35 35 35 35 32 34 23 25 25 35 34 35 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 35 35 35 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 32 31 31 37 37 37 37 37 37 35 35 30 30 30 30 30 32 32 32 32 32 33 28 30 30 32 35 32 32 34 37 37 37 37 37 35 35 35 37 37 37 37 37 37 37 37 37 35 35 35 35 20 19 19 30 30 23 23 23 23 15 15 15 27 17 19 19 24 28 25 27 27 30 31 23 19 16 16 16 19 30 29 32 32 32 32 30 25 25 25 32 30 30 30 35 33 33 32 25 25 25 32 30 32 14 14 13 13 13 25 25 18 18 11 11 11 11 12 12 12 12 12 12 11 11 11 11 26 26 25 23 24 28 24 25 24 22 18 18 13 13 13 17 17 17 18 14 14 24 27 21 23 23 27 19 19 19 27 32 32 25 25 25 25 23 25 25 33 33 32 32 31 31 29 29 29 19 18 19 18 19 27 1!
 9 19 19 19 19 19 24 30 30 31 32 32 31 33 33 33 32 25 23 25 27 32 24 24 23 27 30 19 19 19 23 27 27 27 27 17 19 19 27 18 18 18 23 27 27 29 25 23 23 19 19 18 18 23 17 17 17 20 20 11 11 11 18 12 12 18 11 11 11 11 11 11 11 11 11 18 22 22 19 11 11 11 18 18 15 19 18 14 14 14 15 11 11 11 11 11 11 11 11 11 11 11 11 16 16 16 11 11 11 11 11 8 11 15 13 13 13 13 15 8 11 11 11 13 11 11 11 11 11 11 11 16 19 18 13 11 11 11 13 12 12 12 23 21 12 12 12 17 15 22 23 22 22 22 22 23 22 15 17 15 21 19 18 18 11 11 11 11 11 15 11 11 11 11 11 11 11 15 13 13 11 11 11 13 13 13 18 11 11 11 11 12 19 19 19 19 19 19 23 24 24 21 20 17 17 20 21 21 21 12 12 12 12
+>GGOQ6K301AWPXS
+37 37 37 37 37 37 37 37 37 37 37 37 37 35 35 35 37 37 35 31 18 18 18 18 33 32 32 30 24 20 20 20 23 39 37 37 37 37 37 39 40 40 40 40 40 40 40 39 40 40 40 39 39 30 26 26 32 30 30 30 24 19 15 15 15 15 23 18 21 30 32 32 32 33 35 37 37 37 37 37 37 37 37 37 37 37 37 32 31 31 37 37 37 37 37 37 37 37 37 37 28 28 28 30 27 30 30 30 30 30 23 23 16 16 16 16 16 24 30 30 30 30 30 30 32 35 34 34 34 34 32 32 32 32 32 32 32 32 33 20 20 20 25 25 25 30 29 34 37 35 28 28 26 32 27 24 24 21 21 11 11 11 11 11 11 11 11 11 11 11 11 28 23 23 22 22 21 21 28 26 26 17 17 12 12 12 12 12 27 19 21 21 21 24 19 30 32 33 32 32 32 35 21 21 21 21 21 21 35 22 37 37 37 37 37 37 37 37 37 37 21 21 21 37 37 37 37 30 26 26 25 32 26 27 27 22 20 33 13 13 13 13 35 22 18 18 18 27 31 32 31 30 23 23 23 27 32 32 28 28 26 26 27 22 31 29 27 26 26 27 21 23 23 27 15 15 15 15 24 27 29 30 30 30 27 27 27 28 28 28 27 27 23 24 22 28 28 22 18 13 13 13 18 12 12 12 12 25 24 24 21 21 21 25 29 22 24 24 21 14 14 14 14 14 12 27 27 16 16 1!
 7 15 17 29 30 30 32 32 28 25 20 20 19 19 23 33 33 33 28 28 28 32 32 32 35 35 35 35 35 32 32 29 29 28 28 28 35 33 31 29 24 22 17 18 15 15 15 11 11 11 11 11 11 18 15 15 15 15 19 26 26 29 27 27 25 24 24 21 21 21 21 21 21 13 11 11 11 11 14 22 21 15 15 11 11 11 24 24 17 17 14 18 18 15 15 15 15 17 15 13 15 15 15 16 16 22 19 17 12 12 12 17 17 18 18 23 15 17 17 15 22 23 21 21 19 21 22 22 15 12 12 12 15 18 18 16 13 15 15 13 13 11 11 11 11 11 11 15 11 11 11 11 11 11 11 13 13 15 16 19 19 18 18 15 11 11 11 15 13 15 11 11 11 11 11 11 11 11 11 11 11 8 8 11 11 11 11 11 11 16 13 13 11 11 11 11 11 11 11 13 13 13 11 11 11 11 11 11 13 11 11 11 11 11 11 11 11 11 11 11 11 0 14 14 11 12 12 17 17 21 25 25
+>GGOQ6K301A8J46
+37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 37 37 37 37 40 40 40 40 40 40 40 40 40 40 40 40 37 39 37 37 37 37 37 37 37 37 25 25 25 35 37 37 37 37 37 37 37 37 37 37 37 37 37 35 35 35 37 37 37 37 32 32 32 33 33 35 35 28 18 18 18 18 28 22 33 25 25 24 24 30 22 33 33 33 33 33 32 30 19 19 15 15 15 23 23 14 15 15 15 23 30 30 33 35 35 35 35 37 37 37 37 35 35 33 33 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 30 30 30 35 35 33 31 12 12 11 11 11 28 14 22 11 11 11 11 11 12 25 25 28 28 21 23 27 33 32 37 37 37 37 37 37 37 35 35 35 37 37 37 37 37 37 37 37 37 35 35 35 30 30 30 37 37 37 37 35 33 32 29 24 24 24 30 24 19 14 14 14 14 14 29 18 19 28 26 26 30 29 30 32 33 33 33 20 21 21 21 28 33 33 33 33 30 29 27 28 27 27 24 23 21 13 13 13 13 17 20 20 12 12 12 18 28 28 23 11 11 11 11 11 12 12 18 20 22 11 11 11 11 12 23 22 21 21 28 27 28 17 19 19 19 15 15 15 24 22 22 22 20 22 21 21 19 19 15 15 20 20 19 19 19 19 2!
 7 27 30 31 31 33 35 35 35 35 35 32 32 32 30 30 30 32 32 32 32 32 20 20 20 25 30 30 30 35 27 30 30 29 35 35 28 28 28 35 35 23 23 23 18 18 20 20 18 33 19 19 18 17 18 23 27 22 21 21 20 19 17 17 17 13 13 13 13 11 15 22 14 16 21 21 21 17 17 14 14 14 18 19 20 19 17 24 25 27 23 23 23 23 15 17 17 17 21 18 11 11 11 13 16 18 15 15 11 11 11 15 15 11 15 15 18 19 19 16 18 13 13 11 11 11 11 12 18 18 15 12 11 15 15 15 17 15 22 13 13 17 17 17 15 17 15 17 13 18 19 19 13 15 13 15 13 15 15 15 17 22 25 12 12 12 12 23 25 14 14 17 17 12 12 15 15 11 11 11 11 11 8 11 11 11 11 11 11 11 15 15 12 15 15 15 13 15 13 13 15 15 11 11 11 15 11 11 11 13 15 19 18 15 11 11 11 13 17 15 17 17 21 16 16 13 13 13 16 19 18 11 11 11 11 11 11 11 11 11 11 15 15 15 15 15 15
diff -r cbacbb736899 -r 8833ebe82ed1 test-data/sff_converter_xml_1.dat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sff_converter_xml_1.dat	Mon May 24 15:08:57 2010 -0400
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<trace_volume>
+    <trace>
+        <trace_name>GGOQ6K301BJT46</trace_name>
+        <clip_vector_left>5</clip_vector_left>
+        <clip_vector_right>260</clip_vector_right>
+    </trace>
+    <trace>
+        <trace_name>GGOQ6K301AWPXS</trace_name>
+        <clip_vector_left>5</clip_vector_left>
+        <clip_vector_right>470</clip_vector_right>
+    </trace>
+    <trace>
+        <trace_name>GGOQ6K301A8J46</trace_name>
+        <clip_vector_left>5</clip_vector_left>
+        <clip_vector_right>408</clip_vector_right>
+    </trace>
+</trace_volume>
diff -r cbacbb736899 -r 8833ebe82ed1 test-data/sff_converter_xml_2.dat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sff_converter_xml_2.dat	Mon May 24 15:08:57 2010 -0400
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<trace_volume>
+    <trace>
+        <trace_name>GGOQ6K301BJT46</trace_name>
+        <clip_vector_left>5</clip_vector_left>
+        <clip_vector_right>260</clip_vector_right>
+    </trace>
+    <trace>
+        <trace_name>GGOQ6K301AWPXS</trace_name>
+        <clip_vector_left>5</clip_vector_left>
+        <clip_vector_right>470</clip_vector_right>
+    </trace>
+    <trace>
+        <trace_name>GGOQ6K301A8J46</trace_name>
+        <clip_vector_left>5</clip_vector_left>
+        <clip_vector_right>408</clip_vector_right>
+    </trace>
+</trace_volume>
diff -r cbacbb736899 -r 8833ebe82ed1 tools/filters/sff_extractor.xml
--- a/tools/filters/sff_extractor.xml	Mon May 24 15:05:55 2010 -0400
+++ b/tools/filters/sff_extractor.xml	Mon May 24 15:08:57 2010 -0400
@@ -1,39 +1,58 @@
 <tool id="Sff_extractor" name="SFF converter" version="1.0.0">
-  <description></description>
-  <command interpreter="python">
-    #if   str($fastq_output) == "fastq_false"  #sff_extract.py $clip --seq_file=$out_file3 --qual_file=$out_file4 --xml_file=$out_file2 $input
-    #elif str($fastq_output) == "fastq_true"   #sff_extract.py $clip --fastq --seq_file=$out_file1 --xml_file=$out_file2 $input
-    #end if#
-  </command>
-  <inputs>
-    <param format="sff" name="input" type="data" label="Extract from this dataset"/>
-    <param name="clip" type="select" label="Completely remove ends with low qual and/or adaptor sequence">
-      <option value="">No</option>
-      <option value="--clip">Yes</option>
-    </param>
-    <param name="fastq_output" type="boolean" truevalue="fastq_true" falsevalue="fastq_false" checked="False" label="Do you want FASTQ file instead of FASTA + FASTA quality file?" />
-  </inputs>
-  <outputs>
-    <data format="fastq" name="out_file1" >
-      <filter>fastq_output is True</filter>
-    </data>
-    <data format="xml" name="out_file2">
-    </data>  
-    <data format="fasta" name="out_file3">
-      <filter>fastq_output is False</filter>
-    </data>
-    <data format="qual" name="out_file4">
-      <filter>fastq_output is False</filter>
-    </data>
-  </outputs>
-  <help>
+    <description></description>
+    <command interpreter="python">
+        #if   str($fastq_output) == "fastq_false"  #sff_extract.py $clip --seq_file=$out_file3 --qual_file=$out_file4 --xml_file=$out_file2 $input
+        #elif str($fastq_output) == "fastq_true"   #sff_extract.py $clip --fastq --seq_file=$out_file1 --xml_file=$out_file2 $input
+        #end if#
+    </command>
+    <inputs>
+        <param format="sff" name="input" type="data" label="Extract from this dataset"/>
+        <param name="clip" type="select" label="Completely remove ends with low qual and/or adaptor sequence">
+            <option value="">No</option>
+            <option value="--clip">Yes</option>
+        </param>
+        <param name="fastq_output" type="boolean" truevalue="fastq_true" falsevalue="fastq_false" checked="False" label="Do you want FASTQ file instead of FASTA + FASTA quality file?" />
+    </inputs>
+    <outputs>
+        <data format="fastq" name="out_file1" >
+            <filter>fastq_output is True</filter>
+        </data>
+        <data format="xml" name="out_file2">
+        </data>  
+        <data format="fasta" name="out_file3">
+            <filter>fastq_output is False</filter>
+        </data>
+        <data format="qual" name="out_file4">
+            <filter>fastq_output is False</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="2.sff"/>
+            <param name="clip" value=""/>
+            <param name="fastq_output" value="false"/>
+            <output name="out_file2" file="sff_converter_xml_1.dat"/>
+            <output name="out_file3" file="sff_converter_fasta.dat"/>
+            <output name="out_file4" file="sff_converter_qual.dat"/>
+        </test>
+        <test>
+            <param name="input" value="2.sff"/>
+            <param name="clip" value=""/>
+            <param name="fastq_output" value="true"/>
+            <output name="out_file1" file="sff_converter_fastq.dat"/>
+            <output name="out_file2" file="sff_converter_xml_2.dat"/>
+        </test>
+    </tests>
+    <help>
+
 **What it does**
 
 This tool extracts data from the 454 Sequencer SFF format and creates three files containing the: 
-    Sequences (FASTA),
-    Qualities (QUAL) and 
-    Clippings (XML)
-  </help>
+Sequences (FASTA),
+Qualities (QUAL) and 
+Clippings (XML)
+
+    </help>
 </tool>

    

Nate Coraor

tags

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