| Previous changeset 16:4c6e4d583b8f (2014-02-25) Next changeset 18:381aa262c8cb (2014-03-25) |
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Commit message:
Uploaded v0.0.2 preview 9, more functional tests |
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modified:
tools/mira4/README.rst tools/mira4/mira4_de_novo.xml tools/mira4/mira4_mapping.xml |
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added:
test-data/U13small_m.fastq test-data/U13small_m.mira4_de_novo.fasta |
| b |
| diff -r 4c6e4d583b8f -r 5bbaa930d7fa test-data/U13small_m.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/U13small_m.fastq Mon Mar 03 11:49:21 2014 -0500 |
| b |
| b"@@ -0,0 +1,104 @@\n+@122533a.t3\n+ACGCGTTATTAAAGACTTTTTTTTTGGTTTTTTTCAAGTTCAAGTATTCTTTATTCAAAGTTGAAACATGTACCATACTGCATTATTGCAAAAATTCACTGGTACAAAACACTTTGCAGCTGGTGAGAAGGCAATAAAAAGTTGATTTTTAAACTCATTACTATAAATTATTCTTACAGTACTTTGCAAATTCAGAATTTCAAACTGCATGTTCTTTTTCTAAATTGCCCACAGTACTCGAGGTTCCTGAAGCTAAGGCAGCTGTTTCATAGGAGGGGGAAGAAGTATCAAATCTCTTGGGATTTCCATTTCTCTTTCCATGCCGACATACTTCAGGGCATCTTCCTGACTGTCTCTTTTTTCGGGAAACTTCTCTTCGCCAATCTGGATGGCTCTCTCGGCAAAAATACCTATCCTGTGATCACCGTTAACCATCATAACTTTTGCATACCACTTTGGATTTACCACCGATATGCCACAACGATTTTTGTTACCCTTGCAGGTTGCACCACCCAAAATCGTTGTTCTTTTGCCCTTGCCAAATTCTGGGCCCCAAGGGCCAATTCCCCAAAATTAATCCTTTTAATTTCGTGGGCCGCGTTCCAGCTGTCCCCCTTGTTGAAGGTTTTTTTTCGCCCCCCGGCTCTCCCCCCCCCTTTTTAAACCCCGTAAACCATTATAGTTGGTTAAACCCCCGGGGGGTTCCCCCTTGTAAATTTTACCCCCCCCTCTCCCCCATTTAAAAATATGTGCCCTTTTTCTCCCCCCCACTGGGCCCGGGGTTTTCTCCTATTCCGGGGAAAGAAAAACCCTGTTTTCTCTTCGCCAAAATACTCCCCCCCCCCTTTTTATAAAAAAAAAAAAAACTTGGGGGCCCCCACCCCCCCCCGGGGGGGAAAAAAAAAAGCGCGGGGTTTTTGCGCGTTTTTTTTGGGGGGGGGGGGGTTTCTTTTCCCCCCCTTTTTTCCTTCCCCCCCAAAGGAGAAAAAATCTTTTTTGTTGGGGCGCCTCCCGGCGCCCCTCCCGGGGTTGGCGCGGCGAAAACGCGGTTTTTCCCCCCCCCCCAAAGGGGGGGGCGCAGATACCGCGTTTACTCCCCATAAATACTCCGGGGGGGAATAACATCCCGGGAAAAAAAAATTTTATATCTATATATGGGGCCTCCCAAAAAGGGGCATAAAACACGGAGAAACCGGCGCCCTTGTGTGGGCGTTTTTCTCTCAATGGGCGCCCCCCCCCTCAACAAAAATAAAAA\n++\n+'%+2*(6.+;8:2)+(*).1AA88(-,(88AA=;==99@;BC21-,,-8?91695?=5:7?;11,)(*-55==@:BABBAEABABA?BA??;<?<7AAAA?A<<B=9:620576:;@;4>>;@;;7*0/*22;@BCCBE@F?<??DACAAABDAACD?=<B?BB@DA@?B@<@=9B>@??8??678>0,6?9@>8>;?CAEAD??>@DEA>?4>A?C?8;7:A?ACCAADB>=-5;3>:/6-3:6@A4597->58:6318=B?DAA?72*/+.1)01771-.1.+/+).(610)-7-(,0-8968?:/A/4928,))-+1))21/1-6??>9:3-572629.)2510-+,,/5,3,*+.)*.)*+/.7>-..00,+.40:82+68.;2/,-.)+.-+*)**)626;?988623-37./5/1))78@>G<??>;5:>7:/--68;8?A40/,.1--.5:768.4))(())(+%)))+*))**((+(*(*0*--/;::2,+()))++)**,--:2**2/2(*)+,*))+((0-,/*))*+)*+-2+()++/**,,*-=751,,)((*25;(,,2),(-.(*,-+1-.,,./-%.%*1,,'()+)+('%.*)*))0,&(+(),),+++,/*./*,*,))))*)(%%%+-%**,3.+)0**202%-0,,20*/(*,*++))(0())()'(+))17:84.)+1.)))+))41,)$'''))'*0))&),3-,))++-)*+..*',,),+.+.((.**+++),*+,)%(.,/51+()''),.,*/--+(002/((,&+&*,*,+,,,*)*),*)-))*+*%.***,(+))$'&+%)*-'%*0.*+***///+.,,*)*),-*267<;30-(%)**(,1456;63)*,*,+=759.3-.342-*-+0())'))**,)200,)025))++++(*/466,',$))12*&///,)()*)/)+-),2-,**,*1.1.,***,)/,22-*%)),*&/)+',,++)/,**)((()))*,%(*)+)))(*&)).03&1;5:22))+))'.-))+&+/+)))((+*+,33=36-,,3//,+)+)),./+,)*+))*(*)))))%)),)$'+)+,*&)+++,-))**++7702&**1+)-*(*-+)+*)))/1.0.+,-)*)(**.*)**')'')$*.-)42)**00),+*)))%*,)).+.-.****(()(+)-)(()*.())((-*,(++//+,1*.-()/31/8/,/47;7,+(),324)*))(**0C@\n+@122533a.t7\n+GTTCGAGCAATATCCCTACGATCAACTAGAACAATGATTTTGTGGTGGATGCAACCCGCAAGGGTAACAAAATTCGTTTTGCAAATCATTCGGTAAATCCAAACTGCTATGCAAAAGTTATGATGGTTAACGGTGATCACAGGATAGGTATTTTTGCCAAGAGAGCCATCCAGACTGGCGAAGAGCTGTTTTTTGATTACAGATACAGCCAGGCTGATGCCCTGAAGTATGTCGGCATCGAAAGAGAAATGGAAATCCCTTGACATCTGCTACCTCCTCCCCCTCCTCTGAAACAGCTGCCTTAGCTTCAGGAACCTCGAGTACTGTGGGCAATTTAAAAAAAGAACATGCAGTTTGAAATTCTGAATTTGCAAAGTACTGTAAGAATAATTTATAGTAATGAGTTAAAAATCAACTTTTATTGCCTTCCACCACTGCAAGTGTTTGTACCGTGAATTTTGCAATAATGCCATATGGTACATTTTCCACTTTGAATAAAGAATACTTGAGCTTGAAAAAAAAAAAAAAAAAAGATTCTTTATTTAAGCGGCCGCGAGCTTTTCCCTTTAATAGGGTTAATTTAACTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX\n++\n+&&&,1/?/,/(+)+'('+)(1.+*+,0**1-1574=====EBAABA=:=56;6879=>7-025<???@BA>>>;?ACBA?A?AAAEBEA?ABAA=FF@@??AA?@AA?A=@=A<<ACAAAD?==>@==@=@E=@@A@=A@;2:22-&623@DFBAABB=59;/888B?B?<72;;:@==84.)1,9AAEEFECB???;B?<>??;BCBAAAAAA?==>=@DA??;7.<8<524/37AA??><.,1.87====AEB@AAA===869BA@?=@=?AAAABBABBABAAAAAC==A??ABBBEEDAEEBA97:053064:A7;)2,,2.63:5==>=@:::A@;A=7A==A?AAA?A=9====??=D====B@@=:E=A@AAA?;4:6=64==?AABAB05**33/,116>E@==9=:=:?@=:A=466,-)*..--/1230627:3666;.,*(1,996E<6;5@=8=@8-(/)"..b"AAAACAATAGAAATTAGTTATCCTGTCACGTGGGTTAAATGCAGCTGTTAATAAAATAGGCAAAGTAGTTGTCAAGAGTTAATCAGATACACTTCTGCAAGGATGACTAGTTTTATAAAATAAAATAATGGCATCAAAATGAATACCAGTTGAGTAATGTATTACTTTAAAATAACTGTGGGATCTTAAGTCATTTTATAAACACACTAGACCCATCAGACTCAATTTTTTTTTTCAATTTCAAGTATTCTTTATTCCAAGTTGAAAAATATCCATACTGCATTATTGCAAAAATTCACTGGTACAAAACACTTTGCAGCCGGGTGAGAAGGCCATAAAAAATTGAGTGTTTAAACTCATTGCTATAAATTATTCTTATAGTTCTCTTGCCAATTTCGAAATTTCAAACGGGCCTTTTCTTTTTTCTAAATTGCCCACCGTTTCCCGAAGGTTCCTGAAACCAAACTGAACGGAAGAAGGGAAAGTGTGTGAATAACTC\n++\n+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!=9=;49.-,,66,2(*18=56--1A;CEC?4787<?A;;;A:=BBAA=@@992;A>@D?EAEB894+75??BD?AAAAA??@=B=@?A??B???ABBEAAAABA@@@?CCFBBBAC@A>???>;AA@ACA?;8817AA?=;8;58?DDBAAAC???>CC93.*9.8CAAABAEDA@>D????A@??5:94>?:@BAA=??A?CDA@CCAB@AADC??97176/6;1?ADABAAAAAADAAAAEAAAAAAAAAAAAD??@??@DDAAA??8===?AAAAAAAADAAABABBBCAADAADDFAD@?CADDD?=A<5;2686==AAAC@AA@DDFCAFD??;;:8AA=>@:=9:==>>=88:+363?=;?@@EDFAAAAA?AA?AA??AAA===C?;<?@??=844.97?A@?:9A97B;;=>>AD9::646+6>2>806669>@??;8@???@=<<;@;E@D@AABAD>=>>=@===AAAEFFAAAAAAA??59?=@?20)),.7<@DC>==9=>A@;6532748?@@;<5<==A;==8==61**0-12173>@<@=A@2935<EBAA??AA??B>81..2988:61*25:<B@CCAADDEAAA??B?AA61-+34/836ADAA@98/8:55-397BD:1+,.2,.**/+--0?<8-,2*-24=;;5?>/5+,*24.,.+(+))*(-*(,))-)(-*(9,,,,(*.6@AA>-/-/((),+23;67>61)()(*()****,5:>A8;-,-*())))+))),,-,*+*,%15*43,+)))*(-3+,,65,*++,/-+((+,.36-4,+)+((0,())+&3*.)*++**)/4(5/(3..*)-/0453315702**-*14*-+/+(+.*((++\n+@U13e07f02.t2\n+ACATGCTGCAGTCGATCTAGAGGATCCCATGTCAAGGGATTTCCATTTCTCTTTCAATGCCAACATACTTCAGGGCATCAGCCTGGCTGTATCTGTAATCAAAAAACAGTTCTTCGCAAGTCTGGATGGCTCTCCTGACAAAAACACCTATCCTGTGATCACCATTAACCATCATAACTTTTGCATAGCAGTTTGGATTTACCGAATGATTTGCAAAACGAATTTTGTTACCCTTGCAGGTTGCATCCACCACAAAATCATTGTTCAAGTTGAACAGAAAGCTGCACATGTATTTATCACACACTTTCCCTCTTCCGTCAGCTTAGCTTCAGGAACCTCGAGTACTGTGGGCAATTTAAAAAAAGAAAATGCCGTTTGAAATTCTGAATTTGCAAAGTACTATAAGAATAATTTATAGCAATGAGTTTAAAACTCGACTTTTTATTGCCTTCTCACCAGCTGCAAAGTGTTTTGTACCAGTGAATTTTTGCAACAATGCAGTATGGTTTATTTTTCAACTTTGAATAAAGAATACTTGTAAATTGAAAAAAAAAATTGGAGTTCTGGATGGGTCTACGTGGTGTTTATAAAATAACCTAACGCATCGCCCCATCCAGCTTTTTTTCTGAGAGAGTACAGATACCAGCCACTCCCGCGGGGTTGTTTCGATCTTGCAATGCCCCGCCAACTTTTTAATTTTTAGCAGAAAACCCCAGGTTCTAGCTCCCATTGACCAGAAAAATTGTTTATCCTCGGAAATACAAACGCCCTGTTGGAACCACAACTCATGCCTCTCTGCGCCCCTCAAGTTCGTGTAAATGTGAAAACCAGCGCCCCGCCCCGAGTTTTAGAAACGCCCGCCCCGCCTTGTGGAAGCCTTAGGGGAAGTATAACGCCCAGCGACGTTCTGCTCTCCTGGACAGCGTCGGCGTATGGTATCTGACGGTCTAAACATACGTCACGTAACGGGAGCCCCCCTCTTCCGCATCTCTCCCCACTATTTGTGGCTAGCAGAAGAGAAATAATAAGCCGCAGCGTATCTGATGAGGAGCAGACGTTATCACGCTCTGCGGTGGCGGTCTTTAGAACACAAAATTTCGCTGTTGTCGCGCCCTTCTCCGACGGAAAAGAGAAAAAACCCTCTCTGTCTTTTCTATTAAAATAAGTAATTGGTGGGTTTTTTCTGCTGCCTTCTGACGACGACCGAAGAGAAACGCGGGTTTTGTATAACGCAGATATCACATCGCGCGCCCTCCGCGTCCG\n++\n+*'-,,*55(,++/)''..912.-')).3ABAABAA=02-633===ABBAAA?A?A@AECAAAABADAA<>225*5/.6=?AADDAAAAABB???C?AAAAAEE?AA?A@AAAA??=@;:;77:9=B=>AABCA??B??A?AAAAAAAAAACCA=8<;C==@@@@A?AA?A?AAAAADAAAAADA::>67:5A==????=?9965?>9>?>>ADAAAB39*776??DC?<<?A<??88;69;>;A59A@?@@AAAAA@A?=AC@AC@8A18094130.9525;7;>;=77>>5;@@?=A8:?@>>==A;??>>?@@A<;<7;9-*1(//,0577;231.,+828=92;;@@;?@?A84:197138.705AA@@A@@88889....02;?@>=:?@99>A@@AD=6:6=7395577A;=B84*-)2/8FB@@@<13.*/8=@@??;98181215<<;:=9/.***(++*+),*/2571-65*7/8944/3,0*&+)),28;2*0*.000*/,.7>=>5.1.1389B83;.3.2,(2-())&,)01/.318=84-,**((+)/)22-**,.*+2-+(()(,,**.2659.+-+),,%-)))*())(((,,,)(,,+**)(()*(**)+%*()&*'')'')+)))(+**))')(),*)&+%)-,*-)**,.))**+,,*-.*)-,,)(((()(()*-++*)*-**,)*((((),-,))(()('))((())**)*)+)*+*,.22-),+*++*++**,)*..2-)(+***+&('(+&((()+**,*,)***))())))+,(,.((,*-.***(*)((''('('(*(*)))*,*(%$)(()((().3+(((*-**'%)))+++)+*,*)*+--**)*,(*,&&)%%+-1,+*-)+*''('(')*))()+)++))'())))))*)))*-,*,,)))))(*)(((-)***+,*)(*+-*)&()''*.).('&)'*)-))()++30*+**%***(,))),))-,0))(++***((())*1,-64/2,./.-/()).*)))))(('')++).++,))--))-)6'(''''(-,//,/)%)((+((''***()/*())*+*0'+)*+**),*))+'((&(+**,-+*)+-:;.,*,**)+()'+2-192-*+(+(*$$+$)'))0+,*,2*)-).+'+''*)(+*,))*&*++')(++(+(()+))($(&(*+().'*+)))+)'-))+)&*))))**))*)()*+)*,+))))'+)+/12,)(')+$'*()(*\n" |
| b |
| diff -r 4c6e4d583b8f -r 5bbaa930d7fa test-data/U13small_m.mira4_de_novo.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/U13small_m.mira4_de_novo.fasta Mon Mar 03 11:49:21 2014 -0500 |
| b |
| @@ -0,0 +1,47 @@ +>MIRA_rep_c1 +aaatttcataaaatttctcatttcaaaaacgagaaaattaaggccttgcggggttaaatc +gttatcaagtaatcagtcggctcactgcccagtgtggacactggccaatattatggcacc +agcctttgagaaaaggaaacctttttttgaatccatctccctgacctggggtttgggttg +ggttttatcagcatagggtgacaggcaagttcaatctgattggatcctggatcccatcat +ggggtatctgttcctaaatcattccctgatcctcggtcagagcgagcgcttaggttcccg +ctgcagttaaacacctggttcatctgggcatactaaggttatgactttccacctgggagt +ccacgacaactgaaaaaactcaaaacttctttaagtagaagttgagcctgaagctgaggc +agctgtttcagagaggaggaggaggaggagatagcaaatgtcaagggatttccatttctc +tttcaatgccaacatacttcagggcatcagcctggctgtatctgtaatcaaaaaacagtt +cttcgcaagtctggatggctctcctgacaaaaacacctatcctgtgatcaccattaacca +tcataacttttgcatagcagtttggatttaccgaatgatttgcaaaacgaattttgttac +ccttgcaggttgcatccaccacaaaatcattgttcaagttgaacagaaagctgcacatgt +atttatcacacactttccctcttccgtcagcttagcttcaggaacctcgagtactgtggg +caatttagaaaaagaaaatgccgtttgaaattctgaatttgcaaagtactataagaataa +tttatagcaatgagtttaaaactcaactttttattgccttctcaccagctgcaaagtgtt +ttgtaccagtgaatttttgcaataatgcagtatggtatatttttcaactttgaataaaga +atacttgaaattgaaaaaaaaaattgagtctgatgggtctagtgtgtttataaaatgact +taagatcccacagttattttaaagtaatacattactcaactggtattcattttgatgcca +ttattttattttataaaactagtcatccttgcagaagtgtatctgattaactcttgacaa +ctactttgcctattttattaacagctgcatttaacccacgtgacaggataactaatttct +attgtttttgtatttttgcctcctccttccaagatagcagtagagtactgtgttaaatct +tgcttcagaagagcttgtttaaaatagttataaagaaagtaaaatacatagaaaaacacg +ttataattttaaattaaaaaagaaaaaagatgtctactctgaataaattatgcatacata +taaggtctgaacaaaaacatgaaaagatgggctctgagtatcaattttaaaaatctttac +cagtataacattactcaaacaaaaattaaaatttaatataattaagtacatattccaaga +caacaaatggaccttgactgttaattctgg +>MIRA_rep_c2 +gcaatatcgtgacgatatgtawgataaatacatgtgcagctytctgttcaacttgaacaa +tgattttgtggtggatgcaacccgcaagggtaacaaaattcgttttgcaaatcattcggt +aaatccaaactgctatgcaaaagttatgatggttaacggtgatcacaggatakgtatttt +tgccaagagagccatccagactggcgaaragctgttttttgattacagatacagccaggc +tgatgccctgaagtatgtcggcatcgaaagagaaatggaaatcccttgacatctgctacc +tcctccccctcctctgaaacagctgccttagcttcaggaacctcgagtactgtgggcaat +ttaaaaaaagaacatgcagtttgaaattctgaatttgcaaagtactgtaagaataattta +tagtaatgagtttaaaaatcaactttttattgccttctcaccagctgcaaagtgttttgt +wccagtgaattttgcaataatgcagtatggtacattttcactttgaataaagaatacttg +a +>MIRA_rep_c3 +gcgttattaaagacttttttttwtttttttttcaagttcaagtattctttattcaaagtt +gaaaaatgtaccatactgcattattgcaaaaattcactggtacaaaacactttgcagctg +gtgagaaggcaataaaaagttgatttttaaactcattactataaattattcttacagtac +tttgcaaattcagaatttcaaactgcatgttctttttctaaattgcccacagtactcgag +gttcctgaagctaaggcagctgtttcagaggagggggargaagtaycaaatytcwaggga +tttccatttctctttccatgccgamatacttcagggcatcagcctgactgtmtctgtaat +caaaaaacakctcttcgccavtctggatggctctctyggcaaaaatacctatcctgtgat +caccgttaaccatcataacttttgcatagcattt |
| b |
| diff -r 4c6e4d583b8f -r 5bbaa930d7fa tools/mira4/README.rst --- a/tools/mira4/README.rst Tue Feb 25 13:13:17 2014 -0500 +++ b/tools/mira4/README.rst Mon Mar 03 11:49:21 2014 -0500 |
| b |
| @@ -98,7 +98,7 @@ For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder:: - $ tar -czf mira4_wrapper.tar.gz tools/mira4/README.rst tools/mira4/mira4_de_novo.xml tools/mira4/mira4_mapping.xml tools/mira4/mira4_bait.xml tools/mira4/mira4.py tools/mira4/mira4_make_bam.py tools/mira4/mira4_validator.py tools/mira4/mira4_bait.py tools/mira4/tool_dependencies.xml tools/mira4/repository_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta test-data/tvc_map_ref_strain.fasta test-data/tvc_map_same_strain.fasta test-data/tvc_bait.fasta test-data/tvc_mini_bait_pos.fastq test-data/tvc_mini_bait_strict.fastq test-data/tvc_mini_bait_neg.fastq test-data/ecoli.fastq test-data/ecoli.mira4_de_novo.fasta test-data/empty_file.dat + $ tar -czf mira4_wrapper.tar.gz tools/mira4/README.rst tools/mira4/mira4_de_novo.xml tools/mira4/mira4_mapping.xml tools/mira4/mira4_bait.xml tools/mira4/mira4.py tools/mira4/mira4_make_bam.py tools/mira4/mira4_validator.py tools/mira4/mira4_bait.py tools/mira4/tool_dependencies.xml tools/mira4/repository_dependencies.xml test-data/U13small_m.fastq test-data/U13small_m.mira4_de_novo.fasta test-data/tvc_mini.fastq test-data/tvc_contigs.fasta test-data/tvc_map_ref_strain.fasta test-data/tvc_map_same_strain.fasta test-data/tvc_bait.fasta test-data/tvc_mini_bait_pos.fastq test-data/tvc_mini_bait_strict.fastq test-data/tvc_mini_bait_neg.fastq test-data/ecoli.fastq test-data/ecoli.mira4_de_novo.fasta test-data/empty_file.dat Check this worked:: @@ -113,6 +113,8 @@ tools/mira4/mira4_bait.py tools/mira4/tool_dependencies.xml tools/mira4/repository_dependencies.xml + test-data/U13small_m.fastq + test-data/U13small_m.mira4_de_novo.fasta test-data/tvc_mini.fastq test-data/tvc_contigs.fasta test-data/tvc_map_ref_strain.fasta |
| b |
| diff -r 4c6e4d583b8f -r 5bbaa930d7fa tools/mira4/mira4_de_novo.xml --- a/tools/mira4/mira4_de_novo.xml Tue Feb 25 13:13:17 2014 -0500 +++ b/tools/mira4/mira4_de_novo.xml Mon Mar 03 11:49:21 2014 -0500 |
| b |
| @@ -151,7 +151,7 @@ <!-- Simple assembly based on MIRA's minidemo/demo4 example Note we're using just one repeat group, but several parameters with the repeat - (in order to specify sanger reads, no pairing) + --> <test> <param name="job_type" value="genome" /> <param name="job_quality" value="accurate" /> @@ -159,9 +159,11 @@ <param name="type" value="none" /> <param name="filenames" value="U13small_m.fastq" ftype="fastqsanger" /> <output name="out_fasta" file="U13small_m.mira4_de_novo.fasta" ftype="fasta" /> + <output name="out_bam" file="empty_file.dat" compare="contains" /> + <output name="out_maf" file="empty_file.dat" compare="contains" /> + <output name="out_log" file="empty_file.dat" compare="contains" /> </test> - --> - <!-- Simple assembly based on MIRA's minidemo/solexa1 example + <!-- Simple assembly based on MIRA's minidemo/solexa1 example Note we're using just one repeat group, but two parameters within the repeat (filename, no pairing) --> |
| b |
| diff -r 4c6e4d583b8f -r 5bbaa930d7fa tools/mira4/mira4_mapping.xml --- a/tools/mira4/mira4_mapping.xml Tue Feb 25 13:13:17 2014 -0500 +++ b/tools/mira4/mira4_mapping.xml Mon Mar 03 11:49:21 2014 -0500 |
| b |
| @@ -157,27 +157,30 @@ </configfile> </configfiles> <tests> - <!-- Deliberately using default read_group.technology value "solexa" - as then Galaxy's broken <repeat> handling in tests should work... --> - <!-- Tests currently failing, - TwillException: more than one form; you must select one (use 'fv') before submitting <test> <param name="job_type" value="genome" /> <param name="job_quality" value="accurate" /> <param name="references" value="tvc_contigs.fasta" ftype="fasta" /> <param name="strain_setup" value="default" /> + <param name="type" value="none" /> <param name="filenames" value="tvc_mini.fastq" ftype="fastqsanger" /> - <output name="out_fasta" file="tvc_map_same_strain.fasta" ftype="fasta" /> + <output name="out_fasta" file="tvc_map_ref_strain.fasta" ftype="fasta" /> + <output name="out_bam" file="empty_file.dat" compare="contains" /> + <output name="out_maf" file="empty_file.dat" compare="contains" /> + <output name="out_log" file="empty_file.dat" compare="contains" /> </test> <test> <param name="job_type" value="genome" /> <param name="job_quality" value="accurate" /> <param name="references" value="tvc_contigs.fasta" ftype="fasta" /> <param name="strain_setup" value="same" /> + <param name="type" value="none" /> <param name="filenames" value="tvc_mini.fastq" ftype="fastqsanger" /> - <output name="out_fasta" file="tvc_map_ref_strain.fasta" ftype="fasta" /> + <output name="out_fasta" file="tvc_map_same_strain.fasta" ftype="fasta" /> + <output name="out_bam" file="empty_file.dat" compare="contains" /> + <output name="out_maf" file="empty_file.dat" compare="contains" /> + <output name="out_log" file="empty_file.dat" compare="contains" /> </test> - --> </tests> <help> |