| Previous changeset 0:d35cc8e07d00 (2018-05-08) Next changeset 2:da22667725c7 (2024-03-12) |
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Commit message:
planemo upload for repository https://github.com/AbeelLab/lorikeet commit ac00b82e6df1867b3fedbd09dffa6809f61b7352 |
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modified:
lorikeet.xml |
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added:
test-data/input.fastq test-data/input.fastq.gz |
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| diff -r d35cc8e07d00 -r f9c37d0b3002 lorikeet.xml --- a/lorikeet.xml Tue May 08 04:23:01 2018 -0400 +++ b/lorikeet.xml Tue Jun 19 02:01:02 2018 -0400 |
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| @@ -2,7 +2,7 @@ <description>M. tuberculosis DNA fingerprinting</description> <macros> - <token name="@TOOL_VERSION@">17</token> + <token name="@TOOL_VERSION@">20</token> </macros> <requirements> @@ -21,7 +21,7 @@ ]]> </command> <inputs> - <param name="input" label="Input sequences" type="data" format="bam" help="Reads of sample(s) being spoligotyped" /> + <param name="input" label="Input sequences" type="data" format="bam,fastq,fastq.gz" help="Reads of sample(s) being spoligotyped" /> <conditional name="spacer_source"> <param type="select" name="source_type" label="Source for spacer sequences"> <option selected="true" value="builtin">Built-in</option> @@ -47,6 +47,22 @@ </output> </test> <test> + <param name="input" value="input.fastq" ftype="fastq" /> + <output name="output_txt"> + <assert_contents> + <has_text text="1111111111 1111111011 1111111111 1100001111 111" /> + </assert_contents> + </output> + </test> + <test> + <param name="input" value="input.fastq.gz" ftype="fastq.gz" /> + <output name="output_txt"> + <assert_contents> + <has_text text="1111111111 1111111011 1111111111 1100001111 111" /> + </assert_contents> + </output> + </test> + <test> <param name="input" value="input.bam" ftype="bam" /> <param name="source_type" value="file" /> <param name="spacer" value="custom_spacers.fasta" ftype="fasta" /> |
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| diff -r d35cc8e07d00 -r f9c37d0b3002 test-data/input.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fastq Tue Jun 19 02:01:02 2018 -0400 |
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| b"@@ -0,0 +1,2728 @@\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:100:11753:6254\n+CCATTCCCTCTCCCCACGTGTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAACTTGCGCCAACCCTTTCGGTGTGATGCGGATGGTCGGCTCGGGGGGTCAGA\n++\n+HGFHHEDHDHHHDHHGDDEBEBGGGBDGGGHFHH@GDGGG8C8AEADAAGEDDDBBB<>BB<@BDDDB>BBB8:2+4138@A@=;AA2A@###############\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:100:11933:20378\n+GACCCAAAACCCCGAGAGGGGACGGAAACTCGGGGAGCCGATCAGCGACCACCGCACCCTGTCAGTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAACTTTAT\n++\n+IHIIIIIIIIIIIIFHHIIIIEGHHDGDBBBBDDDBA@BB4.064?A?A?B>=B@>?@B:@8:4=6<=6)6;64;?#############################\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:100:12721:8462\n+AACCCCGAGAGGGGACGGAAACTTGCGCCAACCCTTTCGGTGTGATGCGGATGGTCGGCTCGGGTCGTCAGACCCAAAACCCCGAGCGGGGCCGGAAACCTTGAA\n++\n+GDGGGBF:F<DFB@=BFFFFGGGDDGGDGBGGGBBGGGDG6B4A>:B===?<B<?C?EC,@?B@#########################################\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:100:14437:17065\n+AGCTTTCCGGCTTCTATCAGGTAGTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAACCCTCATGGCGGGACATGGACGAGCGCGACTATCGGGGGCGTCGGGC\n++\n+GGHHHDHDHHHGHHH@GDBGFCEGBGGGGGDEEGDHHGHHGHFHHHDHBHD>EBGDGA<A>AAAAAB/AB9,955>>/;?:@:?#####################\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:100:16279:6982\n+ACCCAAAACCCCGAGAGGGGACGGAAACTCCACATCGATTTCCTTGACCCCGCCAGGAGAGAAGATCACGTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAAC\n++\n+CCC@BCC8CC?>?B8.86@######################################################################################\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:100:4143:5168\n+TCCGGCTTCTATCAGGTAGTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAACCCTCATGGGGGGACATGGACGAGCGCGACTATCGGGGGCGCCGGGCCCCAA\n++\n+IIIIIIIIIIIGIIIIGIIHIIHGIHIHIHIIIIDIIIGFHEHIIIFEIIDEEECD6DA@??'??;5=<4@@?@A=B=B##########################\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:100:5900:20698\n+AGAGGGGACGGAAACTGGATTGCGCTAACTGGCTTGGCGCTGATCCTGGTGGTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAACTCCACATCGATTTCCTTG\n++\n+IHBIIIIAIIIIFGIIIIBGIIIIIIEDGIIHIDHGGGGDDIDFFGEGG@CC?AC?BBDBEHEEIHHBEBIHEHBDBDD5:CC?@####################\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:100:9851:14699\n+CCCCGAGAGGGGACGGAAACTCGCAAGCGCCGTGCTTCCCGTGATCGCCTTCTAGTCGTCAGACCCAAAACCCCGCGAGGGGACGGAAACAACACCTCCGCAGCA\n++\n+>2229'>)03A<:?###########################################################################################\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:101:10857:14814\n+TGACGACTGGCGATTTACGACGCTGACGGGAACTCGTGCGAATGTTTCCGTCCCCTTTCCGGGGTTTGGGGTTGGTCCGGCGAATTTCCCTGGGGGTTTTCCAGG\n++\n+GIIIIIIIHIIIIIIIIIIIIIIIIIIIGIDIIIIGEBGG>DGDDGGDGGGCEEE*.*('8<838CC+AC###################################\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:101:12130:2270\n+CAGCCTGTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAACCTGAGGAGAGCGAGTACTCGGGGCTGCCGTCTGCGCTGGTCGTCAGACCCAAAACCCCGAGAG\n++\n+IIIHIIIIIIIIIIIIIIIIIIIIIIIFIHIIHIFIGIGFGEDBE?CA8?=<??;:7<</@A???@@B8=?;?################################\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:101:13036:18149\n+ACGGAAACTTGGAGCGTGTCACCGCAGACGGCACGATTGAGACAAGTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAACCCTCAGCTCCGCATCGCTGATGCG\n++\n+@<7@@DCEEEG?GGBB>A?>=BB@=7;4>?;B?;B<@@DD?91AA01>406;99;A@DD@E>BCEGGB8@>E>9?##############################\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:101:13889:12365\n+GGGTCTGACGACTTGAACACGCCGATACCTATTTGGTCGGGAGTGATAAAGTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGACTGACAGGGTGCGGTGGTCG\n++\n+IIIIIIIIIIHIIIHIIGIIGIHIIHIIHIGIIIIEFGIIIEIEIEGDGGGEHIHIDEEHHIHHFHFHIH@HFFDFFBDDC@CE@B;D===??############\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:101:14716:2667\n+AGAGGGGACGGAAACGCCCCGTGGATGGCGGATGCGTTGTGCGCGCAAGTGTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAACCCGACGATGGCCAGTAAAT\n++\n+IIIIIIIIIIIHIIIIIIIIGIIIIIGIDGGAGG<FCFBBD<FAFDGGDDGBDGDIHEDHIHIGHIHGIGF8I<FDFDABEGCEEBBDB83?3=?C?@>C#####\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:101:15012:13122\n+GTCGATCAAGTCCGGTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAACTCGGGGAGCCGAACAGCGACCACCGCACCCTGTCAGTCGTCAGACCCAAAACCCC\n++\n+A=?A;=B@;;37?7?:CAA>8A:@;<B??DBE<BE######################################################################\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:101:17565:4787\n+GCAGATATCCCATGTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGACCCGGAAGTCAACTAGAGCGGGTGGCGAAACCTGCCCGGTTTCCGGCCCCCCCCGGG\n++\n+FGDGHFHHHHHFHBHHHEHHGDGEGHDHGHGGBFGGGEG##################################################################\n"..b'########################################\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:98:3431:8100\n+CCCCTCTCGGGGGTTTGGGGCTGACGACCTAAGCCCGCTAATCCCGCACAAGGGGTCAGAAAAGGTTCCGTCCCCCCTCGGGGGTTTGGGGCTGACGGGCCGGGG\n++\n+==<94668/<?<+>?##########################################################################################\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:98:6265:7702\n+TGAACACGCCGATACCTATTTGGTCGGGAGTGATAAAGTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGACTGACAGGGTGCGGTGGGCGCTGATCGGCTCCC\n++\n+IIHIIIIIIIIHIIIIIHIIIIIIIGGGEGBGGGGIIIHIIGHIIIIIIFFCHIHIIDIHFEFFAECCBDDBE@E,=8?##########################\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:99:10729:17741\n+CAAAACCCCGAGAGGGGACGGAAACTTGCGCCAACCCTTTCGGTGTGATGCGGATGGTCGGCCCGGGGCGCCAGACCCAAAACCCCGAGAGGGGGCGGGCAGCCC\n++\n+DD=BB>AC?=4:177A<7ABEEBE>EE3EB88B??>?3EE>AA0>>>75>?<E;?##################################################\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:99:11055:3098\n+GGGGACGGAAACCGGGCAGCGTTCGACACCCGCTCTAGTTGACTTCCGGGGCGTCAGACCCAAAACCCCGAGAGGGGGCGGAAACCAGGTGCGCAACGGCGGCGG\n++\n+A;A@7;=;6;BDD8BBEBEE88::=;:>A>8:82855609GDG>@??:?B#######################################################\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:99:11185:15244\n+TTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGACTGCTGCACCTCCCGCACCCGGTGCGATTCTGCGTCCAGTTTCCGTCCCCTCTCGGGGGTTTGGGGCCGGCG\n++\n+HHHHHHHHHHDGDEGGGGEGGGDGG<DGGBGEEE@;0,=:::=6=DD0A>?8;;?##################################################\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:99:12031:3437\n+CCGCGAAATTCACTGCGCGTTATTCAAGGTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGACCCGAGCCGACCATCCGCATCACACCGAAAGGGGTGGCGCAA\n++\n+HHHGHHGHHHGHHHGHHHHHHDHGFHHHDHHHHHDFGGGGBAAGDBGG>CAAA>B=??A:BDBBB@>6C98/358<,5>=8=6=;?8?#################\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:99:1230:12884\n+TCGTCCACAGTCCCCCTTTCAGGTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAACGCCCCGCGGATGGCGGATGCGTTGTGCGCGCAAGGGGCGTCAGCCCC\n++\n+IIIIIIIIIIIIIIIIIIIHGHFFIIFHIIIIIG>GGGDGGGGBGDDGGDCEFFDDEDEDEDCC&:@:??###################################\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:99:13847:17101\n+GACGACACGGACGAGCTGGACCGCATCAGCGATGCTGAGCTGAGGGTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGACTTGTCTCAATCGTGCCGCCTGCGG\n++\n+HHHHHHHHHGHHHHHHHHHHHHFHFHHGHHHHDHDHEFHHG<<GGGEGGEGGBEGHHEHCBDGAG:BDDDCA=>>A@AA>@=@B515547@@@*@##########\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:99:16432:6752\n+CGACCACCGCACCCTGTCAGTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAACCTTCAGCACCACCATCATCCGGCGCCTCAGCTCAGCATGTCGTCAGACCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIGGGIIIIIIIHIIIIHIHHIIIFIIGBDGEGIIIIIFHGGHGHHIEGGEEIGHHGGEGBGCDGDGE@BF?EE@EBD@BBE\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:99:17053:18786\n+ACCCAAAACCCCGAGAGGGGACGGAAACTCGGGGAGCCGATCAGCGACCACCGCACCCCGTCAGTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAACTTGATA\n++\n+HIIIIIIIIHIHIIIHIIIIHIIIGHIHHIHHI>C=7??89>=>8;8>7<BB@@<:??###############################################\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:99:4304:15292\n+TCTCGGGGTTTTGGGTCTGACGACCACCAGGATCAGCGCCAAGCCAGTTAGCGCAATCCAGTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGACCGGAGTCAT\n++\n+=HHHHGGGEGGGGGGHHHHHHGHHHDGGGGHHDHEHHHHHFBHHHGHGH>FGGGEEEFE8HEHEFHHEHHEEBD96.879%*+,3<=4<5A?D@=A;AA######\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:99:7794:7614\n+GGTTTTGGGTCTGACGACATGCTGAGCTGAGGCGCCGGATGATGGTGGTGCTGAAGGTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGACTGACAGGGGGCGG\n++\n+BDDDB?DD<BBBB7DDDDDBDD>D@DDDB2DD@DDDDBBDD<>BB58=,;2<888D@@DD>;8/6B#######################################\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:99:8705:7811\n+TGACGACCATTAGTTGGTGTTGTGATCGCTAAACGCCGGGGCAGTTTCCGTCCCCTCCCGGGGTTTTGGGTCTGACGACCTATCCGCGGGGGGGGCTCACGAACC\n++\n+8@:8@3A5@@97;9;59//535455@;1>3A@@:1@A,@=C0?BB/::7?6/=6@##################################################\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:9:17689:18646\n+GGTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGACCATTAGTTGGTGTTGTGATCGCTAAAAGCCGGGGCAGCTTCCGTCCCCTCCCGGGGGGTTGGGGTCGG\n++\n+HHHHHHHHHGHHHGHHHGHHHDHHHDGGDBEEDFGCACAAA?A##############################################################\n+@HWUSI-EAS1501:32:FC638CYAAXX:2:9:5600:6496\n+TCACCGCAGACGGCACGATTGAGACAAGTCGTCAGACCCAAAACCCCGAGAGGGGACGGAAACCCTCAGCTCAGCATCGCTGATGCGGGCCAGCTCGCCCGTGGC\n++\n+GGGG@G@@GDDDGBG>BG>GDD>GE;;069<@?B<HHHGBGGEGBGGBDB>@2@;C>BB@#############################################\n' 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| diff -r d35cc8e07d00 -r f9c37d0b3002 test-data/input.fastq.gz |
| b |
| Binary file test-data/input.fastq.gz has changed |