| Next changeset 1:6b865dde1baa (2017-01-21) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit dd85747b08272b72c7161de9b18d19598bb49de1 |
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added:
prinseq.xml test-data/prinseq_good_sequences.fastq test-data/prinseq_input_sequences.fastq tool_dependencies.xml |
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| diff -r 000000000000 -r ba78b984a9eb prinseq.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/prinseq.xml Tue May 31 07:43:42 2016 -0400 |
| [ |
| b'@@ -0,0 +1,764 @@\n+<tool id="prinseq" name="PRINSEQ" version="0.1.0">\n+ <description>to process quality of sequences</description>\n+ \n+ <requirements>\n+ <requirement type="package" version="5.18.1">perl</requirement>\n+ <!--<requirement type="package" version="2.90">perl-json</requirement>\n+ <requirement type="package" version="1.106">perl-cairo</requirement>-->\n+ <requirement type="package" version="0.20.4">prinseq</requirement>\n+ </requirements>\n+\n+ <stdio>\n+ <exit_code range="1:" level="fatal" description="" />\n+ <regex match="ERROR"\n+ source="stderr"\n+ level="fatal"\n+ description="" />\n+ <regex match="WARNING"\n+ source="stderr"\n+ level="warning"\n+ description="" />\n+ </stdio>\n+\n+ <version_command>\n+<![CDATA[\n+ prinseq-lite.pl --version\n+]]>\n+ </version_command>\n+\n+ <command>\n+<![CDATA[\n+ mkdir tmp/\n+\n+ &&\n+\n+ prinseq-lite.pl\n+ #if $seq_type.seq_type_opt == "single":\n+ -fastq "$seq_type.input_singles"\n+ #if $seq_type.input_singles.ext == "fastqillumina":\n+ -phred64\n+ #end if\n+ #else:\n+ -fastq "$seq_type.input_mate1"\n+ -fastq2 "$seq_type.input_mate2"\n+ #if $seq_type.input_mate1.ext != $seq_type.input_mate2.ext:\n+ #import sys\n+ #silent sys.stderr.write( \'Both pairs from your paired-end library need to be from the same filetype.\' )\n+ #end if\n+ #if $seq_type.input_mate1.ext == "fastqillumina":\n+ -phred64\n+ #end if\n+ #end if\n+\n+ -out_good "tmp/good_sequences"\n+ -out_bad "tmp/rejected_sequences"\n+\n+ #if $filter_treatments.apply_filter_treatments == "true":\n+ #set length_filter_treatments=$filter_treatments.length_filter_treatments\n+ #if $length_filter_treatments.apply_length_filter_treatments == "true":\n+ #set min_length_filter_treatments=$length_filter_treatments.min_length_filter_treatments\n+ #if $min_length_filter_treatments.apply_min_length_filter_treatments == "true":\n+ -min_len $min_length_filter_treatments.min_length_filter_treatment_value\n+ #end if\n+\n+ #set max_length_filter_treatments=$length_filter_treatments.max_length_filter_treatments\n+ #if $max_length_filter_treatments.apply_max_length_filter_treatments == "true":\n+ -max_len $max_length_filter_treatments.max_length_filter_treatment_value\n+ #end if\n+ #end if\n+\n+ #set quality_filter_treatments=$filter_treatments.quality_filter_treatments\n+ #if $quality_filter_treatments.apply_quality_filter_treatments == "true":\n+ #set min_quality_filter_treatments=$quality_filter_treatments.min_quality_filter_treatments \n+ #if $min_quality_filter_treatments.apply_min_quality_filter_treatments == "true":\n+ -min_qual_score $min_quality_filter_treatments.min_quality_filter_treatment_value\n+ #end if\n+\n+ #set max_quality_filter_treatments=$quality_filter_treatments.max_quality_filter_treatments\n+ #if $max_quality_filter_treatments.apply_max_quality_filter_treatments == "true":\n+ -max_qual_score $max_quality_filter_treatments.max_quality_filter_treatment_value\n+ #end if\n+\n+ #set mean_quality_filter_treatments=$quality_filter_treatments.mean_quality_filter_treatments\n+ #if $mean_quality_filter_treatments.apply_mean_quality_filter_treatments == "true":\n+ #set min_mean_quality_filter_treat'..b' <param name="input_singles" value="prinseq_input_sequences.fastq"/>\n+ <param name=\'apply_filter_treatments\' value="true"/>\n+ <param name=\'apply_length_filter_treatments\' value="true"/> \n+ <param name=\'apply_min_length_filter_treatments\' value="true"/> \n+ <param name="min_length_filter_treatment_value" value="60"/>\n+ <param name=\'apply_max_length_filter_treatments\' value="false" />\n+ <param name=\'apply_quality_filter_treatments\' value="true"/>\n+ <param name=\'apply_min_quality_filter_treatments\' value="false" />\n+ <param name=\'apply_max_quality_filter_treatments\' value="false"/>\n+ <param name=\'apply_mean_quality_filter_treatments\' value="true"/>\n+ <param name=\'apply_min_mean_quality_filter_treatments\' value="true"/>\n+ <param name="min_mean_quality_filter_treatment_value" value="15"/>\n+ <param name=\'apply_max_mean_quality_filter_treatments\' value="false"/>\n+ <param name=\'apply_base_content_filter_treatments\' value="true"/>\n+ <param name=\'apply_GC_perc_content_filter_treatments\' value="false"/>\n+ <param name=\'apply_N_number_content_filter_treatments\' value="false"/>\n+ <param name=\'apply_N_percentage_content_filter_treatments\' value="true"/> \n+ <param name="N_percentage_content_filter_treatment_value" value="2"/>\n+ <param name=\'apply_other_base_content_filter_treatments\' value="false"/>\n+ <param name=\'apply_complexity_filter_treatments\' value="false"/>\n+ <param name=\'apply_trimming_treatments\' value="true" />\n+ <param name=\'apply_length_trimming_treatments\' value="false"/>\n+ <param name=\'apply_position_trimming_treatments\' value="false"/>\n+ <param name=\'apply_tail_trimming_treatments\' value="false"/>\n+ <param name=\'apply_quality_trimming_treatments\' value="true"/>\n+ <param name=\'apply_left_quality_trimming_treatments\' value="false"/>\n+ <param name=\'apply_right_quality_trimming_treatments\' value="true" />\n+ <param name="right_quality_trimming_treatment_value" value="20"/>\n+ <param name="type_quality_trimming_treatments" value="min"/>\n+ <param name="rule_quality_trimming_treatments" value="lt" />\n+ <param name="window_quality_trimming_treatments" value="1"/>\n+ <param name="step_quality_trimming_treatments" value="1"/>\n+\n+ <output name="good_sequence_file" file="prinseq_good_sequences.fastq"/>\n+ </test>\n+ </tests>\n+\n+ <help><![CDATA[\n+\n+**What it does**\n+\n+PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets.\n+This tool allow to process the sequences with filtering and trimming. \n+More information on `PRINSEQ manual <http://prinseq.sourceforge.net/manual.html>`_.\n+\n+-----\n+\n+**Input**\n+\n+The input file is sequence file in fastq format (sequences and quality)::\n+\n+ @HWI-M00234:263:000000000-ADM55:1:1101:7508:4067 1:N:0:ATCACG\n+ GGTGCACTAGGATCGTAGTTGGCTACTTTCCCGTTTTCAATGTATACGCAAGGTACACGGTCAGCGGT\n+ +\n+ CCCCCGFGED8DDCAFDAEE9DFGGGG9CFAFFCC@@CFGFGGCGFGG>GGGFFGDGEFFEFG8>4GF\n+\n+-----\n+\n+**Parameters**\n+\n+The parameters are numerous in PRINSEQ given the wanted treatments.\n+\n+Several filter treatments are proposed:\n+\n+ - Filters based on sequence length \n+ - Filters based on quality score\n+ - Filters based on base content\n+\n+And several trimming treatments eliminate sequence parts:\n+\n+ - Trim of ends\n+ - Trim of tails\n+ - Trim based quality score\n+\n+All these treaments can be customed using proposed parameters.\n+\n+-----\n+\n+**Output**\n+\n+The output file is a sequence file with sequences and quality from input file\n+which have undergone filter and trimming.\n+\n+ ]]>\n+ </help>\n+\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btr026</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r ba78b984a9eb test-data/prinseq_good_sequences.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prinseq_good_sequences.fastq Tue May 31 07:43:42 2016 -0400 |
| b |
| b'@@ -0,0 +1,13608 @@\n+@HWI-M00234:263:000000000-ADM55:1:1101:7508:4067 1:N:0:ATCACG\n+GGTGCACTAGGATCGTAGTTGGCTACTTTCCCGTTTTCAATGTATACGCAAGGTACACGGTCAGCGGTAGCTGCCATAATGTAATGGTAGTCAAATCCTAAGTCTCCCAATGCACATGGCAGTGGAGCGTTCCAATCTTGTGTACCGGCTTTGTCTCCTAATCCCAAGTGCCATTTTCCGATAGCTCCGGTAGCATAACCGGTACTTTTGAACATATCCGCCATGGTATATTGTTCGGGACGGATAATCATGCCGGCATTTCCGGCAGCTACGTCTGTTCCTTTTTTGCGCCATGCATATTCTCCTG\n++HWI-M00234:263:000000000-ADM55:1:1101:7508:4067 1:N:0:ATCACG\n+CCCCCGFGED8DDCAFDAEE9DFGGGG9CFAFFCC@@CFGFGGCGFGG>GGGFFGDGEFFEFG8>4GF@@FGCFGGCFCFCFFCFG>9=FFGFFGGGGFFFGGGGGFFF=FG<GGGF<F8C=@AC<GDCC:EGGGCCF<FFFFEFGFCGGGGGGD<EGFD;=EFFFGFGGGGAFGGGGGGC>>@DCFGGEFEGFFGF>AFFE>C<DFEFFFFEF8B4DGF9FFEFGGEFDE=GGEEECEFEFF<<FCCDGG<GGGCAGGCEGGFF9EC8FGDGGGGGFFCCDDF:FCGGGGEF9GEFGFCE>CCCB9\n+@HWI-M00234:263:000000000-ADM55:1:1101:26232:4161 1:N:0:ATCACG\n+CTCTTCTTAAGCTCGAACAGCTTCTTCAGTCTTACCTGCCATTTCATCTAAAATTTTTAAAGCTCGCTCTAAAACAGTAGTATCATCAATCATAACCAATCCACCATCTGGTCCAGGTTCCAAGTGAATCCCAACACTTTTCCCCTCCTTAAAATTGTGTCCACCGAAAAAATTTCTTACAGTGTCAACATTCAGTCCAAGTTCATCGGCTATTCTATGCATACTACCACTAGGCAATGAGTCTTTAATCTTACGTAATTCATTAAATGTTATTGTTCTCATATTCATAAATTTAATGGTTAATA\n++HWI-M00234:263:000000000-ADM55:1:1101:26232:4161 1:N:0:ATCACG\n+CCCCCGGFGFFFGEGGGGCFGGGEGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCFGGF=EGFGGGGFGFGFGGGFAFDGCFGG=GFGGGFGFGFGGGGGGGGFGGGG?FFGGFDFFFGGGGGFGGGGGGCE=GC@FGGGGGGGFGGGGGGFBDFGGCGGGGFFFGGGGGGGGDFGGFFGFDGGGGFFFGGGGF>GFFFAGGFFFFFFGGGGGFEEFFFFFFEFE@GGGGGGGGGFGGGGGGGFGFFGGGGGGGGGGGFGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGCCCCC\n+@HWI-M00234:263:000000000-ADM55:1:1101:11727:5103 1:N:0:ATCACG\n+CTCCCGTATAGGATGGATCGAAAGCAATCGTCAGGAATCCACGTTCTGCCAATGTCTGCGCATACAAGCCCGAAGCTTGTTCCTTCACGGCACCAAATGGGCCACTGATGGCAATGGCAGGCAATTTACCCGTCACATTCTTGGGTACATACAAATCGGCGGCAAGTGTAATGCCGTAACGGTTGTGGAAAGTTATCTTTTTATGGTCTACTTTATCACTCTGTGGGAATGTCTTGTCCCACTCTTGAGTCAGATTCAAATTCTCTTCCATAAATTTATTATCATTATTAGGATTATTTTCTGTTGCAGACAAATGTCCTGCAGCACAAAGGCTAATAACCATCGCCGCACATATGTTTT\n++HWI-M00234:263:000000000-ADM55:1:1101:11727:5103 1:N:0:ATCACG\n+CCCCCGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGEGGGEGGGGGGGEGEEGGGGGGGGGGGGGGGGGGGGGEFFGGGGGGGGGFGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGG>GGGGGGGGGGGFGGGGF@GGGGGGGGGGGGDCFGFFGGFGFFEFFFGFAFGFCGDCFGGGGGGGGDEGGFFGGGGGGEFGGGGGGFGFGGFCGGFGGGFFFFAFGGGGGGGGGGGGGG@GGGGGGGFGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGFFGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCCCC\n+@HWI-M00234:263:000000000-ADM55:1:1101:15029:5173 1:N:0:ATCACG\n+GGCCTATTCTCTGCGGCCGCCTTTCGGCGGCACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTAACAATGCTTCTTCCGTCGGCCTTAGGATTCTCTCCTCATCCACCTGTGTCGGTTTACGGTACGGGTACAATATAAACAATAGCGGCTTTTCTTGACGGCCGGCTCATGGGCTTCCCTACTTTAGTTCGGTCCGCATCACGCCTTCGGATTGTTCAGCGGATTTGCCTACTGAACTCCTACCTCGCTTGCACCGGATTTTCCGTTTCCGGCTCCCACTTTCCTTCCGGGTCCCCACAGTTCTGTTATATTGCAGTACAGGAATCTCAACCTGTTGTCCATCGGCTACGGCTTTCGCCCTCGCCTTAGGCCCCGACTTACCCAGAGCAGATCAGCTTTACTCTGGAAACCTTAGATATTCGGCCAAAA\n++HWI-M00234:263:000000000-ADM55:1:1101:15029:5173 1:N:0:ATCACG\n+CCCCCGGGGGGGGGGGGGGGGGGGGEGG7FECGFGGGGGEGGGGGEEGGGGGGGGGGGGGGGFGGGGGGGGGGGGFGGGCGGGGGGGGGGGGGGGFFGGGGGGGGGGFFG9FCGGGFGGGGGFFFDGGEECGGGGGGGGGGGEGGGGGGGGECEGEEGD>ACG>=98E59=CBDDD4D3BGF=FGGGDGFFFFFFFF6BDEFD<88>>DF:C7??3GBB7?:1:@FADC9<C>D>GFFAAF>7:7<4FGCD?AFGGC><9:?2<FECCA,@*;*CDCC@+E@EE>FFFGGDDCGE6C6@6+++GCCE,BCED@B9DFCFCFFEEF,9FGGE9GFF9DFGGGGFGGGGGGGCFFFGGGEGCGGFGFGGGGGGCDDGGGGFEGGGGGGGFGFEFEGGGGCGGGGGGGGCEAGFFGGGGCGGGEGFFCFGECGGCGGDGCC?CC\n+@HWI-M00234:263:000000000-ADM55:1:1101:11799:5476 1:N:0:ATCACG\n+CCTAAATTTTCGAGTATAAGCAGGACCGAAGCCACCAACTTATACCTTATCCTCTAAATTTTCGTAAGAGACATGAAGCGGATCTCTAACTATTCCCGATTTTACTGCACCACTTGATCAAACGCTTCGGAACAAGAGCTTTTGAGTGATGTCTCGTTTCCACCACTTTGGCAGAAATAAAGCTAATCTACTATGATTCGATTAAGCAGCAAGAGCATAATTTTCGTTGCCAGATAAAATTTTGAAAACTGGGATTATAGTGCCAATCAACCACGCACTGCATGCTTACATACCACTTAGCCACGCTGTCAAATCCAG\n++HWI-M00234:263:000000000-ADM55:1:1101:11799:5476 1:N:0:ATCACG\n+CCCC<FFFGGF@FFFGFFGAGCCDGGGEFGGD;CFFGDGGGEGGCFF@DFGGC<CEGGGCEFGEGF@E@@,BFFGFGGGGG7+@AFEAEFDGEGGGGGFFEGGFGGGCEGEFDGFG=FGGGD>CED@DGFFGDCFECCCFDGGGDFGGGGF=DEEEDGFDEGFF@@,==+=FGEGFGG'..b'CFC@C,B@,F<F9GEF7DEF7F@@EEEEGEFC9GGGF<<<A8\n+@HWI-M00234:263:000000000-ADM55:1:2119:14032:23863 1:N:0:ATCACG\n+CGCCCTTCTTTTCCATATAGTTTTTGTAAGTAGCGATGGCTTGTTCGCCCTTACCGTCGCGGCTATACAGTTTAGCCAACTCCTTGTAGTTGTTGAGCTTAGAGGGGTCCTTAGCCAAAGCTTTTTCGTAAGCCGTGATAGCAGCGGGGAAATCCTGCTTTTCCTTAGCCAAAGCAGCAGCATATTCGTAGTCTACCGAAATGTAGTTGCTGTCAGCGTATTCAGGATCGCTGAGGTAAGCCGAAGCTTCTTCAGCCGTTTTGATAGCTGCATCGTAGTCCATAGCTTCGCCAATCTTGTTTACTTTG\n++HWI-M00234:263:000000000-ADM55:1:2119:14032:23863 1:N:0:ATCACG\n+CCCCCFEFGFDGGCABGCCECEFEGGGFAFFEGGCGGFGGGGC<FCGGFGGGGGFFAF++@7FG7FF*C@FGGC?F4CFGCFEGGAFEEFF<FFGGG=?EFGGDGFFGGFGF<FDBGCF><FEFF<4@EFG@ECFGEFGCEFCC@BD9FECFGGFEEGCAGE?EFEGGGGGEFFGGG,DEEACAFCGFAFFECGGG=GGGFB?GGGGGFFDF@AEGGGGGE30B=BCGGFFFFF3F8FCECCFGGGFDGFE@F7EC>GF@FFE9FGGFC>@,;BAGGGGFECGD@@+FCDGGGFE@GCF<GGGCCCCC\n+@HWI-M00234:263:000000000-ADM55:1:2119:16782:24009 1:N:0:ATCACG\n+CGGTAAATATCTTCTGACTCAACACTTTTGGCAGAAGTTCCGCTATCAGTTCGCCGACGGAAGGTTCCACAATGTAATCATTATTAAAACTGCGGGCATCCTCCGGTACATCTTCTGCCGCCTCCTGCGCTACTTGCGTCAGGTCAATGGGCAGATAATTCTCGCGGAGCAGCACCTGCGAACCCATCGATTTGAAGTGATGGTAAATCAGCTCCACATGGTCAATCTGCTTTTCCACAAACTCATGCATCAACTTCTCTGCCAGCTCATACGCTTCAACGTACGAAGGCTTGTCTGCCATCACCTGGTAGCTGCCTTGCGGCACATATCCCATTTTCTTG\n++HWI-M00234:263:000000000-ADM55:1:2119:16782:24009 1:N:0:ATCACG\n+CCCCCGFFGAFGCGGAFG;EFGGGGGGGGFCCEFGGGFFGGGEGCFGGGDFGG@7@FGDFEGDGACFFEFGEDFDGGDEF9FD>EFGGFCEFDGFFFEGG=GFGF?CCEF?GG>GGGFDF>E7FGEF8FCCFGGEFFFGGGGGGGGFCFGFCFFGGGGGGGGGG<GGGGGGGGG>CFGGGEGDECFFGGFGGGFFFGFGGGGGGFFCACF=DCFGFFFGFGEBCGFGFFEFFFGGGGF9FACFEAFGFEAAFBFFEB<EFFGCGGFGGEFFCGFGFFFFGFECBFFC:1@CGFF@FFFGFFDEEFEC@CFCGFGF@GECCEFAFE<GGGGFF@@,GCC<CC\n+@HWI-M00234:263:000000000-ADM55:1:2119:11921:24379 1:N:0:ATCACG\n+CCTTTCGTTCTCGTTCCAAAATTTTATCCGGATATTCTTTTTCTCTTATACTTTTTTCTGTTCAGAAGTCAGATATCAATTTTCTCTTATTATTATAAATTATCAATTTAAAAAATTGTTCTCTACACACTCCGCTTACAAAACGCTCATAACCAAAATGTATAGTTGCTTTTTTAAAACTTTTTAACCTTCAAATAACAATTATTCTTGTTACCCTTTTCTGATCTGGTTCTTCATCTTATACTCTTGGCGAGTATATATGAAACTATGTAACAGATTAAAAAAATATCTTTTTGAAATTCCCTTTTTCTTCAGGAACTT\n++HWI-M00234:263:000000000-ADM55:1:2119:11921:24379 1:N:0:ATCACG\n+BCCCCGGGGGGGGFGGGCD@FGFFGGFFGGDGGGFGAFFG9FFGDFGDGCAFGE9FGEGGGGAFBECFFEEEGGCCDGGGGGGGGGGGGFAFGFGGAE9DFE<FFFFFCGFFGB@EGGGGGE;GFCAB;CEFGGGDGFGGGFEG5GGGGGGGGDGF@F<FDAFFDDEFGGC=@GGGFGFGGGF(DFFGGDCGG<CG9<ECFDGG@FGFA9G<FFGBEFC,EAB7D@FF8:87FEDFF-FFFF0EE86FB6:0<55@4CECCEECC==EE4CEC@F>CC5CEAEGEFGCGCFFEC79DE<C,,,@C6,,6;,6,=,,A--@A\n+@HWI-M00234:263:000000000-ADM55:1:2119:17687:24444 1:N:0:ATCACG\n+CGGCAGGCGTTCTCGGCGTCGTGCACGAGGAACTTCTTGGACTTGATGATGCGCTTGCCGTAAACGGGGTGCATGGCATGCCGGGTCACACGGACAGAGATCGTCTTCTCCATCTTGTCGCTGATAACGATTCCGATTTTCATCTTGCGATGAGGGGTTTTCGCTTCCATTGAGCCTTACCTCCTTCCGGTGTTCACGTTCAGTCCCTGTTCTTTTTCGTGAACAATGGTAAGGACTCTCGCGATGGTCTTCTTGACCTCTTTGATTCTGCTGGTGTTCTTCAACTGGACAACAGCATTCTGGAAGCGCAGGTTAAAAAGCTCTTCTTTGGACTGGTCGTGCTTGTTCATGAGCTC\n++HWI-M00234:263:000000000-ADM55:1:2119:17687:24444 1:N:0:ATCACG\n+CCCC@@FEGGGGGG7<778FFGFFGC<;CGGGGFEFC,;E8<CACFAD9FFCFGCFGF8@8BC@EF77FFBFEGCFG<<BAFACCFCGFGGG@>+CFFC:,?=:F8AD,BED=<,CECAC@FGE*E,A>+3@CD@7@=FEG7=;@CDEC)63@FGEC:BC@E>?CDEGFGG@FGDFECFGCEEEDCCCBEEDGGGF@A38@EB@FGFFEDFGCECCFAC?GEGF=@FEFGGFDEE:FF>69@9584<GFFF9F=F8DGF9GGFGGFFE<<6B6F<BFFCFF<FEC<::*,FEFFF<E<<CFFB,EDGEFFGGFC,<<,9EE<CFFF@FEC,GFEF:B@F8FFFFFFC,<FC,CCCA\n+@HWI-M00234:263:000000000-ADM55:1:2119:12876:24965 1:N:0:ATCACG\n+CTAAATTTTCGAGTATAAGCAGGACCGAAGCCACCAACTTATACCTTATCCTCTAAATTTTCGTAAGAGACATGAAGCGGATCTCTAACTATTCCCGATTTTACTGCACCACTTGATCAAACGCTTCGGAACAAGAGCTTTTGAGTGATGTCTCGTTTCCACCACTTTGGCAGAAATAAAGCTAATCTACTATGATTCGATTAAGCAGCAAGAGCATAATTTTCGTTGCCAGATAAAATTTTGAAAACTGGGATTATAGTGCCAATCAACCACGCACTGCATGCTTACATACCACTTAGCCACGCTGTCAAATCCAG\n++HWI-M00234:263:000000000-ADM55:1:2119:12876:24965 1:N:0:ATCACG\n+CCCCCGGGGGGGGGGGGGFGGGGEGCFCGGGGEFGGGGFGGGGGDCFCFFFGGFFFDFEGGEGGGGGGGGGGGGGGFFGG>FFGGFFFGGGGDEFGEDFGAFEFFAFAFGGGGGD@BCEEEFGGE@BFFECEEGGGGGGFFFCGGGGFGCFFFAEFGFGGFGGGGGGGGGGFEDFF9AECFGFGGGGGGGGGFG@CFFGGGGGGFEGF?CFGFAGGFFFBGEFFCGFGGGDECFFGEGFFFFAGFGGGFFEGGF@GFFGFGCGEFEDGFFFF<GGGFCGFGGGGGFFFGGGGGFECDFEE7EEFGDFF9AADCCC@@\n' |
| b |
| diff -r 000000000000 -r ba78b984a9eb test-data/prinseq_input_sequences.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prinseq_input_sequences.fastq Tue May 31 07:43:42 2016 -0400 |
| b |
| b'@@ -0,0 +1,13812 @@\n+@HWI-M00234:263:000000000-ADM55:1:1101:7508:4067 1:N:0:ATCACG\n+GGTGCACTAGGATCGTAGTTGGCTACTTTCCCGTTTTCAATGTATACGCAAGGTACACGGTCAGCGGTAGCTGCCATAATGTAATGGTAGTCAAATCCTAAGTCTCCCAATGCACATGGCAGTGGAGCGTTCCAATCTTGTGTACCGGCTTTGTCTCCTAATCCCAAGTGCCATTTTCCGATAGCTCCGGTAGCATAACCGGTACTTTTGAACATATCCGCCATGGTATATTGTTCGGGACGGATAATCATGCCGGCATTTCCGGCAGCTACGTCTGTTCCTTTTTTGCGCCATGCATATTCTCCTG\n++\n+CCCCCGFGED8DDCAFDAEE9DFGGGG9CFAFFCC@@CFGFGGCGFGG>GGGFFGDGEFFEFG8>4GF@@FGCFGGCFCFCFFCFG>9=FFGFFGGGGFFFGGGGGFFF=FG<GGGF<F8C=@AC<GDCC:EGGGCCF<FFFFEFGFCGGGGGGD<EGFD;=EFFFGFGGGGAFGGGGGGC>>@DCFGGEFEGFFGF>AFFE>C<DFEFFFFEF8B4DGF9FFEFGGEFDE=GGEEECEFEFF<<FCCDGG<GGGCAGGCEGGFF9EC8FGDGGGGGFFCCDDF:FCGGGGEF9GEFGFCE>CCCB9\n+@HWI-M00234:263:000000000-ADM55:1:1101:26232:4161 1:N:0:ATCACG\n+CTCTTCTTAAGCTCGAACAGCTTCTTCAGTCTTACCTGCCATTTCATCTAAAATTTTTAAAGCTCGCTCTAAAACAGTAGTATCATCAATCATAACCAATCCACCATCTGGTCCAGGTTCCAAGTGAATCCCAACACTTTTCCCCTCCTTAAAATTGTGTCCACCGAAAAAATTTCTTACAGTGTCAACATTCAGTCCAAGTTCATCGGCTATTCTATGCATACTACCACTAGGCAATGAGTCTTTAATCTTACGTAATTCATTAAATGTTATTGTTCTCATATTCATAAATTTAATGGTTAATA\n++\n+CCCCCGGFGFFFGEGGGGCFGGGEGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCFGGF=EGFGGGGFGFGFGGGFAFDGCFGG=GFGGGFGFGFGGGGGGGGFGGGG?FFGGFDFFFGGGGGFGGGGGGCE=GC@FGGGGGGGFGGGGGGFBDFGGCGGGGFFFGGGGGGGGDFGGFFGFDGGGGFFFGGGGF>GFFFAGGFFFFFFGGGGGFEEFFFFFFEFE@GGGGGGGGGFGGGGGGGFGFFGGGGGGGGGGGFGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGCCCCC\n+@HWI-M00234:263:000000000-ADM55:1:1101:11727:5103 1:N:0:ATCACG\n+CTCCCGTATAGGATGGATCGAAAGCAATCGTCAGGAATCCACGTTCTGCCAATGTCTGCGCATACAAGCCCGAAGCTTGTTCCTTCACGGCACCAAATGGGCCACTGATGGCAATGGCAGGCAATTTACCCGTCACATTCTTGGGTACATACAAATCGGCGGCAAGTGTAATGCCGTAACGGTTGTGGAAAGTTATCTTTTTATGGTCTACTTTATCACTCTGTGGGAATGTCTTGTCCCACTCTTGAGTCAGATTCAAATTCTCTTCCATAAATTTATTATCATTATTAGGATTATTTTCTGTTGCAGACAAATGTCCTGCAGCACAAAGGCTAATAACCATCGCCGCACATATGTTTT\n++\n+CCCCCGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGEGGGEGGGGGGGEGEEGGGGGGGGGGGGGGGGGGGGGEFFGGGGGGGGGFGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGG>GGGGGGGGGGGFGGGGF@GGGGGGGGGGGGDCFGFFGGFGFFEFFFGFAFGFCGDCFGGGGGGGGDEGGFFGGGGGGEFGGGGGGFGFGGFCGGFGGGFFFFAFGGGGGGGGGGGGGG@GGGGGGGFGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGFFGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCCCC\n+@HWI-M00234:263:000000000-ADM55:1:1101:15029:5173 1:N:0:ATCACG\n+GGCCTATTCTCTGCGGCCGCCTTTCGGCGGCACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTAACAATGCTTCTTCCGTCGGCCTTAGGATTCTCTCCTCATCCACCTGTGTCGGTTTACGGTACGGGTACAATATAAACAATAGCGGCTTTTCTTGACGGCCGGCTCATGGGCTTCCCTACTTTAGTTCGGTCCGCATCACGCCTTCGGATTGTTCAGCGGATTTGCCTACTGAACTCCTACCTCGCTTGCACCGGATTTTCCGTTTCCGGCTCCCACTTTCCTTCCGGGTCCCCACAGTTCTGTTATATTGCAGTACAGGAATCTCAACCTGTTGTCCATCGGCTACGGCTTTCGCCCTCGCCTTAGGCCCCGACTTACCCAGAGCAGATCAGCTTTACTCTGGAAACCTTAGATATTCGGCCAAAA\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGEGG7FECGFGGGGGEGGGGGEEGGGGGGGGGGGGGGGFGGGGGGGGGGGGFGGGCGGGGGGGGGGGGGGGFFGGGGGGGGGGFFG9FCGGGFGGGGGFFFDGGEECGGGGGGGGGGGEGGGGGGGGECEGEEGD>ACG>=98E59=CBDDD4D3BGF=FGGGDGFFFFFFFF6BDEFD<88>>DF:C7??3GBB7?:1:@FADC9<C>D>GFFAAF>7:7<4FGCD?AFGGC><9:?2<FECCA,@*;*CDCC@+E@EE>FFFGGDDCGE6C6@6+++GCCE,BCED@B9DFCFCFFEEF,9FGGE9GFF9DFGGGGFGGGGGGGCFFFGGGEGCGGFGFGGGGGGCDDGGGGFEGGGGGGGFGFEFEGGGGCGGGGGGGGCEAGFFGGGGCGGGEGFFCFGECGGCGGDGCC?CC\n+@HWI-M00234:263:000000000-ADM55:1:1101:11799:5476 1:N:0:ATCACG\n+CCTAAATTTTCGAGTATAAGCAGGACCGAAGCCACCAACTTATACCTTATCCTCTAAATTTTCGTAAGAGACATGAAGCGGATCTCTAACTATTCCCGATTTTACTGCACCACTTGATCAAACGCTTCGGAACAAGAGCTTTTGAGTGATGTCTCGTTTCCACCACTTTGGCAGAAATAAAGCTAATCTACTATGATTCGATTAAGCAGCAAGAGCATAATTTTCGTTGCCAGATAAAATTTTGAAAACTGGGATTATAGTGCCAATCAACCACGCACTGCATGCTTACATACCACTTAGCCACGCTGTCAAATCCAG\n++\n+CCCC<FFFGGF@FFFGFFGAGCCDGGGEFGGD;CFFGDGGGEGGCFF@DFGGC<CEGGGCEFGEGF@E@@,BFFGFGGGGG7+@AFEAEFDGEGGGGGFFEGGFGGGCEGEFDGFG=FGGGD>CED@DGFFGDCFECCCFDGGGDFGGGGF=DEEEDGFDEGFF@@,==+=FGEGFGGGGGGGGGGFFGFFGFFFFFFFGGGFGFFFEFFFFA8A@GGGFFEGGGFEGEAFGFFGGCEAE>CGFFFF<F@CFFGEAGFEDEGDEEGGGGFCFFCE>CCGC?GDGFFGGGGGGFEFF,FDGDGFGFFE,GDEE<<CCC@\n+@HWI-M00234:263:000000000-ADM55:1:1101:11348:5668 1:N:0:ATCACG\n+GCCTAAATTTTCGTGCAGCGGCAGAACCAAAGCCATCAACCGTTGCCTTATCCTCTAAATTTTCACCCGCGCCACGAGGCTGACACGAACTATCCCCG'..b'GFGF@FGE7FCCEFGCGFGFGFFG@CFFGCGGFFGAF9FDDFDF<B<<FEEEGGC9B?FFCGF,BEBF<?DEFEGGECC@FGFFGGGF=F?DGGGECFGFGEGGGG;7A3@,AD7FGFF997CD>=@DDDC87DCEE;535$F@785CCFF@<ACE:=9E<CFGGGGEDCFCGGGCFGFDFE9;@:3(CCB9FGFF@FCECEF<DEFFFFFGFCCAFEA=<?EA<ECGFGFFFA(EFA?AC:EC><?7CGF@CAF?B:C+FEF:GGEECAEAC,<CFE@CCFECFFCFE<@FFF@+E@9FCCF8C:FCEACFC@C,B@,F<F9GEF7DEF7F@@EEEEGEFC9GGGF<<<A8\n+@HWI-M00234:263:000000000-ADM55:1:2119:14032:23863 1:N:0:ATCACG\n+CGCCCTTCTTTTCCATATAGTTTTTGTAAGTAGCGATGGCTTGTTCGCCCTTACCGTCGCGGCTATACAGTTTAGCCAACTCCTTGTAGTTGTTGAGCTTAGAGGGGTCCTTAGCCAAAGCTTTTTCGTAAGCCGTGATAGCAGCGGGGAAATCCTGCTTTTCCTTAGCCAAAGCAGCAGCATATTCGTAGTCTACCGAAATGTAGTTGCTGTCAGCGTATTCAGGATCGCTGAGGTAAGCCGAAGCTTCTTCAGCCGTTTTGATAGCTGCATCGTAGTCCATAGCTTCGCCAATCTTGTTTACTTTG\n++\n+CCCCCFEFGFDGGCABGCCECEFEGGGFAFFEGGCGGFGGGGC<FCGGFGGGGGFFAF++@7FG7FF*C@FGGC?F4CFGCFEGGAFEEFF<FFGGG=?EFGGDGFFGGFGF<FDBGCF><FEFF<4@EFG@ECFGEFGCEFCC@BD9FECFGGFEEGCAGE?EFEGGGGGEFFGGG,DEEACAFCGFAFFECGGG=GGGFB?GGGGGFFDF@AEGGGGGE30B=BCGGFFFFF3F8FCECCFGGGFDGFE@F7EC>GF@FFE9FGGFC>@,;BAGGGGFECGD@@+FCDGGGFE@GCF<GGGCCCCC\n+@HWI-M00234:263:000000000-ADM55:1:2119:16782:24009 1:N:0:ATCACG\n+CGGTAAATATCTTCTGACTCAACACTTTTGGCAGAAGTTCCGCTATCAGTTCGCCGACGGAAGGTTCCACAATGTAATCATTATTAAAACTGCGGGCATCCTCCGGTACATCTTCTGCCGCCTCCTGCGCTACTTGCGTCAGGTCAATGGGCAGATAATTCTCGCGGAGCAGCACCTGCGAACCCATCGATTTGAAGTGATGGTAAATCAGCTCCACATGGTCAATCTGCTTTTCCACAAACTCATGCATCAACTTCTCTGCCAGCTCATACGCTTCAACGTACGAAGGCTTGTCTGCCATCACCTGGTAGCTGCCTTGCGGCACATATCCCATTTTCTTG\n++\n+CCCCCGFFGAFGCGGAFG;EFGGGGGGGGFCCEFGGGFFGGGEGCFGGGDFGG@7@FGDFEGDGACFFEFGEDFDGGDEF9FD>EFGGFCEFDGFFFEGG=GFGF?CCEF?GG>GGGFDF>E7FGEF8FCCFGGEFFFGGGGGGGGFCFGFCFFGGGGGGGGGG<GGGGGGGGG>CFGGGEGDECFFGGFGGGFFFGFGGGGGGFFCACF=DCFGFFFGFGEBCGFGFFEFFFGGGGF9FACFEAFGFEAAFBFFEB<EFFGCGGFGGEFFCGFGFFFFGFECBFFC:1@CGFF@FFFGFFDEEFEC@CFCGFGF@GECCEFAFE<GGGGFF@@,GCC<CC\n+@HWI-M00234:263:000000000-ADM55:1:2119:11921:24379 1:N:0:ATCACG\n+CCTTTCGTTCTCGTTCCAAAATTTTATCCGGATATTCTTTTTCTCTTATACTTTTTTCTGTTCAGAAGTCAGATATCAATTTTCTCTTATTATTATAAATTATCAATTTAAAAAATTGTTCTCTACACACTCCGCTTACAAAACGCTCATAACCAAAATGTATAGTTGCTTTTTTAAAACTTTTTAACCTTCAAATAACAATTATTCTTGTTACCCTTTTCTGATCTGGTTCTTCATCTTATACTCTTGGCGAGTATATATGAAACTATGTAACAGATTAAAAAAATATCTTTTTGAAATTCCCTTTTTCTTCAGGAACTT\n++\n+BCCCCGGGGGGGGFGGGCD@FGFFGGFFGGDGGGFGAFFG9FFGDFGDGCAFGE9FGEGGGGAFBECFFEEEGGCCDGGGGGGGGGGGGFAFGFGGAE9DFE<FFFFFCGFFGB@EGGGGGE;GFCAB;CEFGGGDGFGGGFEG5GGGGGGGGDGF@F<FDAFFDDEFGGC=@GGGFGFGGGF(DFFGGDCGG<CG9<ECFDGG@FGFA9G<FFGBEFC,EAB7D@FF8:87FEDFF-FFFF0EE86FB6:0<55@4CECCEECC==EE4CEC@F>CC5CEAEGEFGCGCFFEC79DE<C,,,@C6,,6;,6,=,,A--@A\n+@HWI-M00234:263:000000000-ADM55:1:2119:17687:24444 1:N:0:ATCACG\n+CGGCAGGCGTTCTCGGCGTCGTGCACGAGGAACTTCTTGGACTTGATGATGCGCTTGCCGTAAACGGGGTGCATGGCATGCCGGGTCACACGGACAGAGATCGTCTTCTCCATCTTGTCGCTGATAACGATTCCGATTTTCATCTTGCGATGAGGGGTTTTCGCTTCCATTGAGCCTTACCTCCTTCCGGTGTTCACGTTCAGTCCCTGTTCTTTTTCGTGAACAATGGTAAGGACTCTCGCGATGGTCTTCTTGACCTCTTTGATTCTGCTGGTGTTCTTCAACTGGACAACAGCATTCTGGAAGCGCAGGTTAAAAAGCTCTTCTTTGGACTGGTCGTGCTTGTTCATGAGCTC\n++\n+CCCC@@FEGGGGGG7<778FFGFFGC<;CGGGGFEFC,;E8<CACFAD9FFCFGCFGF8@8BC@EF77FFBFEGCFG<<BAFACCFCGFGGG@>+CFFC:,?=:F8AD,BED=<,CECAC@FGE*E,A>+3@CD@7@=FEG7=;@CDEC)63@FGEC:BC@E>?CDEGFGG@FGDFECFGCEEEDCCCBEEDGGGF@A38@EB@FGFFEDFGCECCFAC?GEGF=@FEFGGFDEE:FF>69@9584<GFFF9F=F8DGF9GGFGGFFE<<6B6F<BFFCFF<FEC<::*,FEFFF<E<<CFFB,EDGEFFGGFC,<<,9EE<CFFF@FEC,GFEF:B@F8FFFFFFC,<FC,CCCA\n+@HWI-M00234:263:000000000-ADM55:1:2119:12876:24965 1:N:0:ATCACG\n+CTAAATTTTCGAGTATAAGCAGGACCGAAGCCACCAACTTATACCTTATCCTCTAAATTTTCGTAAGAGACATGAAGCGGATCTCTAACTATTCCCGATTTTACTGCACCACTTGATCAAACGCTTCGGAACAAGAGCTTTTGAGTGATGTCTCGTTTCCACCACTTTGGCAGAAATAAAGCTAATCTACTATGATTCGATTAAGCAGCAAGAGCATAATTTTCGTTGCCAGATAAAATTTTGAAAACTGGGATTATAGTGCCAATCAACCACGCACTGCATGCTTACATACCACTTAGCCACGCTGTCAAATCCAG\n++\n+CCCCCGGGGGGGGGGGGGFGGGGEGCFCGGGGEFGGGGFGGGGGDCFCFFFGGFFFDFEGGEGGGGGGGGGGGGGGFFGG>FFGGFFFGGGGDEFGEDFGAFEFFAFAFGGGGGD@BCEEEFGGE@BFFECEEGGGGGGFFFCGGGGFGCFFFAEFGFGGFGGGGGGGGGGFEDFF9AECFGFGGGGGGGGGFG@CFFGGGGGGFEGF?CFGFAGGFFFBGEFFCGFGGGDECFFGEGFFFFAGFGGGFFEGGF@GFFGFGCGEFEDGFFFF<GGGFCGFGGGGGFFFGGGGGFECDFEE7EEFGDFF9AADCCC@@\n' |
| b |
| diff -r 000000000000 -r ba78b984a9eb tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue May 31 07:43:42 2016 -0400 |
| b |
| @@ -0,0 +1,35 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="perl" version="5.18.1"> + <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <!--<package name="perl-json" version="2.90"> + <repository name="package_perl_json_2_90" owner="iuc" prior_installation_required="True" /> + </package> + <package name="perl-cairo" version="1.106"> + <repository name="package_perl_cairo_1_106" owner="iuc" prior_installation_required="True" /> + </package>--> + <package name="prinseq" version="0.20.4"> + <install version="1.0"> + <actions> + <action sha256sum="9b5e0dce3b7f02f09e1cc7e8a2dd77c0b133e5e35529d570ee901f53ebfeb56f" type="download_by_url">http://downloads.sourceforge.net/project/prinseq/standalone/prinseq-lite-0.20.4.tar.gz</action> + <action type="move_file"> + <source>prinseq-lite.pl</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="chmod"><file mode="755">$INSTALL_DIR/prinseq-lite.pl</file></action> + + <action type="move_file"> + <source>prinseq-graphs-noPCA.pl</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="chmod"><file mode="755">$INSTALL_DIR/prinseq-graphs-noPCA.pl</file></action> + + <action type="set_environment"> + <environment_variable action="set_to" name="PRINSEQ_DIR">$INSTALL_DIR/</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/</environment_variable> + </action> + </actions> + </install> + </package> +</tool_dependency> |