diff --git a/tools/cutadapt/cutadapt.xml b/tools/cutadapt/cutadapt.xml index 8b591056265..bc5fe47f3bd 100644 --- a/tools/cutadapt/cutadapt.xml +++ b/tools/cutadapt/cutadapt.xml @@ -39,15 +39,18 @@ #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier)) #end if -#if $input_1.is_of_type("fastq.gz", "fastqsanger.gz"): - #set ext = ".fq.gz" -#else if $input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): - #set ext = ".fq.bz2" -#else if $input_1.is_of_type('fasta'): - #set ext = ".fa" -#else: +#if $input_1.is_of_type("fastq"): #set ext = ".fq" +#else + #set ext = ".fa" +#end if +#if $input_1.ext.endswith(".gz"): + #set ext=ext+".gz" +#elif $input_1.ext.endswith(".bz2") + #set ext=ext+".bz2" #end if + + #set read1 = $read1 + $ext #set out1 = "out1" + $ext #set rest_output = "rest_output" + $ext @@ -86,7 +89,7 @@ cutadapt -j=\${GALAXY_SLOTS:-4} #if 'json_stats' in $output_selector: - --json stats.json + --json stats.json #end if #if str( $library.type ) == "single": @@ -108,19 +111,20 @@ cutadapt --overlap=$adapter_options.overlap $adapter_options.no_indels $adapter_options.match_read_wildcards +$adapter_options.no_match_adapter_wildcards --action=$adapter_options.action $adapter_options.revcomp $filter_options.discard_trimmed $filter_options.discard_untrimmed -#if str($filter_options.minimum_length) and str($filter_options.length_R2_options.length_R2_status) == 'True': - --minimum-length=$filter_options.minimum_length:$filter_options.length_R2_options.R2_minimum +#if str($filter_options.minimum_length) and str($library.type) != "single" and str($library.minimum_length2) != '': + --minimum-length=$filter_options.minimum_length:$library.minimum_length2 #else if str($filter_options.minimum_length): --minimum-length=$filter_options.minimum_length #end if -#if str($filter_options.maximum_length) and str($filter_options.length_R2_options.length_R2_status) == 'True': - --maximum-length=$filter_options.maximum_length:$filter_options.length_R2_options.R2_maximum +#if str($filter_options.maximum_length) and str($library.type) != "single" and str($library.maximum_length2) != '': + --maximum-length=$filter_options.maximum_length:$library.maximum_length2 #else if str($filter_options.maximum_length): --maximum-length=$filter_options.maximum_length #end if @@ -137,6 +141,10 @@ $filter_options.discard_untrimmed #end if $filter_options.discard_cassava +#if $input_1.ext.startswith("fastqillumina") or $input_1.ext.startswith("fastqsolexa") + --quality-base=64 +#end if + #if str($read_mod_options.quality_cutoff) != '0': --quality-cutoff=$read_mod_options.quality_cutoff #end if @@ -144,6 +152,7 @@ $filter_options.discard_cassava --nextseq-trim=$read_mod_options.nextseq_trim #end if $read_mod_options.trim_n +$read_mod_options.poly_a #if $read_mod_options.strip_suffix != '' --strip-suffix $read_mod_options.strip_suffix #end if @@ -206,72 +215,56 @@ $read_mod_options.zero_cap
- + - - - - - + - - - - - - + + +
- - - - - - - - - - - - - - - - - - - + + + + + + + - - + + +
+ - [0-9,]+ + [0-9]+(,[0-9])? - + + - + @@ -283,7 +276,7 @@ $read_mod_options.zero_cap - + @@ -296,7 +289,7 @@ $read_mod_options.zero_cap [A-Za-z0-9 =-_/+]+ - + @@ -308,11 +301,11 @@ $read_mod_options.zero_cap [A-Za-z0-9 {}=_]+ - +
- + @@ -326,20 +319,20 @@ $read_mod_options.zero_cap - + library['type'] != 'paired_collection' and 'multiple_output' not in output_selector - + library['type'] == 'paired' and 'multiple_output' not in output_selector library['type'] == 'paired_collection' and 'multiple_output' not in output_selector - - + + @@ -422,7 +415,7 @@ $read_mod_options.zero_cap - + @@ -439,14 +432,14 @@ $read_mod_options.zero_cap
- - - + + +
- - + + @@ -475,23 +468,15 @@ $read_mod_options.zero_cap
- - - + + +
- - - - - - - - - - + + @@ -520,7 +505,7 @@ $read_mod_options.zero_cap
- +
@@ -540,8 +525,8 @@ $read_mod_options.zero_cap - - + + @@ -557,7 +542,7 @@ $read_mod_options.zero_cap - + @@ -588,17 +573,17 @@ $read_mod_options.zero_cap
- - - - + + + + - - - - + + + +
@@ -620,21 +605,18 @@ $read_mod_options.zero_cap
- - - + + +
- - - - - - + + + @@ -667,7 +649,7 @@ $read_mod_options.zero_cap - + @@ -737,8 +719,8 @@ $read_mod_options.zero_cap - +
@@ -845,22 +827,19 @@ $read_mod_options.zero_cap
- - - + + + +
- - - -
- - + + @@ -881,22 +860,19 @@ $read_mod_options.zero_cap
- - - + + + +
- - - -
- - + + @@ -922,20 +898,17 @@ $read_mod_options.zero_cap +
- - - -
- - + + - + @@ -959,21 +932,18 @@ $read_mod_options.zero_cap +
- - - -
- - + + - + @@ -1035,6 +1005,7 @@ $read_mod_options.zero_cap + @@ -1043,13 +1014,10 @@ $read_mod_options.zero_cap - + -
- -
@@ -1063,25 +1031,22 @@ $read_mod_options.zero_cap - +
- - - + + +
-
- -
- - + + - + @@ -1095,12 +1060,9 @@ $read_mod_options.zero_cap -
- -
- + @@ -1123,16 +1085,16 @@ $read_mod_options.zero_cap
- - - + + +
- - + + @@ -1155,17 +1117,200 @@ $read_mod_options.zero_cap
- - - + + +
- - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + +
+ + + + + + + + + + + + +
+ + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + +
+
+ +
+ + + + + + + + + + + +
+ + + + + + +
+
+ + +
+ + + + + + diff --git a/tools/cutadapt/macros.xml b/tools/cutadapt/macros.xml index d950ca6727f..e1b6a59efaf 100644 --- a/tools/cutadapt/macros.xml +++ b/tools/cutadapt/macros.xml @@ -1,7 +1,7 @@ - 4.4 + 4.6 0 - fastq.gz,fastq,fasta + fastq.bz2,fastq.gz,fastq,fasta.bz2,fasta.gz,fasta topic_0632 @@ -25,46 +25,41 @@ cutadapt + + + + #if $a.adapter_source.adapter_source_list == 'builtin': + $ADAPTER_ARGUMENT '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}${a.single_noindels}' + #else if $a.adapter_source.adapter_source_list == 'file': + $ADAPTER_ARGUMENT file:'${a.adapter_source.adapter_file}${a.single_noindels}' + #else if str($a.adapter_source.adapter_name) != "": + $ADAPTER_ARGUMENT '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}${a.single_noindels}' + #else + $ADAPTER_ARGUMENT '${a.adapter_source.adapter}${a.single_noindels}' + #end if + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - -
- +
- - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - + - - -
- @@ -281,84 +204,29 @@ -
- +
- - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - + - - - - - - [0-9,]+ - + + + + + + + [0-9]+(,[0-9])? + + + +
- diff --git a/tools/cutadapt/test-data/cutadapt/cut/illumina64.fastq b/tools/cutadapt/test-data/cutadapt/cut/illumina64.fastq new file mode 100644 index 00000000000..bbfce73cf0b --- /dev/null +++ b/tools/cutadapt/test-data/cutadapt/cut/illumina64.fastq @@ -0,0 +1,80 @@ +@14569 +AAGTTTATTCCTGGACGAAGGAAGAAAAGGCCAGATGGGAAACAAGAACAAGCCCCTGTTGAAGACGCAGGGCC ++ +cceeeeceeeee`dedbdbdb_^b`abU_cacadabd`dLMZ[XTcT^a^adaaaddcd`aL^`^_`Y\]^`Y_ +@19211 +AGA ++ +^\` +@9180 +GAGGG ++ +b`bLb +@19132 +TGTGATTATCCACTGGTATAT ++ +Z[QZZLZ[]J[SHZNaZ[_Ia +@15868 +CTGCCAAGGCTGCCCCCAAA ++ +`c`cc\`\Lb]bL`[`a]L` +@1424 +GGCCCCAGACTTGCTCCCCCAACAAGGACAATGTCCAAGGAGTGTCCCC ++ +eeeeeeeea`bbdaaadad`Oaaaaccada_aa_d`_X`_^`[`_[_W^ +@7855 +GTGGGGGCT ++ +]^\]FW]Z` +@17943 +ACATGGGACCAGAAAACACCACCAGGGGTTTGGGGCTGTCCTGAG ++ +ccc`\^`aba\b^`\FR`OOPYG[[W```[Ra_RR_\]\\P\_H_ +@11100 +CGGATAACTGAAAATGCATTTTTAACGCCATGACCGTGTCTCAAGGACCCGCTGTGGAAG ++ +b`b_b_a\bc^Tabadaddcddd``bdaa_^aJ\^_\]\\__O[___L^\_aaa^^^UJ^ +@15663 +AGGT ++ +aaKa +@4698 +CCAATTGGCACCCCTCTGCCTTCAGCCATT ++ +cccc\`ccc\caccZccccc]^`LY\bL_b +@20649 +TCTGGACTGGATCTTTAGGATGGTGGAGATGATCTGGATGTAGGACAAAAGAACCAGGCAGAAGGGTG ++ +eeeeeaddadacdddebeccdddadd\^abbT_]bccTac]]b]L^][]Ve[^ZaY_^_^`\\Y]^Y` +@17259 + ++ + +@6003 +CTTCAACTCATCTTGTTATTAATACCATCAATATCCCATGAGGCTCATAAAACGAGTCTTTCTTCTTGGAAACATGACCAAGATTGGGCAAACGT ++ +fffffffffffffffffdffecfcefeffdcfdeeebbbdbccccc\db\`^aa`^Y^^^cbcbaa`bbWY^^^__S_YYR]GWY]\]]XX\_`S +@4118 +TCAAATTGTACTGCAAAGAAGGTCCCAGCTGGTCTCTTCTGGGAGTGATCTAACTAACTTAAG ++ +dc^ddeeeeeedeee`ceceddadadddcbde_dedc_ec_a^^b\b\\]VIPZY^T^^^\L_ +@18416 +GTGGGGAAGCCGAAGAAGCAGCGGAGATCGATTGTAAGAACGACG ++ +dddacaabdbea\d^cce\da`dd_^__`a`a`b[_^__^\^^^_ +@20115 +TGAAAAAGGAAAACATGGTAGTTTTCTTGTATGAGAGAGCCAGAGCCACCTTGGAGATTTTGTTCTCTCTGTGCG ++ +ed^eeafffaddfecdddabc^_badd`bd_ddadaa^bbcad\d\__^_\aaa_aY____aaN_\cdc\^aaYb +@16139 +TCATCCGAAGAGTTGGCAGGCCCTGTGAATTGTGAAAACAGTATACCCACCCCTTTCCC ++ +cabacacY^c\daaddaadad^\ad_a\Y`[ZQ]Y^^OYQ^X^YT\\]U\^RRX^\YJ^ +@14123 +GATTTGGGGAAAGGAAACAATAGTTGAGTTTGGGCCACGGGAAATTCAAGATGCCTGGTATGTC ++ +cccccccac^bYbbT_aa_Yb^^Ta\\^]]aaTaaaaab\b\XL`VZZV]QYYY[aa^^^^_^^ +@8766 +ACCTGTAAGGTCCGCTCCTGGTGGACACCCACGAAGTCCAGGGCCTCAGGCAGGAAGTTGTAGCGCAGAGTTTTGAGCAGCTGCTCCATC ++ +fcfffffcffeffeeefdefddeecdccacddfdYd`d^\_^`\_abbc\b[ba^Y^Z_^^H^Z_^Y_Y_OKWPZR]]Z]`Z``Z^UHZ^ diff --git a/tools/cutadapt/test-data/cutadapt/cut/maxee.fastq b/tools/cutadapt/test-data/cutadapt/cut/maxee.fastq new file mode 100644 index 00000000000..0cdd9218bf6 --- /dev/null +++ b/tools/cutadapt/test-data/cutadapt/cut/maxee.fastq @@ -0,0 +1,8 @@ +@empty + ++ + +@ee_0.8 +ACGTTGCA ++ +++++++++ diff --git a/tools/cutadapt/test-data/cutadapt/cut/polya.1.fasta b/tools/cutadapt/test-data/cutadapt/cut/polya.1.fasta new file mode 100644 index 00000000000..9b8fd8f4bc3 --- /dev/null +++ b/tools/cutadapt/test-data/cutadapt/cut/polya.1.fasta @@ -0,0 +1,8 @@ +>polyA +AAACTTCAGAACAG +>polyAlong +CTTAGTTCAATWTTAACCAAACTTCAGAACAG +>polyA2 +AAACTTAACAAGAACAAG +>nopoly +GAAGAGTATCTCTCTGTCCTCTTGTCCGGCGTTACAGTAATGATCG diff --git a/tools/cutadapt/test-data/cutadapt/cut/polya.2.fasta b/tools/cutadapt/test-data/cutadapt/cut/polya.2.fasta new file mode 100644 index 00000000000..9eee1995b62 --- /dev/null +++ b/tools/cutadapt/test-data/cutadapt/cut/polya.2.fasta @@ -0,0 +1,8 @@ +>polyA +CTGTTCTGAAGTTT +>polyAlong +CTGTTCTGAAGTTTGGTTAAWATTGAACTAAG +>polyA2 +CTTGTTCTTGTTAAGTTT +>nopoly +TCTGAAGTTTGGTTAAWATTGAACTAA diff --git a/tools/cutadapt/test-data/cutadapt/cut/polya.legacy.1.fasta b/tools/cutadapt/test-data/cutadapt/cut/polya.legacy.1.fasta new file mode 100644 index 00000000000..f0a5c35ea04 --- /dev/null +++ b/tools/cutadapt/test-data/cutadapt/cut/polya.legacy.1.fasta @@ -0,0 +1,8 @@ +>polyA +AAACTTCAG +>polyAlong +CTTAGTTCAATWTTAACCAAACTTCAGAACAG +>polyA2 +AAACTTAAC +>nopoly +GAAGAGTATCTCTCTGTCCTCTTGTCCGGCGTTACAGTAATGATCG diff --git a/tools/cutadapt/test-data/cutadapt/cut/simple.fasta b/tools/cutadapt/test-data/cutadapt/cut/simple.fasta new file mode 100644 index 00000000000..a86f5f1599b --- /dev/null +++ b/tools/cutadapt/test-data/cutadapt/cut/simple.fasta @@ -0,0 +1,4 @@ +>first_sequence +SEQUENCE1 +>second_sequence +SEQUENCE2 diff --git a/tools/cutadapt/test-data/cutadapt/cut/simple.fasta.gz b/tools/cutadapt/test-data/cutadapt/cut/simple.fasta.gz new file mode 100644 index 00000000000..cd721a9fcd9 Binary files /dev/null and b/tools/cutadapt/test-data/cutadapt/cut/simple.fasta.gz differ diff --git a/tools/cutadapt/test-data/cutadapt/cut/wildcard.fa b/tools/cutadapt/test-data/cutadapt/cut/wildcard.fa new file mode 100644 index 00000000000..2dae07a4519 --- /dev/null +++ b/tools/cutadapt/test-data/cutadapt/cut/wildcard.fa @@ -0,0 +1,4 @@ +>1 +TGCATGCA +>2 +TGCATGCA diff --git a/tools/cutadapt/test-data/cutadapt/cut/wildcardN.fa b/tools/cutadapt/test-data/cutadapt/cut/wildcardN.fa new file mode 100644 index 00000000000..ef44dbc368f --- /dev/null +++ b/tools/cutadapt/test-data/cutadapt/cut/wildcardN.fa @@ -0,0 +1,6 @@ +>perfect +TTT +>withN +TTT +>1mism +TTTGGGGCGG diff --git a/tools/cutadapt/test-data/cutadapt/data/illumina64.fastq b/tools/cutadapt/test-data/cutadapt/data/illumina64.fastq new file mode 100644 index 00000000000..bc5b10246e1 --- /dev/null +++ b/tools/cutadapt/test-data/cutadapt/data/illumina64.fastq @@ -0,0 +1,80 @@ +@14569 +AAGTTTATTCCTGGACGAAGGAAGAAAAGGCCAGATGGGAAACAAGAACAAGCCCCTGTTGAAGACGCAGGGCCAACAGGGGCCAACGAAGCTGC ++ +cceeeeceeeee`dedbdbdb_^b`abU_cacadabd`dLMZ[XTcT^a^adaaaddcd`aL^`^_`Y\]^`Y_BBBBBBBBBBBBBBBBBBBBB +@19211 +AGAGGGCGTGTGATTGCTGGATGTGGGCGGGGGGCCGGGGGAGCCCCATGGGCAGGAGACCTGAGAGCCAGGCGGTGAGGCACTATGAACGCGAG ++ +^\`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@9180 +GAGGGGCAGCGACTAGTCACCGGACCTGTCAGGCAAGCATAAGCCGTGCGTCAGCACCACGCTGACGGTGCTCCCGCACTCGCGGGACGCGCCAC ++ +b`bLbBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@19132 +TGTGATTATCCACTGGTATATCGGCGTGCCGTCCGCACGAGGAAAAAAGGCATTATTGTTGTGGATCTGTACCATCGTTTGTCCCGTTACCCTTC ++ +Z[QZZLZ[]J[SHZNaZ[_IaBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@15868 +CTGCCAAGGCTGCCCCCAAACCTGGCCCTCCGCGCACCCCACCACGGATCCTGACGTCCTGTCCCCCGCGGCTATGACAGCCAAGTCCCGTCAGC ++ +`c`cc\`\Lb]bL`[`a]L`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@1424 +GGCCCCAGACTTGCTCCCCCAACAAGGACAATGTCCAAGGAGTGTCCCCTGGGAAGGGTGGGCCTCCCCAGGTGCGGGCGGTGGGCACTGCCCCC ++ +eeeeeeeea`bbdaaadad`Oaaaaccada_aa_d`_X`_^`[`_[_W^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@7855 +GTGGGGGCTACAATGTGGCTCCAAGTTTTTTCCCGGGAGGTAAGGCCGGGAGCCCCCGCCCTGAGGGGGCGGGAAAGAGGAAGCCCGACGCGGAC ++ +]^\]FW]Z`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@17943 +ACATGGGACCAGAAAACACCACCAGGGGTTTGGGGCTGTCCTGAGGCTCGGGTAGCAAGCAGCGGGGCTCCGTGTCCAAGCACGCCGGTGTCACC ++ +ccc`\^`aba\b^`\FR`OOPYG[[W```[Ra_RR_\]\\P\_H_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@11100 +CGGATAACTGAAAATGCATTTTTAACGCCATGACCGTGTCTCAAGGACCCGCTGTGGAAGGGGCGCCGCAGCCAGAAGCTGGCCATGTCAGCGCG ++ +b`b_b_a\bc^Tabadaddcddd``bdaa_^aJ\^_\]\\__O[___L^\_aaa^^^UJ^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@15663 +AGGTGAAGTGGCAGGAGGACCGCCGGAAGAAGCTCTTCAGAACTCAGGGGGAGGGGGAAAGCAGAAACCAGAAGTCCAGTGAGCAGGGGGCTGAG ++ +aaKaBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@4698 +CCAATTGGCACCCCTCTGCCTTCAGCCATTCCCTCTGGCTACTGCTCTCTGGTCGGGGCGCCTGGGCGACAGACTCTCTCCCCCCACCCCCCCGC ++ +cccc\`ccc\caccZccccc]^`LY\bL_bBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@20649 +TCTGGACTGGATCTTTAGGATGGTGGAGATGATCTGGATGTAGGACAAAAGAACCAGGCAGAAGGGTGTCATCAGAAGAACACTGCTAGACACCA ++ +eeeeeaddadacdddebeccdddadd\^abbT_]bccTac]]b]L^][]Ve[^ZaY_^_^`\\Y]^Y`BBBBBBBBBBBBBBBBBBBBBBBBBBB +@17259 +GCCTTGTGTTGTTCCTGGCATCACCGCAGGGAGCCCTGGGGGGCCAGGCGGGCGCTGACCCTGGGCACTGCCGCGCCTGGAGGGGCTGAGCACCG ++ +BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@6003 +CTTCAACTCATCTTGTTATTAATACCATCAATATCCCATGAGGCTCATAAAACGAGTCTTTCTTCTTGGAAACATGACCAAGATTGGGCAAACGT ++ +fffffffffffffffffdffecfcefeffdcfdeeebbbdbccccc\db\`^aa`^Y^^^cbcbaa`bbWY^^^__S_YYR]GWY]\]]XX\_`S +@4118 +TCAAATTGTACTGCAAAGAAGGTCCCAGCTGGTCTCTTCTGGGAGTGATCTAACTAACTTAAGCTGACCCTGTGACTGGCTGAGGATAATCCCTT ++ +dc^ddeeeeeedeee`ceceddadadddcbde_dedc_ec_a^^b\b\\]VIPZY^T^^^\L_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@18416 +GTGGGGAAGCCGAAGAAGCAGCGGAGATCGATTGTAAGAACGACGTCCATGACCAGGGTTGGTGGAGACTGCTTCTCTGCATGCGGGGGAAGGCG ++ +dddacaabdbea\d^cce\da`dd_^__`a`a`b[_^__^\^^^_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@20115 +TGAAAAAGGAAAACATGGTAGTTTTCTTGTATGAGAGAGCCAGAGCCACCTTGGAGATTTTGTTCTCTCTGTGCGCACCAGTGATGACACAGGGG ++ +ed^eeafffaddfecdddabc^_badd`bd_ddadaa^bbcad\d\__^_\aaa_aY____aaN_\cdc\^aaYbBBBBBBBBBBBBBBBBBBBB +@16139 +TCATCCGAAGAGTTGGCAGGCCCTGTGAATTGTGAAAACAGTATACCCACCCCTTTCCCGGAGCAGGACGCTGAATGTCCAGAGGATGCCAGACC ++ +cabacacY^c\daaddaadad^\ad_a\Y`[ZQ]Y^^OYQ^X^YT\\]U\^RRX^\YJ^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@14123 +GATTTGGGGAAAGGAAACAATAGTTGAGTTTGGGCCACGGGAAATTCAAGATGCCTGGTATGTCAAGTCTGGCAGTTGAAGCAGCAGGGCTGGCG ++ +cccccccac^bYbbT_aa_Yb^^Ta\\^]]aaTaaaaab\b\XL`VZZV]QYYY[aa^^^^_^^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@8766 +ACCTGTAAGGTCCGCTCCTGGTGGACACCCACGAAGTCCAGGGCCTCAGGCAGGAAGTTGTAGCGCAGAGTTTTGAGCAGCTGCTCCATCAGGGA ++ +fcfffffcffeffeeefdefddeecdccacddfdYd`d^\_^`\_abbc\b[ba^Y^Z_^^H^Z_^Y_Y_OKWPZR]]Z]`Z``Z^UHZ^BBBBB diff --git a/tools/cutadapt/test-data/cutadapt/data/maxee.fastq b/tools/cutadapt/test-data/cutadapt/data/maxee.fastq new file mode 100644 index 00000000000..256f94c2ecb --- /dev/null +++ b/tools/cutadapt/test-data/cutadapt/data/maxee.fastq @@ -0,0 +1,16 @@ +@empty + ++ + +@ee_1 +A ++ +! +@ee_0.8 +ACGTTGCA ++ +++++++++ +@ee_1.01 +TGGACGTTGCA ++ ++5+++++++++ diff --git a/tools/cutadapt/test-data/cutadapt/data/polya.1.fasta b/tools/cutadapt/test-data/cutadapt/data/polya.1.fasta new file mode 100644 index 00000000000..dd6d5b9b3e9 --- /dev/null +++ b/tools/cutadapt/test-data/cutadapt/data/polya.1.fasta @@ -0,0 +1,8 @@ +>polyA +AAACTTCAGAACAGAAAAAAAAAAAAAAAAAAAAA +>polyAlong +CTTAGTTCAATWTTAACCAAACTTCAGAACAGAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAA +>polyA2 +AAACTTAACAAGAACAAGAAAAAAAAAAAAAAAAAAAAA +>nopoly +GAAGAGTATCTCTCTGTCCTCTTGTCCGGCGTTACAGTAATGATCG diff --git a/tools/cutadapt/test-data/cutadapt/data/polya.2.fasta b/tools/cutadapt/test-data/cutadapt/data/polya.2.fasta new file mode 100644 index 00000000000..6f333bfc06a --- /dev/null +++ b/tools/cutadapt/test-data/cutadapt/data/polya.2.fasta @@ -0,0 +1,8 @@ +>polyA +TTTTTTTTTTTTTTTTTTTTTCTGTTCTGAAGTTT +>polyAlong +TTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTCTGTTCTGAAGTTTGGTTAAWATTGAACTAAG +>polyA2 +TTTTTTTTTTTTTTTTTTTTTCTTGTTCTTGTTAAGTTT +>nopoly +TCTGAAGTTTGGTTAAWATTGAACTAA diff --git a/tools/cutadapt/test-data/cutadapt/data/simple.fasta b/tools/cutadapt/test-data/cutadapt/data/simple.fasta new file mode 100644 index 00000000000..e5c1d4c31c2 --- /dev/null +++ b/tools/cutadapt/test-data/cutadapt/data/simple.fasta @@ -0,0 +1,7 @@ +# a comment +# another one +>first_sequence +SEQUENCE1 +>second_sequence +SEQUEN +CE2 diff --git a/tools/cutadapt/test-data/cutadapt/data/simple.fasta.gz b/tools/cutadapt/test-data/cutadapt/data/simple.fasta.gz new file mode 100644 index 00000000000..b4a329ffc56 Binary files /dev/null and b/tools/cutadapt/test-data/cutadapt/data/simple.fasta.gz differ diff --git a/tools/cutadapt/test-data/cutadapt/data/wildcard.fa b/tools/cutadapt/test-data/cutadapt/data/wildcard.fa new file mode 100644 index 00000000000..f482927106e --- /dev/null +++ b/tools/cutadapt/test-data/cutadapt/data/wildcard.fa @@ -0,0 +1,4 @@ +>1 +ANGTACGTTGCATGCA +>2 +ACGTANGTTGCATGCA diff --git a/tools/cutadapt/test-data/cutadapt/data/wildcardN.fa b/tools/cutadapt/test-data/cutadapt/data/wildcardN.fa new file mode 100644 index 00000000000..5c152660dca --- /dev/null +++ b/tools/cutadapt/test-data/cutadapt/data/wildcardN.fa @@ -0,0 +1,6 @@ +>perfect +TTTGGGGGGG +>withN +TTTGGNGGGG +>1mism +TTTGGGGCGG diff --git a/tools/cutadapt/test-data/cutadapt_rest.json b/tools/cutadapt/test-data/cutadapt_rest.json index c245a713b6a..63a84f58e11 100644 --- a/tools/cutadapt/test-data/cutadapt_rest.json +++ b/tools/cutadapt/test-data/cutadapt_rest.json @@ -46,6 +46,9 @@ "quality_trimmed": null, "quality_trimmed_read1": null, "quality_trimmed_read2": null, + "poly_a_trimmed": null, + "poly_a_trimmed_read1": null, + "poly_a_trimmed_read2": null, "output": 35, "output_read1": 35, "output_read2": null @@ -81,5 +84,7 @@ } } ], - "adapters_read2": null + "adapters_read2": null, + "poly_a_trimmed_read1": null, + "poly_a_trimmed_read2": null }