| Previous changeset 34:8c0175e03cee (2023-05-19) Next changeset 36:64172f1c1202 (2024-01-04) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418 |
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modified:
cutadapt.xml macros.xml test-data/cutadapt_rest.json |
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added:
test-data/cutadapt/cut/illumina64.fastq test-data/cutadapt/cut/maxee.fastq test-data/cutadapt/cut/polya.1.fasta test-data/cutadapt/cut/polya.2.fasta test-data/cutadapt/cut/polya.legacy.1.fasta test-data/cutadapt/cut/simple.fasta test-data/cutadapt/cut/simple.fasta.gz test-data/cutadapt/cut/wildcard.fa test-data/cutadapt/cut/wildcardN.fa test-data/cutadapt/data/illumina64.fastq test-data/cutadapt/data/maxee.fastq test-data/cutadapt/data/polya.1.fasta test-data/cutadapt/data/polya.2.fasta test-data/cutadapt/data/simple.fasta test-data/cutadapt/data/simple.fasta.gz test-data/cutadapt/data/wildcard.fa test-data/cutadapt/data/wildcardN.fa |
| b |
| diff -r 8c0175e03cee -r 9845c649f41b cutadapt.xml --- a/cutadapt.xml Fri May 19 21:42:14 2023 +0000 +++ b/cutadapt.xml Sun Dec 17 18:52:25 2023 +0000 |
| [ |
| b'@@ -39,15 +39,18 @@\n #set read1 = re.sub(\'[^\\w\\-\\s]\', \'_\', str($library.input_1.element_identifier))\n #end if\n \n-#if $input_1.is_of_type("fastq.gz", "fastqsanger.gz"):\n- #set ext = ".fq.gz"\n-#else if $input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n- #set ext = ".fq.bz2"\n-#else if $input_1.is_of_type(\'fasta\'):\n+#if $input_1.is_of_type("fastq"):\n+ #set ext = ".fq"\n+#else\n #set ext = ".fa"\n-#else:\n- #set ext = ".fq"\n #end if\n+#if $input_1.ext.endswith(".gz"):\n+ #set ext=ext+".gz"\n+#elif $input_1.ext.endswith(".bz2")\n+ #set ext=ext+".bz2"\n+#end if\n+\n+\n #set read1 = $read1 + $ext\n #set out1 = "out1" + $ext\n #set rest_output = "rest_output" + $ext\n@@ -86,7 +89,7 @@\n -j=\\${GALAXY_SLOTS:-4}\n \n #if \'json_stats\' in $output_selector:\n- --json stats.json\n+ --json stats.json\n #end if\n \n #if str( $library.type ) == "single":\n@@ -108,19 +111,20 @@\n --overlap=$adapter_options.overlap\n $adapter_options.no_indels\n $adapter_options.match_read_wildcards\n+$adapter_options.no_match_adapter_wildcards\n --action=$adapter_options.action\n $adapter_options.revcomp\n \n $filter_options.discard_trimmed\n $filter_options.discard_untrimmed\n \n-#if str($filter_options.minimum_length) and str($filter_options.length_R2_options.length_R2_status) == \'True\':\n- --minimum-length=$filter_options.minimum_length:$filter_options.length_R2_options.R2_minimum\n+#if str($filter_options.minimum_length) and str($library.type) != "single" and str($library.minimum_length2) != \'\':\n+ --minimum-length=$filter_options.minimum_length:$library.minimum_length2\n #else if str($filter_options.minimum_length):\n --minimum-length=$filter_options.minimum_length\n #end if\n-#if str($filter_options.maximum_length) and str($filter_options.length_R2_options.length_R2_status) == \'True\':\n- --maximum-length=$filter_options.maximum_length:$filter_options.length_R2_options.R2_maximum\n+#if str($filter_options.maximum_length) and str($library.type) != "single" and str($library.maximum_length2) != \'\':\n+ --maximum-length=$filter_options.maximum_length:$library.maximum_length2\n #else if str($filter_options.maximum_length):\n --maximum-length=$filter_options.maximum_length\n #end if\n@@ -137,6 +141,10 @@\n #end if\n $filter_options.discard_cassava\n \n+#if $input_1.ext.startswith("fastqillumina") or $input_1.ext.startswith("fastqsolexa")\n+ --quality-base=64\n+#end if\n+\n #if str($read_mod_options.quality_cutoff) != \'0\':\n --quality-cutoff=$read_mod_options.quality_cutoff\n #end if\n@@ -144,6 +152,7 @@\n --nextseq-trim=$read_mod_options.nextseq_trim\n #end if\n $read_mod_options.trim_n\n+$read_mod_options.poly_a\n #if $read_mod_options.strip_suffix != \'\'\n --strip-suffix $read_mod_options.strip_suffix\n #end if\n@@ -206,72 +215,56 @@\n <!-- Adapter Options -->\n <section name="adapter_options" title="Adapter Options">\n <param name="action" type="select" label="What to do if a match is found">\n- <option value="trim" selected="True">Trim: trim adapter and upstream or downstream sequence</option>\n+ <option value="trim" selected="true">Trim: trim adapter and upstream or downstream sequence</option>\n <option value="retain">Retain: the read is trimmed, but the adapter sequence is not removed</option>\n <option value="mask">Mask: mask adapters with \'N\' characters instead of trimming them</option>\n <option value="lowercase">Lowercase: convert to lowercase</option>\n <option value="none">None: leave unchanged</option>\n </param>\n- <param name="internal" type="select" label="Disallow internal adaptor ocurrences" help="The non-internal 5\xe2\x80\x99 and 3\xe2\x80\x99 adapter types disallow internal occurrences of the adapter sequence. The adapter must always be at one of the ends of the read, but partial occurrences are also ok.">\n- <option value="X">Enabled</option>\n- <option value="" selected="True">Disabled</option>\n'..b'ommandline.py#L257 -->\n+ <test expect_num_outputs="1">\n+ <param name="type" value="single" />\n+ <param name="input_1" ftype="fastqillumina" value="cutadapt/data/illumina64.fastq" />\n+ <param name="quality_cutoff" value="10"/>\n+ <output name="out1" file="cutadapt/cut/illumina64.fastq" ftype="fastqillumina"/>\n+ <assert_command>\n+ <has_text text="--quality-cutoff=10"/>\n+ <has_text text="--quality-base=64"/>\n+ </assert_command>\n+ </test>\n+\n+ <!-- https://github.com/marcelm/cutadapt/blame/3407ac0004d04b11ae7157934a6665ecaf82c328/tests/test_commandline.py#L1028 --> \n+ <test expect_num_outputs="3">\n+ <param name="type" value="single" />\n+ <param name="input_1" ftype="fastqillumina" value="cutadapt/data/maxee.fastq" />\n+ <param name="max_expected_errors" value="0.9"/>\n+ <param name="output_selector" value="report,info_file"/>\n+ <output name="out1" file="cutadapt/cut/maxee.fastq" ftype="fastqillumina"/>\n+ <output name="report">\n+ <assert_contents>\n+ <has_text text="Reads with too many exp. errors: 2"/>\n+ </assert_contents>\n+ </output>\n+ <output name="info_file">\n+ <assert_contents>\n+ <has_n_lines n="4"/>\n+ <has_text text="ee_0.8	-1	ACGTTGCA	++++++++"/>\n+ </assert_contents>\n+ </output>\n+ <assert_command>\n+ <has_text text="--max-expected-errors=0.9"/>\n+ </assert_command>\n+ </test>\n+\n+ <!-- https://github.com/marcelm/cutadapt/blob/3407ac0004d04b11ae7157934a6665ecaf82c328/tests/test_commandline.py#L335 -->\n+ <test expect_num_outputs="1">\n+ <param name="type" value="single" />\n+ <param name="input_1" ftype="fasta" value="cutadapt/data/wildcard.fa" />\n+ <section name="r1">\n+ <repeat name="anywhere_adapters">\n+ <conditional name="adapter_source">\n+ <param name="adapter_source_list" value="user"/>\n+ <param name="adapter" value="ACGTACGT"/>\n+ </conditional>\n+ </repeat>\n+ </section>\n+ <section name="adapter_options">\n+ <param name="match_read_wildcards" value="true"/>\n+ </section>\n+ <output name="out1" file="cutadapt/cut/wildcard.fa" ftype="fasta" sort="true"/>\n+ <assert_command>\n+ <has_text text="--match-read-wildcards"/>\n+ <has_text text="-b \'ACGTACGT\'"/>\n+ </assert_command>\n+ </test>\n+\n+ <!-- https://github.com/marcelm/cutadapt/blob/3407ac0004d04b11ae7157934a6665ecaf82c328/tests/test_commandline.py#L368 -->\n+ <test expect_num_outputs="1">\n+ <param name="type" value="single" />\n+ <param name="input_1" ftype="fasta" value="cutadapt/data/wildcardN.fa" />\n+ <section name="r1">\n+ <repeat name="adapters">\n+ <conditional name="adapter_source">\n+ <param name="adapter_source_list" value="user"/>\n+ <param name="adapter" value="GGGGGGG"/>\n+ </conditional>\n+ </repeat>\n+ </section>\n+ <section name="adapter_options">\n+ <param name="match_read_wildcards" value="true"/>\n+ <param name="error_rate" value="0"/>\n+ </section>\n+ <output name="out1" file="cutadapt/cut/wildcardN.fa" ftype="fasta" sort="true"/>\n+ <assert_command>\n+ <has_text text="--match-read-wildcards"/>\n+ <has_text text="--error-rate=0.0"/>\n+ <has_text text="-a \'GGGGGGG\'"/>\n+ </assert_command>\n </test>\n </tests>\n \n' |
| b |
| diff -r 8c0175e03cee -r 9845c649f41b macros.xml --- a/macros.xml Fri May 19 21:42:14 2023 +0000 +++ b/macros.xml Sun Dec 17 18:52:25 2023 +0000 |
| [ |
| b'@@ -1,7 +1,7 @@\n <macros>\n- <token name="@TOOL_VERSION@">4.4</token>\n+ <token name="@TOOL_VERSION@">4.6</token>\n <token name="@VERSION_SUFFIX@">0</token>\n- <token name="@FASTQ_TYPES@">fastq.gz,fastq,fasta</token>\n+ <token name="@FASTQ_TYPES@">fastq.bz2,fastq.gz,fastq,fasta.bz2,fasta.gz,fasta</token>\n <xml name="edam_ontology">\n <edam_topics> \n <edam_topic>topic_0632</edam_topic>\n@@ -25,46 +25,41 @@\n <xref type=\'bio.tools\'>cutadapt</xref>\n </xrefs>\n </xml>\n+\n+ <!-- parametrized token - you need to set `$ADAPTER_ARGUMENT` -->\n+ <token name="@adapter_cli@">\n+ #if $a.adapter_source.adapter_source_list == \'builtin\':\n+ $ADAPTER_ARGUMENT \'${a.adapter_source.adapter.fields.name}\'=\'${a.adapter_source.adapter}${a.single_noindels}\'\n+ #else if $a.adapter_source.adapter_source_list == \'file\':\n+ $ADAPTER_ARGUMENT file:\'${a.adapter_source.adapter_file}${a.single_noindels}\'\n+ #else if str($a.adapter_source.adapter_name) != "":\n+ $ADAPTER_ARGUMENT \'${a.adapter_source.adapter_name}\'=\'${a.adapter_source.adapter}${a.single_noindels}\'\n+ #else\n+ $ADAPTER_ARGUMENT \'${a.adapter_source.adapter}${a.single_noindels}\'\n+ #end if\n+ </token>\n+\n <token name="@read1_options@"><![CDATA[\n \n ## Read1 trimming\n \n+ #set ADAPTER_ARGUMENT="-a"\n #for $a in $library.r1.adapters\n- #if $a.adapter_source.adapter_source_list == \'builtin\':\n- -a \'${a.adapter_source.adapter.fields.name}\'=\'${a.adapter_source.adapter}${adapter_options.internal}${a.single_noindels}\'\n- #else if $a.adapter_source.adapter_source_list == \'file\':\n- -a file:\'${a.adapter_source.adapter_file}${adapter_options.internal}${a.single_noindels}\'\n- #else if str($a.adapter_source.adapter_name) != "":\n- -a \'${a.adapter_source.adapter_name}\'=\'${a.adapter_source.adapter}${adapter_options.internal}${a.single_noindels}\'\n- #else\n- -a \'${a.adapter_source.adapter}${adapter_options.internal}${a.single_noindels}\'\n- #end if\n+ @adapter_cli@\n #end for\n- #for $aa in $library.r1.anywhere_adapters\n- #if $aa.anywhere_adapter_source.anywhere_adapter_source_list == \'builtin\':\n- -b \'${aa.anywhere_adapter_source.anywhere_adapter.fields.name}\'=\'${aa.anywhere_adapter_source.anywhere_adapter}${aa.single_noindels}\'\n- #else if $aa.anywhere_adapter_source.anywhere_adapter_source_list == \'file\':\n- -b file:\'${aa.anywhere_adapter_source.anywhere_adapter_file}${aa.single_noindels}\'\n- #else if str($aa.anywhere_adapter_source.anywhere_adapter_name) != "":\n- -b \'${aa.anywhere_adapter_source.anywhere_adapter_name}\'=\'${aa.anywhere_adapter_source.anywhere_adapter}${aa.single_noindels}\'\n- #else\n- -b \'${aa.anywhere_adapter_source.anywhere_adapter}${aa.single_noindels}\'\n- #end if\n+ \n+ #set ADAPTER_ARGUMENT="-b"\n+ #for $a in $library.r1.anywhere_adapters\n+ @adapter_cli@\n #end for\n- #for $fa in $library.r1.front_adapters\n- #if $fa.front_adapter_source.front_adapter_source_list == \'builtin\':\n- -g \'${fa.front_adapter_source.front_adapter.fields.name}\'=\'${adapter_options.internal}${fa.front_adapter_source.front_adapter}${fa.single_noindels}\'\n- #else if $fa.front_adapter_source.front_adapter_source_list == \'file\':\n- -g file:\'${adapter_options.internal}${fa.front_adapter_source.front_adapter_file}${fa.single_noindels}\'\n- #else if str($fa.front_adapter_source.front_adapter_name) != "":\n- -g \'${fa.front_adapter_source.front_adapter_name}\'=\'${adapter_options.internal}${fa.front_adapter_source.front_adapter}${fa.single_noindels}'..b'param name="anywhere_adapter_source_list2" type="select" label="Source">\n- <option value="builtin" selected="True">Standard (select from the list below)</option>\n- <option value="user">Enter custom sequence</option>\n- <option value="file">File from history</option>\n- </param>\n-\n- <when value="user">\n- <param name="anywhere_adapter_name2" type="text" value="" optional="True" label="Enter custom 5\' or 3\' adapter name (Optional)" />\n- <expand macro="adapter" name="anywhere_adapter2" argument="-B" label="Enter custom 5\' or 3\' adapter sequence" value="AATTGGCC" />\n- </when>\n- <when value="builtin">\n- <expand macro="adapter_select" name="anywhere_adapter2" argument="-B" type="select" label="Choose 5\' or 3\' adapter"/>\n- </when>\n- <when value="file">\n- <param name="anywhere_adapter_file2" argument="-b" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 3\' or 5\' adapters" />\n- </when>\n- </conditional>\n- <param name="single_noindels" type="boolean" truevalue=";noindels" falsevalue="" checked="false" label="Disallow indels for this adapter"/>\n- </repeat>\n-\n- <param name="cut2" argument="-U" type="integer" value="0" optional="True" label="Cut bases from the second read in each pair." help="Remove bases from the beginning or end of each read before trimming adapters. If positive, the bases are removed from the beginning of each read. If negative, the bases are removed from the end of each read." />\n- <param name="quality_cutoff2" type="text" optional="true" label="Optional separate quality cutoff for Read 2" help="Trim low-quality bases from 5\' and/or 3\' ends of each read before adapter removal. If one value is given, only the 3\' end is trimmed. If two comma-separated cutoffs are given, the 5\' end is trimmed with the first cutoff, the 3\' end with the second. Leave blank to use the same value as for Read 1">\n- <sanitizer>\n- <valid initial="string.digits"><add value="," /></valid>\n- </sanitizer>\n- <validator type="regex">[0-9,]+</validator>\n- </param>\n+ <!-- read modification -->\n+ <param name="cut2" argument="-U" type="integer" value="0" optional="true" label="Cut bases from the second read in each pair." help="Remove bases from the beginning or end of each read before trimming adapters. If positive, the bases are removed from the beginning of each read. If negative, the bases are removed from the end of each read." />\n+ <param name="quality_cutoff2" argument="-Q" type="text" optional="true" label="Optional separate quality cutoff for Read 2" help="Trim low-quality bases from 5\' and/or 3\' ends of each read before adapter removal. If one value is given, only the 3\' end is trimmed. If two comma-separated cutoffs are given, the 5\' end is trimmed with the first cutoff, the 3\' end with the second. Leave blank to use the same value as for Read 1">\n+ <sanitizer>\n+ <valid initial="string.digits"><add value="," /></valid>\n+ </sanitizer>\n+ <validator type="regex">[0-9]+(,[0-9])?</validator>\n+ </param>\n+ <!-- read filtering-->\n+ <param name="minimum_length2" type="integer" min="0" value="" optional="true" label="Minimum length (R2)" />\n+ <param name="maximum_length2" type="integer" min="0" value="" optional="true" label="Maximum length (R2)" />\n </section>\n-\n </xml>\n \n <xml name="inherit_format_1">\n' |
| b |
| diff -r 8c0175e03cee -r 9845c649f41b test-data/cutadapt/cut/illumina64.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt/cut/illumina64.fastq Sun Dec 17 18:52:25 2023 +0000 |
| [ |
| @@ -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^ |
| b |
| diff -r 8c0175e03cee -r 9845c649f41b test-data/cutadapt/cut/maxee.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt/cut/maxee.fastq Sun Dec 17 18:52:25 2023 +0000 |
| b |
| @@ -0,0 +1,8 @@ +@empty + ++ + +@ee_0.8 +ACGTTGCA ++ +++++++++ |
| b |
| diff -r 8c0175e03cee -r 9845c649f41b test-data/cutadapt/cut/polya.1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt/cut/polya.1.fasta Sun Dec 17 18:52:25 2023 +0000 |
| b |
| @@ -0,0 +1,8 @@ +>polyA +AAACTTCAGAACAG +>polyAlong +CTTAGTTCAATWTTAACCAAACTTCAGAACAG +>polyA2 +AAACTTAACAAGAACAAG +>nopoly +GAAGAGTATCTCTCTGTCCTCTTGTCCGGCGTTACAGTAATGATCG |
| b |
| diff -r 8c0175e03cee -r 9845c649f41b test-data/cutadapt/cut/polya.2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt/cut/polya.2.fasta Sun Dec 17 18:52:25 2023 +0000 |
| b |
| @@ -0,0 +1,8 @@ +>polyA +CTGTTCTGAAGTTT +>polyAlong +CTGTTCTGAAGTTTGGTTAAWATTGAACTAAG +>polyA2 +CTTGTTCTTGTTAAGTTT +>nopoly +TCTGAAGTTTGGTTAAWATTGAACTAA |
| b |
| diff -r 8c0175e03cee -r 9845c649f41b test-data/cutadapt/cut/polya.legacy.1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt/cut/polya.legacy.1.fasta Sun Dec 17 18:52:25 2023 +0000 |
| b |
| @@ -0,0 +1,8 @@ +>polyA +AAACTTCAG +>polyAlong +CTTAGTTCAATWTTAACCAAACTTCAGAACAG +>polyA2 +AAACTTAAC +>nopoly +GAAGAGTATCTCTCTGTCCTCTTGTCCGGCGTTACAGTAATGATCG |
| b |
| diff -r 8c0175e03cee -r 9845c649f41b test-data/cutadapt/cut/simple.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt/cut/simple.fasta Sun Dec 17 18:52:25 2023 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>first_sequence +SEQUENCE1 +>second_sequence +SEQUENCE2 |
| b |
| diff -r 8c0175e03cee -r 9845c649f41b test-data/cutadapt/cut/simple.fasta.gz |
| b |
| Binary file test-data/cutadapt/cut/simple.fasta.gz has changed |
| b |
| diff -r 8c0175e03cee -r 9845c649f41b test-data/cutadapt/cut/wildcard.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt/cut/wildcard.fa Sun Dec 17 18:52:25 2023 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>1 +TGCATGCA +>2 +TGCATGCA |
| b |
| diff -r 8c0175e03cee -r 9845c649f41b test-data/cutadapt/cut/wildcardN.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt/cut/wildcardN.fa Sun Dec 17 18:52:25 2023 +0000 |
| b |
| @@ -0,0 +1,6 @@ +>perfect +TTT +>withN +TTT +>1mism +TTTGGGGCGG |
| b |
| diff -r 8c0175e03cee -r 9845c649f41b test-data/cutadapt/data/illumina64.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt/data/illumina64.fastq Sun Dec 17 18:52:25 2023 +0000 |
| [ |
| @@ -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 |
| b |
| diff -r 8c0175e03cee -r 9845c649f41b test-data/cutadapt/data/maxee.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt/data/maxee.fastq Sun Dec 17 18:52:25 2023 +0000 |
| b |
| @@ -0,0 +1,16 @@ +@empty + ++ + +@ee_1 +A ++ +! +@ee_0.8 +ACGTTGCA ++ +++++++++ +@ee_1.01 +TGGACGTTGCA ++ ++5+++++++++ |
| b |
| diff -r 8c0175e03cee -r 9845c649f41b test-data/cutadapt/data/polya.1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt/data/polya.1.fasta Sun Dec 17 18:52:25 2023 +0000 |
| b |
| @@ -0,0 +1,8 @@ +>polyA +AAACTTCAGAACAGAAAAAAAAAAAAAAAAAAAAA +>polyAlong +CTTAGTTCAATWTTAACCAAACTTCAGAACAGAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAA +>polyA2 +AAACTTAACAAGAACAAGAAAAAAAAAAAAAAAAAAAAA +>nopoly +GAAGAGTATCTCTCTGTCCTCTTGTCCGGCGTTACAGTAATGATCG |
| b |
| diff -r 8c0175e03cee -r 9845c649f41b test-data/cutadapt/data/polya.2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt/data/polya.2.fasta Sun Dec 17 18:52:25 2023 +0000 |
| b |
| @@ -0,0 +1,8 @@ +>polyA +TTTTTTTTTTTTTTTTTTTTTCTGTTCTGAAGTTT +>polyAlong +TTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTCTGTTCTGAAGTTTGGTTAAWATTGAACTAAG +>polyA2 +TTTTTTTTTTTTTTTTTTTTTCTTGTTCTTGTTAAGTTT +>nopoly +TCTGAAGTTTGGTTAAWATTGAACTAA |
| b |
| diff -r 8c0175e03cee -r 9845c649f41b test-data/cutadapt/data/simple.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt/data/simple.fasta Sun Dec 17 18:52:25 2023 +0000 |
| b |
| @@ -0,0 +1,7 @@ +# a comment +# another one +>first_sequence +SEQUENCE1 +>second_sequence +SEQUEN +CE2 |
| b |
| diff -r 8c0175e03cee -r 9845c649f41b test-data/cutadapt/data/simple.fasta.gz |
| b |
| Binary file test-data/cutadapt/data/simple.fasta.gz has changed |
| b |
| diff -r 8c0175e03cee -r 9845c649f41b test-data/cutadapt/data/wildcard.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt/data/wildcard.fa Sun Dec 17 18:52:25 2023 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>1 +ANGTACGTTGCATGCA +>2 +ACGTANGTTGCATGCA |
| b |
| diff -r 8c0175e03cee -r 9845c649f41b test-data/cutadapt/data/wildcardN.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt/data/wildcardN.fa Sun Dec 17 18:52:25 2023 +0000 |
| b |
| @@ -0,0 +1,6 @@ +>perfect +TTTGGGGGGG +>withN +TTTGGNGGGG +>1mism +TTTGGGGCGG |
| b |
| diff -r 8c0175e03cee -r 9845c649f41b test-data/cutadapt_rest.json --- a/test-data/cutadapt_rest.json Fri May 19 21:42:14 2023 +0000 +++ b/test-data/cutadapt_rest.json Sun Dec 17 18:52:25 2023 +0000 |
| b |
| @@ -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 } |