| Previous changeset 23:c4b82dce8335 (2021-04-30) Next changeset 25:4e5056fefd88 (2021-07-02) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf" |
|
modified:
cutadapt.xml macros.xml test-data/A1.fastq.gz test-data/A2.fastq.gz test-data/cutadapt_nextseq_out.fq.gz test-data/cutadapt_out1.fq.gz test-data/cutadapt_out2.fq.gz test-data/cutadapt_trimmed.out.gz test-data/cutadapt_untrimmed.out.gz test-data/unknown.fastq.gz |
|
added:
test-data/bwa-mem-fastq1_assimetric.fq.gz test-data/bwa-mem-fastq2_assimetric.fq.gz test-data/cutadapt_action_lowercase.out test-data/cutadapt_action_mask.out test-data/cutadapt_action_none.out test-data/cutadapt_action_retain.out test-data/cutadapt_builtin_internal_adapter.out test-data/cutadapt_out1_internal_adapter.fq.gz test-data/cutadapt_out1_max_length.fq.gz test-data/cutadapt_out1_max_min_01.fq.gz test-data/cutadapt_out1_max_min_02.fq.gz test-data/cutadapt_out1_min_length.fq.gz test-data/cutadapt_out2_internal_adapter.fq.gz test-data/cutadapt_out2_max_length.fq.gz test-data/cutadapt_out2_max_min_01.fq.gz test-data/cutadapt_out2_max_min_02.fq.gz test-data/cutadapt_out2_min_length.fq.gz test-data/cutadapt_revcomp.out test-data/cutadapt_shorten_3prime.out test-data/cutadapt_shorten_5prime.out test-data/cutadapt_shorten_expected_errors.out test-data/cutadapt_shorten_internal_adapters.out test-data/cutadapt_small_cut.out test-data/cutadapt_small_rename.out |
| b |
| diff -r c4b82dce8335 -r 288f97432497 cutadapt.xml --- a/cutadapt.xml Fri Apr 30 10:13:37 2021 +0000 +++ b/cutadapt.xml Wed Jun 02 22:47:34 2021 +0000 |
| [ |
| b'@@ -1,12 +1,11 @@\n-<tool id="cutadapt" name="Cutadapt" version="1.16.9" profile="17.09">\n- <description>Remove adapter sequences from Fastq/Fasta</description>\n+<tool id="cutadapt" name="Cutadapt" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01">\n+ <description>Remove adapter sequences from FASTQ/FASTA</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n- <requirements>\n- <requirement type="package" version="1.16">cutadapt</requirement>\n- </requirements>\n-\n+ <expand macro=\'edam_ontology\' />\n+ <expand macro=\'requirements\' />\n+ <expand macro=\'xrefs\'/>\n <version_command>cutadapt --version</version_command>\n \n <command detect_errors="exit_code"><![CDATA[\n@@ -18,20 +17,20 @@\n #set paired = False\n #set library_type = str($library.type)\n #if $library_type == \'paired\':\n-#set paired = True\n-#set read1 = re.sub(\'[^\\w\\-\\s]\', \'_\', str($library.input_1.element_identifier))\n-#set read2 = re.sub(\'[^\\w\\-\\s]\', \'_\', str($library.input_2.element_identifier))\n-#set input_1 = $library.input_1\n-#set input_2 = $library.input_2\n+ #set paired = True\n+ #set read1 = re.sub(\'[^\\w\\-\\s]\', \'_\', str($library.input_1.element_identifier))\n+ #set read2 = re.sub(\'[^\\w\\-\\s]\', \'_\', str($library.input_2.element_identifier))\n+ #set input_1 = $library.input_1\n+ #set input_2 = $library.input_2\n #else if $library_type == \'paired_collection\'\n-#set paired = True\n-#set input_1 = $library.input_1.forward\n-#set input_2 = $library.input_1.reverse\n-#set read1 = re.sub(\'[^\\w\\-\\s]\', \'_\', str($library.input_1.name)) + "_1"\n-#set read2 = re.sub(\'[^\\w\\-\\s]\', \'_\', str($library.input_1.name)) + "_2"\n+ #set paired = True\n+ #set input_1 = $library.input_1.forward\n+ #set input_2 = $library.input_1.reverse\n+ #set read1 = re.sub(\'[^\\w\\-\\s]\', \'_\', str($library.input_1.name)) + "_1"\n+ #set read2 = re.sub(\'[^\\w\\-\\s]\', \'_\', str($library.input_1.name)) + "_2"\n #else\n-#set input_1 = $library.input_1\n-#set read1 = re.sub(\'[^\\w\\-\\s]\', \'_\', str($library.input_1.element_identifier))\n+ #set input_1 = $library.input_1\n+ #set read1 = re.sub(\'[^\\w\\-\\s]\', \'_\', str($library.input_1.element_identifier))\n #end if\n \n #if $input_1.is_of_type("fastq.gz", "fastqsanger.gz"):\n@@ -72,20 +71,17 @@\n \n ## Run Cutadapt\n \n-#if $output_options.multiple_output:\n+#if \'multiple_output\' in $output_selector:\n mkdir split &&\n #end if\n \n cutadapt\n \n-## cutadapt (up to version 1.16) can\'t be run in multicore mode with these options\n-#if not any(($output_options.info_file, $output_options.rest_file, $output_options.wildcard_file, $output_options.too_short_file, $output_options.too_long_file, $output_options.untrimmed_file))\n- -j \\${GALAXY_SLOTS:-1}\n-#end if\n+-j=\\${GALAXY_SLOTS:-4}\n \n #if str( $library.type ) == "single":\n @read1_options@\n- #if $output_options.multiple_output:\n+ #if \'multiple_output\' in $output_selector:\n --output=\'split/{name}.${input_1.ext}\'\n #else:\n --output=\'$out1\'\n@@ -103,20 +99,25 @@\n #end if\n \n --error-rate=$adapter_options.error_rate\n---times=$adapter_options.count\n+--times=$adapter_options.times\n --overlap=$adapter_options.overlap\n $adapter_options.no_indels\n $adapter_options.match_read_wildcards\n-$adapter_options.no_trim\n-$adapter_options.mask_adapter\n+--action=$adapter_options.action\n+$adapter_options.revcomp\n \n-$filter_options.discard\n+$filter_options.discard_trimmed\n $filter_options.discard_untrimmed\n-#if str($filter_options.min):\n- --minimum-length=$filter_options.min\n+\n+#if str($filter_options.minimum_length) and str($filter_options.length_R2_options.length_R2_status) == \'True\':\n+ --minimum-length=$filter_options.minimum_length:$filter_options.length_R2_options.R2_minimum\n+#else if str($filter_options.minimum_length):\n+ --minimum-length=$filter_options.minimum_length\n #end if\n-#if str($filter_options.max):\n- --maximum-length=$filter_options.max\n+#if str($filter_options.maximum_length) and str($filter_options.length_R2_options.length_R'..b'to do multiple rounds of adapter matching, this is the name of the last found adapter.\n+ * {cut_prefix} \xe2\x80\x93 the prefix removed by the --cut (or -u) option (that is, when used with a positive length argument)\n+ * {cut_suffix} \xe2\x80\x93 the suffix removed by the --cut (or -u) option (that is, when used with a negative length argument)\n+\n+If the --rename option is used with paired-end data, the template is applied separately to both R1 and R2. That is, for R1, the placeholders are replaced with values from R1, and for R2, the placeholders are replaced with values from R2. For example, {comment} becomes R1\xe2\x80\x99s comment in R1 and it becomes R2\xe2\x80\x99s comment in R2.\n+\n+\n --------------------\n \n **More Information**\n@@ -712,27 +1067,5 @@\n Author: Lance Parsons <lparsons@princeton.edu>\n \n ]]></help>\n-\n- <citations>\n- <citation type="bibtex">\n-@article{marcel_cutadapt_2011,\n-\ttitle = {Cutadapt removes adapter sequences from high-throughput sequencing reads},\n-\tvolume = {17},\n-\tcopyright = {Authors who publish with this journal agree to the following terms: Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work\'s authorship and initial publication in this journal. Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal\'s published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal. Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access ).},\n-\turl = {http://journal.embnet.org/index.php/embnetjournal/article/view/200},\n-\tabstract = {When small RNA is sequenced on current sequencing machines, the resulting reads are usually longer than the RNA and therefore contain parts of the 3\' adapter. That adapter must be found and removed error-tolerantly from each read before read mapping. Previous solutions are either hard to use or do not offer required features, in particular support for color space data. As an easy to use alternative, we developed the command-line tool cutadapt, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features.\n-\n-Cutadapt, including its MIT-licensed source code, is available for download at http://code.google.com/p/cutadapt/},\n-\tnumber = {1},\n-\turldate = {2011-08-02},\n-\tjournal = {EMBnet.journal},\n-\tauthor = {Marcel, Martin},\n-\tyear = {2011},\n-\tnote = {When small RNA is sequenced on current sequencing machines, the resulting reads are usually longer than the RNA and therefore contain parts of the 3\' adapter. That adapter must be found and removed error-tolerantly from each read before read mapping. Previous solutions are either hard to use or do not offer required features, in particular support for color space data. As an easy to use alternative, we developed the command-line tool cutadapt, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features. Cutadapt, including its MIT-licensed source code, is available for download at http://code.google.com/p/cutadapt/},\n-\tkeywords = {Adapter removal;, fastq, MicroRNA, Sequencing, Small RNA, software},\n-\tfile = {Cutadapt removes adapter sequences from high-throughput sequencing reads | Martin | EMBnet.journal:/Users/lparsons/Library/Application Support/Firefox/Profiles/thd2t4je.default/zotero/storage/ZXZT4PSE/200.html:text/html}\n-}\n- </citation>\n- </citations>\n-\n+ <expand macro="citations" />\n </tool>\n' |
| b |
| diff -r c4b82dce8335 -r 288f97432497 macros.xml --- a/macros.xml Fri Apr 30 10:13:37 2021 +0000 +++ b/macros.xml Wed Jun 02 22:47:34 2021 +0000 |
| [ |
| b'@@ -1,18 +1,42 @@\n <macros>\n-\n+ <token name="@TOOL_VERSION@">3.4</token>\n+ <token name="@GALAXY_TOOL_VERSION@">galaxy0</token>\n+ <xml name="edam_ontology">\n+ <edam_topics> \n+ <edam_topic>topic_0632</edam_topic>\n+ </edam_topics>\n+ <edam_operations>\n+ <edam_operation>operation_0231</edam_operation>\n+ </edam_operations>\n+ </xml>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">cutadapt</requirement>\n+ </requirements>\n+ </xml>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.14806/ej.17.1.200</citation>\n+ </citations>\n+ </xml>\n+ <xml name="xrefs">\n+ <xrefs>\n+ <xref type=\'bio.tools\'>cutadapt</xref>\n+ </xrefs>\n+ </xml>\n <token name="@read1_options@"><![CDATA[\n \n ## Read1 trimming\n \n #for $a in $library.r1.adapters\n #if $a.adapter_source.adapter_source_list == \'builtin\':\n- -a \'${a.adapter_source.adapter.fields.name}\'=\'${a.adapter_source.adapter}\'\n+ -a \'${a.adapter_source.adapter.fields.name}\'=\'${a.adapter_source.adapter}${adapter_options.internal}\'\n #else if $a.adapter_source.adapter_source_list == \'file\':\n- -a file:\'${a.adapter_source.adapter_file}\'\n+ -a file:\'${a.adapter_source.adapter_file}${adapter_options.internal}\'\n #else if str($a.adapter_source.adapter_name) != "":\n- -a \'${a.adapter_source.adapter_name}\'=\'${a.adapter_source.adapter}\'\n+ -a \'${a.adapter_source.adapter_name}\'=\'${a.adapter_source.adapter}${adapter_options.internal}\'\n #else\n- -a \'${a.adapter_source.adapter}\'\n+ -a \'${a.adapter_source.adapter}${adapter_options.internal}\'\n #end if\n #end for\n #for $aa in $library.r1.anywhere_adapters\n@@ -28,13 +52,13 @@\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}\'=\'${fa.front_adapter_source.front_adapter}\'\n+ -g \'${fa.front_adapter_source.front_adapter.fields.name}\'=\'${adapter_options.internal}${fa.front_adapter_source.front_adapter}\'\n #else if $fa.front_adapter_source.front_adapter_source_list == \'file\':\n- -g file:\'${fa.front_adapter_source.front_adapter_file}\'\n+ -g file:\'${adapter_options.internal}${fa.front_adapter_source.front_adapter_file}\'\n #else if str($fa.front_adapter_source.front_adapter_name) != "":\n- -g \'${fa.front_adapter_source.front_adapter_name}\'=\'${fa.front_adapter_source.front_adapter}\'\n+ -g \'${fa.front_adapter_source.front_adapter_name}\'=\'${adapter_options.internal}${fa.front_adapter_source.front_adapter}\'\n #else\n- -g \'${fa.front_adapter_source.front_adapter}\'\n+ -g \'${adapter_options.internal}${fa.front_adapter_source.front_adapter}\'\n #end if\n #end for\n \n@@ -44,22 +68,22 @@\n \n ## Additional Outputs\n \n- #if $output_options.info_file:\n+ #if \'info_file\' in $output_selector:\n --info-file=$info_file\n #end if\n- #if $output_options.rest_file:\n+ #if \'rest_file\' in $output_selector:\n --rest-file=\'${rest_output}\'\n #end if\n- #if $output_options.wildcard_file:\n+ #if \'wildcard_file\' in $output_selector:\n --wildcard-file=\'${wild_output}\'\n #end if\n- #if $output_options.too_short_file:\n+ #if \'too_short_file\' in $output_selector:\n --too-short-output=\'${too_short_output}\'\n #end if\n- #if $output_options.too_long_file:\n+ #if \'too_long_fil'..b'{adapter_options.internal}${fa.front_adapter_source2.front_adapter2}\'\n #end if\n #end for\n \n@@ -109,13 +133,13 @@\n \n ## Additional Outputs - Read 2\n \n- #if $output_options.too_short_file:\n+ #if \'too_short_file\' in $output_selector:\n --too-short-paired-output=\'${too_short_paired_output}\'\n #end if\n- #if $output_options.too_long_file:\n+ #if \'too_long_file\' in $output_selector:\n --too-long-paired-output=\'${too_long_paired_output}\'\n #end if\n- #if $output_options.untrimmed_file:\n+ #if \'untrimmed_file\' in $output_selector:\n --untrimmed-paired-output=\'${untrimmed_paired_output}\'\n #end if\n \n@@ -181,7 +205,7 @@\n <param name="adapter_source_list" 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+ <option value="file">File from history</option>\n </param>\n \n <when value="user">\n@@ -204,7 +228,7 @@\n <param name="front_adapter_source_list" 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+ <option value="file">File from history</option>\n </param>\n \n <when value="user">\n@@ -225,7 +249,7 @@\n <param name="anywhere_adapter_source_list" 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+ <option value="file">File from history</option>\n </param>\n \n <when value="user">\n@@ -260,7 +284,7 @@\n <param name="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+ <option value="file">File from history</option>\n </param>\n \n <when value="user">\n@@ -282,7 +306,7 @@\n <param name="front_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+ <option value="file">File from history</option>\n </param>\n \n <when value="user">\n@@ -303,7 +327,7 @@\n <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+ <option value="file">File from history</option>\n </param>\n \n <when value="user">\n' |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/A1.fastq.gz |
| b |
| Binary file test-data/A1.fastq.gz has changed |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/A2.fastq.gz |
| b |
| Binary file test-data/A2.fastq.gz has changed |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/bwa-mem-fastq1_assimetric.fq.gz |
| b |
| Binary file test-data/bwa-mem-fastq1_assimetric.fq.gz has changed |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/bwa-mem-fastq2_assimetric.fq.gz |
| b |
| Binary file test-data/bwa-mem-fastq2_assimetric.fq.gz has changed |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_action_lowercase.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt_action_lowercase.out Wed Jun 02 22:47:34 2021 +0000 |
| b |
| @@ -0,0 +1,12 @@ +@prefix:1_13_573/1 +cgtccgaantagctaccaccctgattagacaaat ++ +)3%)&&&&!.1&(6:<'67..*,:75)'77&&&5 +@prefix:1_13_1259/1 +AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT ++ +;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<& +@prefix:1_13_1440/1 +CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC ++ +<=A:A=57!7<';<6?5;;6:+:=)71>70<,=: |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_action_mask.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt_action_mask.out Wed Jun 02 22:47:34 2021 +0000 |
| b |
| @@ -0,0 +1,12 @@ +@prefix:1_13_573/1 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ++ +)3%)&&&&!.1&(6:<'67..*,:75)'77&&&5 +@prefix:1_13_1259/1 +AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT ++ +;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<& +@prefix:1_13_1440/1 +CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC ++ +<=A:A=57!7<';<6?5;;6:+:=)71>70<,=: |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_action_none.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt_action_none.out Wed Jun 02 22:47:34 2021 +0000 |
| b |
| @@ -0,0 +1,12 @@ +@prefix:1_13_573/1 +CGTCCGAANTAGCTACCACCCTGATTAGACAAAT ++ +)3%)&&&&!.1&(6:<'67..*,:75)'77&&&5 +@prefix:1_13_1259/1 +AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT ++ +;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<& +@prefix:1_13_1440/1 +CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC ++ +<=A:A=57!7<';<6?5;;6:+:=)71>70<,=: |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_action_retain.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt_action_retain.out Wed Jun 02 22:47:34 2021 +0000 |
| b |
| @@ -0,0 +1,12 @@ +@prefix:1_13_573/1 +CGTCCGAANTAG ++ +)3%)&&&&!.1& +@prefix:1_13_1259/1 +AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT ++ +;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<& +@prefix:1_13_1440/1 +CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC ++ +<=A:A=57!7<';<6?5;;6:+:=)71>70<,=: |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_builtin_internal_adapter.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt_builtin_internal_adapter.out Wed Jun 02 22:47:34 2021 +0000 |
| b |
| @@ -0,0 +1,12 @@ +@prefix:1_13_573/1 +CGTCCGAANTAGCTACCACCCTGATTAGACAAAT ++ +)3%)&&&&!.1&(6:<'67..*,:75)'77&&&5 +@prefix:1_13_1259/1 +AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT ++ +;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<& +@prefix:1_13_1440/1 +CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC ++ +<=A:A=57!7<';<6?5;;6:+:=)71>70<,=: |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_nextseq_out.fq.gz |
| b |
| Binary file test-data/cutadapt_nextseq_out.fq.gz has changed |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_out1.fq.gz |
| b |
| Binary file test-data/cutadapt_out1.fq.gz has changed |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_out1_internal_adapter.fq.gz |
| b |
| Binary file test-data/cutadapt_out1_internal_adapter.fq.gz has changed |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_out1_max_length.fq.gz |
| b |
| Binary file test-data/cutadapt_out1_max_length.fq.gz has changed |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_out1_max_min_01.fq.gz |
| b |
| Binary file test-data/cutadapt_out1_max_min_01.fq.gz has changed |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_out1_max_min_02.fq.gz |
| b |
| Binary file test-data/cutadapt_out1_max_min_02.fq.gz has changed |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_out1_min_length.fq.gz |
| b |
| Binary file test-data/cutadapt_out1_min_length.fq.gz has changed |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_out2.fq.gz |
| b |
| Binary file test-data/cutadapt_out2.fq.gz has changed |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_out2_internal_adapter.fq.gz |
| b |
| Binary file test-data/cutadapt_out2_internal_adapter.fq.gz has changed |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_out2_max_length.fq.gz |
| b |
| Binary file test-data/cutadapt_out2_max_length.fq.gz has changed |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_out2_max_min_01.fq.gz |
| b |
| Binary file test-data/cutadapt_out2_max_min_01.fq.gz has changed |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_out2_max_min_02.fq.gz |
| b |
| Binary file test-data/cutadapt_out2_max_min_02.fq.gz has changed |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_out2_min_length.fq.gz |
| b |
| Binary file test-data/cutadapt_out2_min_length.fq.gz has changed |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_revcomp.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt_revcomp.out Wed Jun 02 22:47:34 2021 +0000 |
| b |
| @@ -0,0 +1,12 @@ +@prefix:1_13_573/1 +CGTCCGAANTAGCTACCACCCTGATTAGACAAAT ++ +)3%)&&&&!.1&(6:<'67..*,:75)'77&&&5 +@prefix:1_13_1259/1 +AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT ++ +;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<& +@prefix:1_13_1440/1 +CAAGATCTNCCCTGCCACATTGCCCTAGT ++ +<=A:A=57!7<';<6?5;;6:+:=)71>7 |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_shorten_3prime.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt_shorten_3prime.out Wed Jun 02 22:47:34 2021 +0000 |
| b |
| @@ -0,0 +1,12 @@ +@prefix:1_13_573/1 +CGTCCGAANT ++ +)3%)&&&&!. +@prefix:1_13_1259/1 + ++ + +@prefix:1_13_1440/1 +CAAGATCTNC ++ +<=A:A=57!7 |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_shorten_5prime.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt_shorten_5prime.out Wed Jun 02 22:47:34 2021 +0000 |
| b |
| @@ -0,0 +1,12 @@ +@prefix:1_13_573/1 +TTAGACAAAT ++ +75)'77&&&5 +@prefix:1_13_1259/1 + ++ + +@prefix:1_13_1440/1 +CTAGTTAAAC ++ +)71>70<,=: |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_shorten_expected_errors.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt_shorten_expected_errors.out Wed Jun 02 22:47:34 2021 +0000 |
| b |
| @@ -0,0 +1,12 @@ +@prefix:1_13_573/1 +CGTCCGAANTAGCTACCACCCTGATTAGACAAAT ++ +)3%)&&&&!.1&(6:<'67..*,:75)'77&&&5 +@prefix:1_13_1259/1 +AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT ++ +;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<& +@prefix:1_13_1440/1 +CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC ++ +<=A:A=57!7<';<6?5;;6:+:=)71>70<,=: |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_shorten_internal_adapters.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt_shorten_internal_adapters.out Wed Jun 02 22:47:34 2021 +0000 |
| b |
| @@ -0,0 +1,12 @@ +@prefix:1_13_573/1 +CGTCCGAANTAGCTACCACCCTGATTAGACAAAT ++ +)3%)&&&&!.1&(6:<'67..*,:75)'77&&&5 +@prefix:1_13_1259/1 +AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT ++ +;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<& +@prefix:1_13_1440/1 +CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC ++ +<=A:A=57!7<';<6?5;;6:+:=)71>70<,=: |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_small_cut.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt_small_cut.out Wed Jun 02 22:47:34 2021 +0000 |
| b |
| @@ -0,0 +1,12 @@ +@prefix:1_13_573/1 +GAANTAGCTACCACCCTGATTAGACAAAT ++ +&&&!.1&(6:<'67..*,:75)'77&&&5 +@prefix:1_13_1259/1 +CTANGACGGGTTGGCCCTTAGACGTATCT ++ +A;A!9<<<,7:<=3=;:<&<?<?8<;=<& +@prefix:1_13_1440/1 +TCTNCCCTGCCACATTGCCCTAGTTAAAC ++ +=57!7<';<6?5;;6:+:=)71>70<,=: |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_small_rename.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt_small_rename.out Wed Jun 02 22:47:34 2021 +0000 |
| b |
| @@ -0,0 +1,12 @@ +@prefix:1_13_573/1 barcode=CGTCC +GAANTAGCTACCACCCTGATTAGACAAAT ++ +&&&!.1&(6:<'67..*,:75)'77&&&5 +@prefix:1_13_1259/1 barcode=AGCCG +CTANGACGGGTTGGCCCTTAGACGTATCT ++ +A;A!9<<<,7:<=3=;:<&<?<?8<;=<& +@prefix:1_13_1440/1 barcode=CAAGA +TCTNCCCTGCCACATTGCCCTAGTTAAAC ++ +=57!7<';<6?5;;6:+:=)71>70<,=: |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_trimmed.out.gz |
| b |
| Binary file test-data/cutadapt_trimmed.out.gz has changed |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/cutadapt_untrimmed.out.gz |
| b |
| Binary file test-data/cutadapt_untrimmed.out.gz has changed |
| b |
| diff -r c4b82dce8335 -r 288f97432497 test-data/unknown.fastq.gz |
| b |
| Binary file test-data/unknown.fastq.gz has changed |