| Previous changeset 10:01d94df2e32a (2015-05-26) Next changeset 12:78e1cf88d133 (2018-05-24) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4 |
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modified:
cutadapt.xml test-data/cutadapt_rest.fa test-data/cutadapt_small.out |
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added:
macros.xml static/images/adapters.svg test-data/adapters.loc test-data/bwa-mem-fastq1.fq test-data/bwa-mem-fastq1.fq.gz test-data/bwa-mem-fastq2.fq.gz test-data/cutadapt_builtin.out test-data/cutadapt_info_out.txt test-data/cutadapt_nextseq_out.fq.gz test-data/cutadapt_out1.fq.gz test-data/cutadapt_out2.fq.gz tool-data/adapters.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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removed:
README cutadapt_adapters.txt.sample tool_dependencies.xml |
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| diff -r 01d94df2e32a -r 8665bcc8b847 README --- a/README Tue May 26 16:02:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,55 +0,0 @@ -Galaxy tool definition for cutadapt (http://code.google.com/p/cutadapt/) - - -Installation - Tool Shed ------------------------- - -The recommended way to install cutadapt as a tool in Galaxy is to the use the -Galaxy Tool Shed (http://wiki.galaxyproject.org/Tool%20Shed). - -This will allow cutadapt to be installed automatically and keep track of older -versions of cutadapt and the tool wrapper. - - -Installation - Manual ---------------------- - -1. Install the cutadapt package and make sure it is in path for Galaxy - -2. Copy cutadapt.xml to $GALAXY_HOME/tools/cutadapt - -3. Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file - - **Optional steps to setup and run Galaxy functional tests** - -4. Copy test-data/* to $GALAXY_HOME/test-data/ - -5. Set GALAXY_TEST_TOOL_CONF environment variable to a tool_conf.xml file that - contains the tools you want to test. (e.g. 'tool_conf.xml') - -6. $GALAXY_HOME/run_functional_tests.sh -id cutadapt - See the Galaxy Wiki for more information: http://wiki.g2.bx.psu.edu/ - - -Configuration of Adapters -------------------------- - -A list of predefined adapters may be specified in the cutadapt_adapters.txt -file which resides in the tool-data directory underneath the Galaxy root. A sample -file is provided. - - -Limitations of the Galaxy wrapper ---------------------------------- - -Reading adapters from a fasta file is not supported -Colorspace data support is not implemented -Only one "Strip suffix" is suppored - - -Galaxy Wrapper Development --------------------------- - -Author: Lance Parsons <lparsons@princeton.edu> - -Repository: [https://bitbucket.org/lance_parsons/cutadapt\_galaxy\_wrapper](https://bitbucket.org/lance_parsons/cutadapt_galaxy_wrapper) |
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| diff -r 01d94df2e32a -r 8665bcc8b847 cutadapt.xml --- a/cutadapt.xml Tue May 26 16:02:19 2015 -0400 +++ b/cutadapt.xml Mon Mar 05 11:02:48 2018 -0500 |
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| b'@@ -1,462 +1,582 @@\n-<tool id="cutadapt" name="Cutadapt" version="1.6">\n+<tool id="cutadapt" name="Cutadapt" version="1.16">\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="1.6">cutadapt</requirement>\n+ <requirement type="package" version="1.16">cutadapt</requirement>\n </requirements>\n \n- <stdio>\n- <exit_code range="1" level="fatal" description="IOError, FormatError, or Interrupt" />\n- <exit_code range="2" level="fatal" description="Invalid options specified" />\n- <exit_code range="3:" level="fatal" description="Unknown error" />\n- </stdio>\n-\n <version_command>cutadapt --version</version_command>\n \n- <command>cutadapt\n- #if $input.extension.startswith( "fastq"):\n- --format=fastq\n- #if $input.extension == "fastqillumina":\n- --quality-base=64\n- #end if\n- #if $input.extension == "fastqsolexa":\n- --quality-base=64\n+ <command detect_errors="exit_code"><![CDATA[\n+\n+ ## Link in the input and output files, so Cutadapt can tell their type\n+\n+ #set compressed="False"\n+ #set format = "fastq"\n+\n+ #if str($library.type) == \'paired\':\n+\n+ #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):\n+ #set read1 = "input_f.fastq.gz"\n+ #set compressed = "GZ"\n+ #set out1 = "out1.gz"\n+ #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+ #set read1 = "input_f.fastq.bz2"\n+ #set compressed = "BZ2"\n+ #set out1 = "out1.bz2"\n+ #else if $library.input_1.is_of_type(\'fasta\'):\n+ #set format = "fasta"\n+ #set read1 = "input_f.fasta"\n+ #set out1 = "out1.fa"\n+ #else:\n+ #set read1 = "input_f.fastq"\n+ #set out1 = "out1.fq"\n #end if\n- #else\n- --format=$input.extension\n- #end if\n- #for $a in $adapters\n- #if $a.adapter_source.adapter_source_list == \'prebuilt\':\n- --adapter="${a.adapter_source.adapter.fields.name}"=\'${a.adapter_source.adapter}\'\n- #else if str($a.adapter_source.adapter_name) != "":\n- --adapter=\'${a.adapter_source.adapter_name}\'=\'${a.adapter_source.adapter}\'\n- #else\n- --adapter=\'${a.adapter_source.adapter}\'\n+ ln -f -s \'${library.input_1}\' ${read1} &&\n+\n+ #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"):\n+ #set read2 = "input_r.fastq.gz"\n+ #set compressed = "GZ"\n+ #set out2 = "out2.gz"\n+ #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+ #set read2 = "input_r.fastq.bz2"\n+ #set compressed = "BZ2"\n+ #set out2 = "out2.bz2"\n+ #else if $library.input_2.is_of_type(\'fasta\'):\n+ #set read2 = "input_r.fasta"\n+ #set out2 = "out2.fa"\n+ #set format = "fasta"\n+ #else:\n+ #set read2 = "input_r.fastq"\n+ #set out2 = "out2.fq"\n+ #end if\n+ ln -f -s \'${library.input_2}\' ${read2} &&\n+\n+\n+ #else if str($library.type) == \'paired_collection\':\n+\n+ #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):\n+ #set read1 = "input_f.fastq.gz"\n+ #set compressed = "GZ"\n+ #set out1 = "out1.gz"\n+ #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+ #set read1 = "input_f.fastq.bz2"\n+ #set compressed = "BZ2"\n+ #set out1 = "out1.bz2"\n+ #else if $library.input_1.forward.is_of_type(\'fas'..b'and trim the fourth not at all.\n+ *Sequence: AGATCGGAAGAGC; Type: regular 3\'; Length: 13; Trimmed: 0 times.*\n \n \n-Format of the info file\n------------------------\n-The info file contains information about the found adapters. The output is a tab-separated text file. Each line corresponds to one read of the input file. The fields are:\n+**Info file**\n+\n+The info file contains information about the found adapters. The output is a tab-separated text file. Each line corresponds to one read of the input file.\n+\n+Columns contain the following data:\n \n-1. Read name\n-2. Number of errors\n-3. 0-based start coordinate of the adapter match\n-4. 0-based end coordinate of the adapter match\n-5. Sequence of the read to the left of the adapter match (can be empty)\n-6. Sequence of the read that was matched to the adapter\n-7. Sequence of the read to the right of the adapter match (can be empty)\n-8. Name of the found adapter.\n+ * **1st**: Read name\n+ * **2nd**: Number of errors\n+ * **3rd**: 0-based start coordinate of the adapter match\n+ * **4th**: 0-based end coordinate of the adapter match\n+ * **5th**: Sequence of the read to the left of the adapter match (can be empty)\n+ * **6th**: Sequence of the read that was matched to the adapter\n+ * **7th**: Sequence of the read to the right of the adapter match (can be empty)\n+ * **8th**: Name of the found adapter\n+ * **9th**: Quality values corresponding to sequence left of the adapter match (can be empty)\n+ * **10th**: Quality values corresponding to sequence matched to the adapter (can be empty)\n+ * **11th**: Quality values corresponding to sequence to the right of the adapter (can be empty)\n \n-The concatenation of the fields 5-7 yields the full read sequence. In column 8, adapters without a name are numbered starting from 1.\n+The concatenation of columns 5-7 yields the full read sequence. Column 8 identifies the found adapter. Adapters without a name are numbered starting from 1. Fields 9-11 are empty if quality values are not available. Concatenating them yields the full sequence of quality values.\n \n If no adapter was found, the format is as follows:\n \n-1. Read name\n-2. The value -1\n-3. The read sequence\n+ #. Read name\n+ #. The value -1\n+ #. The read sequence\n+ #. Quality values\n+\n+When parsing the file, be aware that additional columns may be added in the future. Note also that some fields can be empty, resulting in consecutive tabs within a line.\n+\n+If the --times option is used and greater than 1, each read can appear more than once in the info file. There will be one line for each found adapter, all with identical read names. Only for the first of those lines will the concatenation of columns 5-7 be identical to the original read sequence (and accordingly for columns 9-11). For subsequent lines, the shown sequence are the ones that were used in subsequent rounds of adapter trimming, that is, they get successively shorter.\n+\n+--------------------\n+\n+**More Information**\n+\n+--------------------\n \n-When parsing that file, be aware that additional columns may be added in the future. Note also that some fields can be empty, resulting in consecutive tabs within a line. Also, in the current version, when the *Match times* option is set to a value other than 1 (the default value), multiple lines are written to the info file for each read.\n+See the excellent `Cutadapt documentation`_\n+\n+.. _Cutadapt: https://cutadapt.readthedocs.io/en/stable/\n+.. _`Cutadapt documentation`: https://cutadapt.readthedocs.io/en/latest/index.html\n+.. _`Illumina TruSeq Adapters De-Mystified`: http://tucf-genomics.tufts.edu/documents/protocols/TUCF_Understanding_Illumina_TruSeq_Adapters.pdf\n+\n \n-.. _cutadapt: http://code.google.com/p/cutadapt/\n- </help>\n+--------------------\n+\n+**Galaxy Wrapper Development**\n+\n+--------------------\n+\n+Author: Lance Parsons <lparsons@princeton.edu>\n+\n+ ]]></help>\n \n <citations>\n <citation type="bibtex">\n' |
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| diff -r 01d94df2e32a -r 8665bcc8b847 cutadapt_adapters.txt.sample --- a/cutadapt_adapters.txt.sample Tue May 26 16:02:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,14 +0,0 @@ -# -# Adapter/Linker sequences for FASTX-Clipper tool. -# Also used by cutadapt tool -# -# Format: -# Adapter Sequence <TAB> Descriptive name -# -# Example: -# AAATTTGATAAGATA Our-Adapter -# -# Some adapters can be found here: -# http://seqanswers.com/forums/showthread.php?t=198 - -TGTAGGCC Dummy-Adapter (do not use me) |
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| diff -r 01d94df2e32a -r 8665bcc8b847 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Mar 05 11:02:48 2018 -0500 |
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| b'@@ -0,0 +1,264 @@\n+<macros>\n+\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}"=\'${a.adapter_source.adapter}\'\n+ #else if str($a.adapter_source.adapter_name) != "":\n+ -a \'${a.adapter_source.adapter_name}\'=\'${a.adapter_source.adapter}\'\n+ #else\n+ -a \'${a.adapter_source.adapter}\'\n+ #end if\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}\'\n+ #else if str($aa.anywhere_adapter_source.anywhere_adapter_name) != "":\n+ -b \'${aa.anywhere_adapter_source.anywhere_adapter_name}\'=\'${aa.anywhere_adapter_source.anywhere_adapter}\'\n+ #else\n+ -b \'${aa.anywhere_adapter_source.anywhere_adapter}\'\n+ #end if\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}"=\'${fa.front_adapter_source.front_adapter}\'\n+ #else if str($fa.front_adapter_source.front_adapter_name) != "":\n+ -g \'${fa.front_adapter_source.front_adapter_name}\'=\'${fa.front_adapter_source.front_adapter}\'\n+ #else\n+ -g \'${fa.front_adapter_source.front_adapter}\'\n+ #end if\n+ #end for\n+\n+ #if str($library.r1.cut) != \'0\':\n+ -u $library.r1.cut\n+ #end if\n+\n+ ## Additional Outputs\n+\n+ #if $output_options.info_file:\n+ --info-file=$info_file\n+ #end if\n+ #if $output_options.rest_file:\n+ --rest-file=$rest_output\n+ #end if\n+ #if $output_options.wildcard_file:\n+ --wildcard-file=$wild_output\n+ #end if\n+ #if $output_options.too_short_file:\n+ --too-short-output=$too_short_output\n+ #end if\n+ #if $output_options.too_long_file:\n+ --too-long-output=$too_long_output\n+ #end if\n+ #if $output_options.untrimmed_file:\n+ --untrimmed-output=$untrimmed_output\n+ #end if\n+\n+ ]]></token>\n+\n+ <token name="@read2_options@"><