Previous changeset 12:78e1cf88d133 (2018-05-24) Next changeset 14:c76ee709ffb9 (2018-08-05) |
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830 |
modified:
cutadapt.xml |
b |
diff -r 78e1cf88d133 -r f5fdf41c08b8 cutadapt.xml --- a/cutadapt.xml Thu May 24 18:24:08 2018 -0400 +++ b/cutadapt.xml Tue Jun 12 15:38:04 2018 -0400 |
[ |
b'@@ -10,138 +10,135 @@\n <version_command>cutadapt --version</version_command>\n \n <command detect_errors="exit_code"><![CDATA[\n-\n- ## Link in the input and output files, so Cutadapt can tell their type\n+## Link in the input and output files, so Cutadapt can tell their type\n \n- #import re\n- #set format = "fastq"\n- #set read1 = "input_f"\n- #set read2 = "input_r"\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- #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))\n- #else\n- #set input_1 = $library.input_1\n- #set read1 = re.sub(\'[^\\w\\-\\s]\', \'_\', str($library.input_1.element_identifier))\n- #end if\n+#import re\n+#set read1 = "input_f"\n+#set read2 = "input_r"\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+#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))\n+#else\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- #set read1 = $read1 + ".fq.gz"\n- #set out1 = "out1.gz"\n- #else if $input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n- #set read1 = $read1 + ".fq.bz2"\n- #set out1 = "out1.bz2"\n- #else if $input_1.is_of_type(\'fasta\'):\n- #set format = "fasta"\n- #set read1 = $read1 + ".fa"\n- #set out1 = "out1.fa"\n- #else:\n- #set read1 = $read1 + ".fq"\n- #set out1 = "out1.fq"\n- #end if\n- ln -f -s \'${input_1}\' \'$read1\' &&\n+#if $input_1.is_of_type("fastq.gz", "fastqsanger.gz"):\n+ #set read1 = $read1 + ".fq.gz"\n+ #set out1 = "out1.gz"\n+#else if $input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+ #set read1 = $read1 + ".fq.bz2"\n+ #set out1 = "out1.bz2"\n+#else if $input_1.is_of_type(\'fasta\'):\n+ #set read1 = $read1 + ".fa"\n+ #set out1 = "out1.fa"\n+#else:\n+ #set read1 = $read1 + ".fq"\n+ #set out1 = "out1.fq"\n+#end if\n+ln -f -s \'${input_1}\' \'$read1\' &&\n \n- #if $paired:\n- #if $input_2.is_of_type("fastq.gz", "fastqsanger.gz"):\n- #set read2 = $read2 + ".fq.gz"\n- #set out2 = "out2.gz"\n- #else if $input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n- #set read2 = $read2 + ".fq.bz2"\n- #set out2 = "out2.bz2"\n- #else if $input_2.is_of_type(\'fasta\'):\n- #set format = "fasta"\n- #set read2 = $read2 + ".fa"\n- #set out2 = "out2.fa"\n- #else:\n- #set read2 = $read2 + ".fq"\n- #set out2 = "out2.fq"\n- #end if\n- ln -f -s \'${input_2}\' \'$read2\' &&\n- #end if\n+#if $paired:\n+ #if $input_2.is_of_type("fastq.gz", "fastqsanger.gz"):\n+ #set read2 = $read2 + ".fq.gz"\n+ #set out2 = "out2.gz"\n+ #else if $input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+ #set read2 = $read2 + ".fq.bz2'..b' run in multicore mode with these options\n+#if not any(($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 \n- #if str( $library.type ) == "single":\n- @read1_options@\n- --output=\'$out1\'\n- #else:\n- @read1_options@\n- @read2_options@\n- --output=\'$out1\'\n- --paired-output=\'$out2\'\n- #end if\n+#if str( $library.type ) == "single":\n+ @read1_options@\n+ --output=\'$out1\'\n+#else:\n+ @read1_options@\n+ @read2_options@\n+ --output=\'$out1\'\n+ --paired-output=\'$out2\'\n+#end if\n \n- --error-rate=$adapter_options.error_rate\n- --times=$adapter_options.count\n- --overlap=$adapter_options.overlap\n- $adapter_options.no_indels\n- $adapter_options.match_read_wildcards\n+--error-rate=$adapter_options.error_rate\n+--times=$adapter_options.count\n+--overlap=$adapter_options.overlap\n+$adapter_options.no_indels\n+$adapter_options.match_read_wildcards\n \n \n- $filter_options.discard\n- $filter_options.discard_untrimmed\n- $filter_options.no_trim\n- $filter_options.mask_adapter\n- #if str($filter_options.min) != \'0\':\n- --minimum-length=$filter_options.min\n- #end if\n- #if str($filter_options.max) != \'0\':\n- --maximum-length=$filter_options.max\n- #end if\n- #if $filter_options.max_n:\n- --max-n=$filter_options.max_n\n- #end if\n- #if str( $library.type ) != "single":\n- #if $filter_options.pair_filter:\n- --pair-filter=$filter_options.pair_filter\n- #end if\n- #end if\n+$filter_options.discard\n+$filter_options.discard_untrimmed\n+$filter_options.no_trim\n+$filter_options.mask_adapter\n+#if str($filter_options.min) != \'0\':\n+ --minimum-length=$filter_options.min\n+#end if\n+#if str($filter_options.max) != \'0\':\n+ --maximum-length=$filter_options.max\n+#end if\n+#if $filter_options.max_n:\n+ --max-n=$filter_options.max_n\n+#end if\n+#if str( $library.type ) != "single":\n+ #if $filter_options.pair_filter:\n+ --pair-filter=$filter_options.pair_filter\n+ #end if\n+#end if\n \n \n- #if str($read_mod_options.quality_cutoff) != \'0\':\n- --quality-cutoff=$read_mod_options.quality_cutoff\n- #end if\n- #if str($read_mod_options.nextseq_trim) != \'0\':\n- --nextseq-trim=$read_mod_options.nextseq_trim\n- #end if\n- $read_mod_options.trim_n\n- #if $read_mod_options.prefix != \'\':\n- --prefix="$read_mod_options.prefix"\n- #end if\n- #if $read_mod_options.suffix != \'\':\n- --suffix="$read_mod_options.suffix"\n- #end if\n- #if str($read_mod_options.length) != \'0\':\n- --length=$$read_mod_options.length\n- #end if\n- #if $read_mod_options.length_tag != \'\':\n- --length-tag="$read_mod_options.length_tag"\n- #end if\n+#if str($read_mod_options.quality_cutoff) != \'0\':\n+ --quality-cutoff=$read_mod_options.quality_cutoff\n+#end if\n+#if str($read_mod_options.nextseq_trim) != \'0\':\n+ --nextseq-trim=$read_mod_options.nextseq_trim\n+#end if\n+$read_mod_options.trim_n\n+#if $read_mod_options.prefix != \'\':\n+ --prefix="$read_mod_options.prefix"\n+#end if\n+#if $read_mod_options.suffix != \'\':\n+ --suffix="$read_mod_options.suffix"\n+#end if\n+#if str($read_mod_options.length) != \'0\':\n+ --length=$$read_mod_options.length\n+#end if\n+#if $read_mod_options.length_tag != \'\':\n+ --length-tag="$read_mod_options.length_tag"\n+#end if\n \n- \'${read1}\'\n- #if $paired:\n- \'${read2}\'\n- #end if\n+\'${read1}\'\n+#if $paired:\n+ \'${read2}\'\n+#end if\n \n- #if $output_options.report:\n- > report.txt\n- #end if\n+#if $output_options.report:\n+ > report.txt\n+#end if\n ]]></command>\n <inputs>\n \n' |