| Previous changeset 10:a9d4f71dbfb0 (2016-03-22) Next changeset 12:781e3a3b9d31 (2017-01-08) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd |
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modified:
bowtie2_wrapper.xml |
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| diff -r a9d4f71dbfb0 -r b4e9cf5f2ae8 bowtie2_wrapper.xml --- a/bowtie2_wrapper.xml Tue Mar 22 14:58:55 2016 -0400 +++ b/bowtie2_wrapper.xml Tue Jan 03 10:51:03 2017 -0500 |
| [ |
| b'@@ -1,22 +1,22 @@\n-<tool id="bowtie2" name="Bowtie2" version="2.2.6.2">\n+<tool id="bowtie2" name="Bowtie2" version="2.2.8">\n <description>- map reads against reference genome</description>\n <macros>\n <import>read_group_macros.xml</import>\n </macros>\n+ <requirements>\n+ <requirement type="package" version="2.2.8">bowtie2</requirement>\n+ <requirement type="package" version="1.3.1">samtools</requirement>\n+ </requirements>\n <version_command>bowtie2 --version</version_command>\n- <requirements>\n- <requirement type="package" version="2.2.6">bowtie2</requirement>\n- <requirement type="package" version="1.2">samtools</requirement>\n- </requirements>\n- <command>\n+ <command detect_errors="exit_code"><![CDATA[\n ## prepare bowtie2 index\n #set index_path = \'\'\n #if str($reference_genome.source) == "history":\n- bowtie2-build "$reference_genome.own_file" genome &&\n- ln -s "$reference_genome.own_file" genome.fa &&\n+ bowtie2-build --threads \\${GALAXY_SLOTS:-4} \'$reference_genome.own_file\' genome &&\n+ ln -s -f \'$reference_genome.own_file\' genome.fa &&\n #set index_path = \'genome\'\n #else:\n- #set index_path = $reference_genome.index.fields.path\n+ #set index_path = \'$reference_genome.index.fields.path\'\n #end if\n \n ## execute bowtie2\n@@ -27,20 +27,20 @@\n -p \\${GALAXY_SLOTS:-4}\n \n ## index file path\n- -x $index_path\n+ -x \'$index_path\'\n \n ## Fastq inputs\n #if str( $library.type ) == "single":\n- -U "${library.input_1}"\n+ -U \'${library.input_1}\'\n #if str( $library.unaligned_file ) == "true":\n- --un $output_unaligned_reads_l\n+ --un \'$output_unaligned_reads_l\'\n #end if\n #if str( $library.aligned_file ) == "true":\n- --al $output_aligned_reads_l\n+ --al \'$output_aligned_reads_l\'\n #end if\n #elif str( $library.type ) == "paired":\n- -1 "${library.input_1}"\n- -2 "${library.input_2}"\n+ -1 \'${library.input_1}\'\n+ -2 \'${library.input_2}\'\n #if str( $library.paired_options.paired_options_selector ) == "yes":\n -I "${library.paired_options.I}"\n -X "${library.paired_options.X}"\n@@ -72,7 +72,7 @@\n ${library.paired_options.no_overlap}\n #end if\n #if str( $library.unaligned_file ) == "true":\n- --un-conc $output_unaligned_reads_l\n+ --un-conc \'$output_unaligned_reads_l\'\n #end if\n #end if\n \n@@ -174,36 +174,31 @@\n \n ## mapping stats (i.e. stderr from bowtie2)\n #if $save_mapping_stats\n-\t 2> "$mapping_stats"\n+ 2> \'$mapping_stats\'\n #end if\n \n ## output file\n #if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ):\n- | samtools view -Su - | samtools sort -o - - > $output\n+ | samtools sort -O bam -o \'$output\'\n #else\n- > $output_sam\n+ > \'$output_sam\'\n #end if\n \n ## rename unaligned sequence files\n #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:\n #from os.path import splitext\n #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )\n- && mv "${ _unaligned_root }.1${_unaligned_ext}" "${ output_unaligned_reads_l }"\n- && mv "${ _unaligned_root }.2${_unaligned_ext}" "${ output_unaligned_reads_r }"\n+ && mv "${ _unaligned_root }.1${_unaligned_ext}" \'$output_unaligned_reads_l\'\n+ && mv "${ _unaligned_root }.2${_unaligned_ext}" \'$output_unaligned_reads_r\'\n #end if\n #if $library.type == "pa'..b're-seed" reads with\n+ -R <int>\n+ `<int>` is the maximum number of times Bowtie 2 will "re-seed" reads with\n repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads\n (same length, same number of mismatches allowed) at different offsets and\n searches for more alignments. A read is considered to have repetitive seeds if\n the total number of seed hits divided by the number of seeds that aligned at\n least once is greater than 300. Default: 2.\n- \n+\n -----\n \n **Paired-end options**::\n \n- -I/--minins <int>\n+ -I/--minins <int>\n The minimum fragment length for valid paired-end alignments. E.g. if `-I 60` is\n specified and a paired-end alignment consists of two 20-bp alignments in the\n appropriate orientation with a 20-bp gap between them, that alignment is\n@@ -944,9 +939,9 @@\n For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very\n efficient.\n \n- Default: 0 (essentially imposing no minimum) \n+ Default: 0 (essentially imposing no minimum)\n \n- -X/--maxins <int>\n+ -X/--maxins <int>\n The maximum fragment length for valid paired-end alignments. E.g. if `-X 100`\n is specified and a paired-end alignment consists of two 20-bp alignments in the\n proper orientation with a 60-bp gap between them, that alignment is considered\n@@ -998,19 +993,19 @@\n --no-overlap\n If one mate alignment overlaps the other at all, consider that to be\n non-concordant. Default: mates can overlap in a concordant alignment.\n- \n+\n ------\n \n **SAM options**::\n \n- --rg-id <text>\n- Set the read group ID to `<text>`. This causes the SAM `@RG` header line to be\n- printed, with `<text>` as the value associated with the `ID:` tag. It also\n+ --rg-id <text>\n+ Set the read group ID to `<text>`. This causes the SAM `@RG` header line to be\n+ printed, with `<text>` as the value associated with the `ID:` tag. It also\n causes the `RG:Z:` extra field to be attached to each SAM output record, with\n- value set to `<text>`.\n+ value set to `<text>`.\n \n- --rg <text>\n- Add `<text>` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the\n+ --rg <text>\n+ Add `<text>` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the\n `@RG` header line. Note: in order for the `@RG` line to appear, `--rg-id`\n must also be specified. This is because the `ID` tag is required by the SAM\n Specification. Specify `--rg` multiple times to set multiple fields. See the\n@@ -1020,7 +1015,7 @@\n When printing secondary alignments, Bowtie 2 by default will write out the `SEQ`\n and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterix\n in those fields instead.\n- \n+\n -----\n \n **Other options**::\n@@ -1033,8 +1028,8 @@\n not specified. Has no effect if `-p` is set to 1, since output order will\n naturally correspond to input order in that case.\n \n- --seed <int>\n- Use `<int>` as the seed for pseudo-random number generator. Default: 0.\n+ --seed <int>\n+ Use `<int>` as the seed for pseudo-random number generator. Default: 0.\n \n --non-deterministic\n Normally, Bowtie 2 re-initializes its pseudo-random generator for each read. It\n@@ -1049,7 +1044,7 @@\n but might be more appropriate in situations where the input consists of many\n identical reads.\n \n- </help>\n+ ]]></help>\n <citations>\n <citation type="doi">10.1186/gb-2009-10-3-r25</citation>\n <citation type="doi">10.1038/nmeth.1923</citation>\n' |