| Previous changeset 13:12450efac659 (2017-01-09) Next changeset 15:43d12513224b (2017-06-01) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f |
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modified:
bowtie2_wrapper.xml |
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added:
test-data/bowtie2-fq1.fq.bz2 test-data/bowtie2-fq1.fq.gz test-data/bowtie2-fq2.fq.bz2 test-data/bowtie2-fq2.fq.gz |
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| diff -r 12450efac659 -r 937aa69e715f bowtie2_wrapper.xml --- a/bowtie2_wrapper.xml Mon Jan 09 04:31:00 2017 -0500 +++ b/bowtie2_wrapper.xml Wed Apr 12 17:09:42 2017 -0400 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="bowtie2" name="Bowtie2" version="2.3.0">\n+<tool id="bowtie2" name="Bowtie2" version="2.3.0.1" profile="17.01">\n <description>- map reads against reference genome</description>\n <macros>\n <import>read_group_macros.xml</import>\n@@ -19,6 +19,66 @@\n #set index_path = $reference_genome.index.fields.path\n #end if\n \n+ ## Link in the input files, so bowtie2 can tell their type\n+\n+ #set compressed="False"\n+ #if str($library.type) == \'paired\':\n+ #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):\n+ #set read1 = "input_f.fastq.gz"\n+ #set compressed = "GZ"\n+ #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+ #set read1 = "input_f.fastq.bz2"\n+ #set compressed = "BZ2"\n+ #else:\n+ #set read1 = "input_f.fastq"\n+ #end if\n+ ln -f -s \'${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+ #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+ #set read2 = "input_r.fastq.bz2"\n+ #set compressed = "BZ2"\n+ #else:\n+ #set read2 = "input_r.fastq"\n+ #end if\n+ ln -f -s \'${library.input_2}\' ${read2} &&\n+ #else if str($library.type) == \'paired_collection\':\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+ #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+ #set read1 = "input_f.fastq.bz2"\n+ #set compressed = "BZ2"\n+ #else:\n+ #set read1 = "input_f.fastq"\n+ #end if\n+ ln -s \'${library.input_1.forward}\' ${read1} &&\n+\n+ #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):\n+ #set read2 = "input_r.fastq.gz"\n+ #set compressed = "GZ"\n+ #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+ #set read2 = "input_r.fastq.bz2"\n+ #set compressed = "BZ2"\n+ #else:\n+ #set read2 = "input_r.fastq"\n+ #end if\n+ ln -s \'${library.input_1.reverse}\' ${read2} &&\n+ #else:\n+ #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):\n+ #set read1 = "input_f.fastq.gz"\n+ #set compressed = "GZ"\n+ #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+ #set read1 = "input_f.fastq.bz2"\n+ #set compressed = "BZ2"\n+ #else:\n+ #set read1 = "input_f.fastq"\n+ #end if\n+ ln -s \'${library.input_1}\' ${read1} &&\n+ #end if\n+\n ## execute bowtie2\n \n bowtie2\n@@ -31,16 +91,46 @@\n \n ## Fastq inputs\n #if str( $library.type ) == "single":\n- -U \'${library.input_1}\'\n+ -U \'${read1}\'\n #if str( $library.unaligned_file ) == "true":\n- --un \'$output_unaligned_reads_l\'\n+ #if $compressed == "GZ":\n+ --un-gz \'${output_unaligned_reads_l}\'\n+ #else if $compressed == "BZ2":\n+ --un-bz2 \'${output_unaligned_reads_l}\'\n+ #else:\n+ --un \'${output_unaligned_reads_l}\'\n+ #end if\n #end if\n #if str( $library.aligned_file ) == "true":\n- --al \'$output_aligned_reads_l\'\n+ #if $compressed == "GZ":\n+ --al-gz \'${output_aligned_reads_l}\'\n+ #else if $compressed == "BZ2":\n+ --al-bz2 \'$'..b'ype="select" label="Do you want to set paired-end options?" help="See "Alignment Options" section of Help below for information">\n <option value="no" selected="True">No</option>\n@@ -243,9 +310,9 @@\n </conditional>\n </when>\n <when value="paired_collection">\n- <param name="input_1" format="fastqsanger" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype "fastqsanger"" />\n- <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc; This triggers --un parameter for single reads and --un-conc for paired reads" />\n- <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" help="--al/--al-conc; This triggers --al parameter for single reads and --al-conc for paired reads" />\n+ <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype "fastqsanger"" />\n+ <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc (possibly with -gz or -bz2); This triggers --un parameter for single reads and --un-conc for paired reads" />\n+ <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" help="--al/--al-conc (possibly with -gz or -bz2); This triggers --al parameter for single reads and --al-conc for paired reads" />\n <conditional name="paired_options">\n <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See "Alignment Options" section of Help below for information">\n <option value="no" selected="True">No</option>\n@@ -622,6 +689,32 @@\n <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>\n <output name="mapping_stats" file="bowtie2-stats.out" ftype="txt"/>\n </test>\n+ <test>\n+ <!-- test fastqsanger.gz input -->\n+ <param name="type" value="paired"/>\n+ <param name="selection" value="no"/>\n+ <param name="paired_options_selector" value="no"/>\n+ <param name="unaligned_file" value="false"/>\n+ <param name="analysis_type_selector" value="simple"/>\n+ <param name="source" value="history" />\n+ <param name="input_1" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz"/>\n+ <param name="input_2" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz"/>\n+ <param name="own_file" value="bowtie2-ref.fasta" />\n+ <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>\n+ </test>\n+ <test>\n+ <!-- test fastqsanger.bz2 input -->\n+ <param name="type" value="paired"/>\n+ <param name="selection" value="no"/>\n+ <param name="paired_options_selector" value="no"/>\n+ <param name="unaligned_file" value="false"/>\n+ <param name="analysis_type_selector" value="simple"/>\n+ <param name="source" value="history" />\n+ <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/>\n+ <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/>\n+ <param name="own_file" value="bowtie2-ref.fasta" />\n+ <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>\n+ </test>\n </tests>\n \n <help><![CDATA[\n' |
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