Mercurial > repos > devteam > bowtie2
comparison bowtie2_wrapper.xml @ 16:8ccbdbe9a695 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
| author | iuc |
|---|---|
| date | Thu, 01 Jun 2017 11:14:22 -0400 |
| parents | 43d12513224b |
| children | 66f992977578 |
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| 15:43d12513224b | 16:8ccbdbe9a695 |
|---|---|
| 1 <tool id="bowtie2" name="Bowtie2" version="2.3.2.1" profile="17.01"> | 1 <tool id="bowtie2" name="Bowtie2" version="2.3.2.2" profile="17.01"> |
| 2 <description>- map reads against reference genome</description> | 2 <description>- map reads against reference genome</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>bowtie2_macros.xml</import> | 4 <import>bowtie2_macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <requirements> | 6 <requirements> |
| 20 #end if | 20 #end if |
| 21 | 21 |
| 22 ## Link in the input files, so bowtie2 can tell their type | 22 ## Link in the input files, so bowtie2 can tell their type |
| 23 | 23 |
| 24 #set compressed="False" | 24 #set compressed="False" |
| 25 #set reads_are_fastq = True | |
| 25 #if str($library.type) == 'paired': | 26 #if str($library.type) == 'paired': |
| 26 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): | 27 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): |
| 27 #set read1 = "input_f.fastq.gz" | 28 #set read1 = "input_f.fastq.gz" |
| 28 #set compressed = "GZ" | 29 #set compressed = "GZ" |
| 29 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): | 30 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
| 30 #set read1 = "input_f.fastq.bz2" | 31 #set read1 = "input_f.fastq.bz2" |
| 31 #set compressed = "BZ2" | 32 #set compressed = "BZ2" |
| 33 #else if $library.input_1.is_of_type('fasta'): | |
| 34 #set reads_are_fastq = False | |
| 35 #set read1 = "input_f.fasta" | |
| 32 #else: | 36 #else: |
| 33 #set read1 = "input_f.fastq" | 37 #set read1 = "input_f.fastq" |
| 34 #end if | 38 #end if |
| 35 ln -f -s '${library.input_1}' ${read1} && | 39 ln -f -s '${library.input_1}' ${read1} && |
| 36 | 40 |
| 38 #set read2 = "input_r.fastq.gz" | 42 #set read2 = "input_r.fastq.gz" |
| 39 #set compressed = "GZ" | 43 #set compressed = "GZ" |
| 40 #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"): | 44 #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
| 41 #set read2 = "input_r.fastq.bz2" | 45 #set read2 = "input_r.fastq.bz2" |
| 42 #set compressed = "BZ2" | 46 #set compressed = "BZ2" |
| 47 #else if $library.input_2.is_of_type('fasta'): | |
| 48 #set read2 = "input_r.fasta" | |
| 43 #else: | 49 #else: |
| 44 #set read2 = "input_r.fastq" | 50 #set read2 = "input_r.fastq" |
| 45 #end if | 51 #end if |
| 46 ln -f -s '${library.input_2}' ${read2} && | 52 ln -f -s '${library.input_2}' ${read2} && |
| 47 #else if str($library.type) == 'paired_collection': | 53 #else if str($library.type) == 'paired_collection': |
| 49 #set read1 = "input_f.fastq.gz" | 55 #set read1 = "input_f.fastq.gz" |
| 50 #set compressed = "GZ" | 56 #set compressed = "GZ" |
| 51 #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"): | 57 #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
| 52 #set read1 = "input_f.fastq.bz2" | 58 #set read1 = "input_f.fastq.bz2" |
| 53 #set compressed = "BZ2" | 59 #set compressed = "BZ2" |
| 60 #else if $library.input_1.forward.is_of_type('fasta'): | |
| 61 #set reads_are_fastq = False | |
| 62 #set read1 = "input_f.fasta" | |
| 54 #else: | 63 #else: |
| 55 #set read1 = "input_f.fastq" | 64 #set read1 = "input_f.fastq" |
| 56 #end if | 65 #end if |
| 57 ln -s '${library.input_1.forward}' ${read1} && | 66 ln -s '${library.input_1.forward}' ${read1} && |
| 58 | 67 |
| 60 #set read2 = "input_r.fastq.gz" | 69 #set read2 = "input_r.fastq.gz" |
| 61 #set compressed = "GZ" | 70 #set compressed = "GZ" |
| 62 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"): | 71 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
| 63 #set read2 = "input_r.fastq.bz2" | 72 #set read2 = "input_r.fastq.bz2" |
| 64 #set compressed = "BZ2" | 73 #set compressed = "BZ2" |
| 74 #else if $library.input_1.reverse.is_of_type("fasta"): | |
| 75 #set read2 = "input_r.fasta" | |
| 65 #else: | 76 #else: |
| 66 #set read2 = "input_r.fastq" | 77 #set read2 = "input_r.fastq" |
| 67 #end if | 78 #end if |
| 68 ln -s '${library.input_1.reverse}' ${read2} && | 79 ln -s '${library.input_1.reverse}' ${read2} && |
| 69 | 80 |
| 72 #set read1 = "input_il.fastq.gz" | 83 #set read1 = "input_il.fastq.gz" |
| 73 #set compressed = "GZ" | 84 #set compressed = "GZ" |
| 74 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): | 85 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
| 75 #set read1 = "input_il.fastq.bz2" | 86 #set read1 = "input_il.fastq.bz2" |
| 76 #set compressed = "BZ2" | 87 #set compressed = "BZ2" |
| 88 #else if $library.input_1.is_of_type("fasta"): | |
| 89 #set reads_are_fastq = False | |
| 90 #set read1 = "input_il.fasta" | |
| 77 #else: | 91 #else: |
| 78 #set read1 = "input_il.fastq" | 92 #set read1 = "input_il.fastq" |
| 79 #end if | 93 #end if |
| 80 ln -s '${library.input_1}' ${read1} && | 94 ln -s '${library.input_1}' ${read1} && |
| 81 #else: | 95 #else: |
| 83 #set read1 = "input_f.fastq.gz" | 97 #set read1 = "input_f.fastq.gz" |
| 84 #set compressed = "GZ" | 98 #set compressed = "GZ" |
| 85 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): | 99 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
| 86 #set read1 = "input_f.fastq.bz2" | 100 #set read1 = "input_f.fastq.bz2" |
| 87 #set compressed = "BZ2" | 101 #set compressed = "BZ2" |
| 102 #else if $library.input_1.is_of_type("fasta"): | |
| 103 #set reads_are_fastq = False | |
| 104 #set read1 = "input_f.fasta" | |
| 88 #else: | 105 #else: |
| 89 #set read1 = "input_f.fastq" | 106 #set read1 = "input_f.fastq" |
| 90 #end if | 107 #end if |
| 91 ln -s '${library.input_1}' ${read1} && | 108 ln -s '${library.input_1}' ${read1} && |
| 92 #end if | 109 #end if |
| 99 -p \${GALAXY_SLOTS:-4} | 116 -p \${GALAXY_SLOTS:-4} |
| 100 | 117 |
| 101 ## index file path | 118 ## index file path |
| 102 -x '$index_path' | 119 -x '$index_path' |
| 103 | 120 |
| 104 ## Fastq inputs | 121 ## Input reads are fasta? |
| 122 #if not reads_are_fastq: | |
| 123 -f | |
| 124 #end if | |
| 125 | |
| 126 ## Input reads | |
| 105 #if str( $library.type ) == "single": | 127 #if str( $library.type ) == "single": |
| 106 -U '${read1}' | 128 -U '${read1}' |
| 107 #if str( $library.unaligned_file ) == "true": | 129 #if str( $library.unaligned_file ) == "true": |
| 108 #if $compressed == "GZ": | 130 #if $compressed == "GZ": |
| 109 --un-gz '${output_unaligned_reads_l}' | 131 --un-gz '${output_unaligned_reads_l}' |
| 308 <option value="paired_collection">Paired-end Dataset Collection</option> | 330 <option value="paired_collection">Paired-end Dataset Collection</option> |
| 309 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option> | 331 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option> |
| 310 </param> | 332 </param> |
| 311 | 333 |
| 312 <when value="single"> | 334 <when value="single"> |
| 313 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTQ file" help="Must be of datatype "fastqsanger"" /> | 335 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file" help="Must be of datatype "fastqsanger" or "fasta"" /> |
| 314 | 336 |
| 315 <expand macro="align_unalign" /> | 337 <expand macro="align_unalign" /> |
| 316 | 338 |
| 317 </when> | 339 </when> |
| 318 <when value="paired"> | 340 <when value="paired"> |
| 319 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTQ file #1" help="Must be of datatype "fastqsanger"" /> | 341 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #1" help="Must be of datatype "fastqsanger"or "fasta"" /> |
| 320 <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTQ file #2" help="Must be of datatype "fastqsanger"" /> | 342 <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #2" help="Must be of datatype "fastqsanger"or "fasta"" /> |
| 321 | 343 |
| 322 <expand macro="align_unalign" /> | 344 <expand macro="align_unalign" /> |
| 323 <expand macro="paired_end_options" /> | 345 <expand macro="paired_end_options" /> |
| 324 | 346 |
| 325 </when> | 347 </when> |
| 326 <when value="paired_collection"> | 348 <when value="paired_collection"> |
| 327 <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"" /> | 349 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype "fastqsanger" or "fasta"" /> |
| 328 | 350 |
| 329 <expand macro="align_unalign" /> | 351 <expand macro="align_unalign" /> |
| 330 <expand macro="paired_end_options" /> | 352 <expand macro="paired_end_options" /> |
| 331 | 353 |
| 332 </when> | 354 </when> |
| 333 <when value="paired_interleaved"> | 355 <when value="paired_interleaved"> |
| 334 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="Interleaved FASTQ file" help="Must be of datatype "fastqsanger". --interleaved"/> | 356 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="Interleaved FASTQ file" help="Must be of datatype "fastqsanger" or "fasta". --interleaved"/> |
| 335 | 357 |
| 336 <expand macro="align_unalign" /> | 358 <expand macro="align_unalign" /> |
| 337 <expand macro="paired_end_options" /> | 359 <expand macro="paired_end_options" /> |
| 338 | 360 |
| 339 </when> | 361 </when> |
| 726 <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/> | 748 <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/> |
| 727 <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/> | 749 <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/> |
| 728 <param name="own_file" value="bowtie2-ref.fasta" /> | 750 <param name="own_file" value="bowtie2-ref.fasta" /> |
| 729 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> | 751 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> |
| 730 </test> | 752 </test> |
| 753 <test> | |
| 754 <!-- test fasta input --> | |
| 755 <param name="type" value="paired"/> | |
| 756 <param name="paired_options_selector" value="no"/> | |
| 757 <param name="unaligned_file" value="false"/> | |
| 758 <param name="analysis_type_selector" value="simple"/> | |
| 759 <param name="source" value="history" /> | |
| 760 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/> | |
| 761 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/> | |
| 762 <param name="own_file" value="bowtie2-ref.fasta" /> | |
| 763 <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/> | |
| 764 </test> | |
| 731 </tests> | 765 </tests> |
| 732 | 766 |
| 733 <help><![CDATA[ | 767 <help><![CDATA[ |
| 734 | 768 |
| 735 **Bowtie2 Overview** | 769 **Bowtie2 Overview** |