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comparison bowtie2_wrapper.xml @ 16:def46fdb3909 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
author iuc
date Thu, 01 Jun 2017 11:14:09 -0400
parents 7e0b333f39e1
children 69f044db2445
comparison
equal deleted inserted replaced
15:7e0b333f39e1 16:def46fdb3909
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 &quot;fastqsanger&quot;" /> 335 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
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 &quot;fastqsanger&quot;" /> 341 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #1" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" />
320 <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTQ file #2" help="Must be of datatype &quot;fastqsanger&quot;" /> 342 <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #2" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" />
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 &quot;fastqsanger&quot;" /> 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 &quot;fastqsanger&quot; or &quot;fasta&quot;" />
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 &quot;fastqsanger&quot;. --interleaved"/> 356 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="Interleaved FASTQ file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;. --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**