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comparison bowtie2_wrapper.xml @ 14:85f0e9edb32d draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
author devteam
date Wed, 12 Apr 2017 17:09:24 -0400
parents 55dcd6aad1ab
children 7e0b333f39e1
comparison
equal deleted inserted replaced
13:55dcd6aad1ab 14:85f0e9edb32d
1 <tool id="bowtie2" name="Bowtie2" version="2.3.0"> 1 <tool id="bowtie2" name="Bowtie2" version="2.3.0.1" 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>read_group_macros.xml</import> 4 <import>read_group_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
17 #set index_path = 'genome' 17 #set index_path = 'genome'
18 #else: 18 #else:
19 #set index_path = $reference_genome.index.fields.path 19 #set index_path = $reference_genome.index.fields.path
20 #end if 20 #end if
21 21
22 ## Link in the input files, so bowtie2 can tell their type
23
24 #set compressed="False"
25 #if str($library.type) == 'paired':
26 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
27 #set read1 = "input_f.fastq.gz"
28 #set compressed = "GZ"
29 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
30 #set read1 = "input_f.fastq.bz2"
31 #set compressed = "BZ2"
32 #else:
33 #set read1 = "input_f.fastq"
34 #end if
35 ln -f -s '${library.input_1}' ${read1} &&
36
37 #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
38 #set read2 = "input_r.fastq.gz"
39 #set compressed = "GZ"
40 #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
41 #set read2 = "input_r.fastq.bz2"
42 #set compressed = "BZ2"
43 #else:
44 #set read2 = "input_r.fastq"
45 #end if
46 ln -f -s '${library.input_2}' ${read2} &&
47 #else if str($library.type) == 'paired_collection':
48 #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
49 #set read1 = "input_f.fastq.gz"
50 #set compressed = "GZ"
51 #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
52 #set read1 = "input_f.fastq.bz2"
53 #set compressed = "BZ2"
54 #else:
55 #set read1 = "input_f.fastq"
56 #end if
57 ln -s '${library.input_1.forward}' ${read1} &&
58
59 #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
60 #set read2 = "input_r.fastq.gz"
61 #set compressed = "GZ"
62 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
63 #set read2 = "input_r.fastq.bz2"
64 #set compressed = "BZ2"
65 #else:
66 #set read2 = "input_r.fastq"
67 #end if
68 ln -s '${library.input_1.reverse}' ${read2} &&
69 #else:
70 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
71 #set read1 = "input_f.fastq.gz"
72 #set compressed = "GZ"
73 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
74 #set read1 = "input_f.fastq.bz2"
75 #set compressed = "BZ2"
76 #else:
77 #set read1 = "input_f.fastq"
78 #end if
79 ln -s '${library.input_1}' ${read1} &&
80 #end if
81
22 ## execute bowtie2 82 ## execute bowtie2
23 83
24 bowtie2 84 bowtie2
25 85
26 ## number of threads 86 ## number of threads
29 ## index file path 89 ## index file path
30 -x '$index_path' 90 -x '$index_path'
31 91
32 ## Fastq inputs 92 ## Fastq inputs
33 #if str( $library.type ) == "single": 93 #if str( $library.type ) == "single":
34 -U '${library.input_1}' 94 -U '${read1}'
35 #if str( $library.unaligned_file ) == "true": 95 #if str( $library.unaligned_file ) == "true":
36 --un '$output_unaligned_reads_l' 96 #if $compressed == "GZ":
97 --un-gz '${output_unaligned_reads_l}'
98 #else if $compressed == "BZ2":
99 --un-bz2 '${output_unaligned_reads_l}'
100 #else:
101 --un '${output_unaligned_reads_l}'
102 #end if
37 #end if 103 #end if
38 #if str( $library.aligned_file ) == "true": 104 #if str( $library.aligned_file ) == "true":
39 --al '$output_aligned_reads_l' 105 #if $compressed == "GZ":
40 #end if 106 --al-gz '${output_aligned_reads_l}'
41 #elif str( $library.type ) == "paired": 107 #else if $compressed == "BZ2":
42 -1 '${library.input_1}' 108 --al-bz2 '${output_aligned_reads_l}'
43 -2 '${library.input_2}' 109 #else:
110 --al '${output_aligned_reads_l}'
111 #end if
112 #end if
113 #else:
114 -1 '${read1}'
115 -2 '${read2}'
116 #if str( $library.unaligned_file ) == "true":
117 #if $compressed == "GZ":
118 --un-conc-gz '${output_unaligned_reads_l}'
119 #else if $compressed == "BZ2":
120 --un-conc-bz2 '${output_unaligned_reads_l}'
121 #else:
122 --un-conc '${output_unaligned_reads_l}'
123 #end if
124 #end if
125 #if str( $library.aligned_file ) == "true":
126 #if $compressed == "GZ":
127 --al-conc-gz '${output_aligned_reads_l}'
128 #else if $compressed == "BZ2":
129 --al-conc-bz2 '${output_aligned_reads_l}'
130 #else:
131 --al-conc '${output_aligned_reads_l}'
132 #end if
133 #end if
44 #if str( $library.paired_options.paired_options_selector ) == "yes": 134 #if str( $library.paired_options.paired_options_selector ) == "yes":
45 -I "${library.paired_options.I}" 135 -I "${library.paired_options.I}"
46 -X "${library.paired_options.X}" 136 -X "${library.paired_options.X}"
47 ${library.paired_options.fr_rf_ff} 137 ${library.paired_options.fr_rf_ff}
48 ${library.paired_options.no_mixed} 138 ${library.paired_options.no_mixed}
49 ${library.paired_options.no_discordant} 139 ${library.paired_options.no_discordant}
50 ${library.paired_options.dovetail} 140 ${library.paired_options.dovetail}
51 ${library.paired_options.no_contain} 141 ${library.paired_options.no_contain}
52 ${library.paired_options.no_overlap} 142 ${library.paired_options.no_overlap}
53 #end if
54 #if str( $library.unaligned_file ) == "true":
55 --un-conc $output_unaligned_reads_l
56 #end if
57 #if str( $library.aligned_file ) == "true":
58 --al-conc $output_aligned_reads_l
59 #end if
60 #else
61 ## prepare collection
62 -1 $library.input_1.forward
63 -2 $library.input_1.reverse
64 #if str( $library.paired_options.paired_options_selector ) == "yes":
65 -I "${library.paired_options.I}"
66 -X "${library.paired_options.X}"
67 ${library.paired_options.fr_rf_ff}
68 ${library.paired_options.no_mixed}
69 ${library.paired_options.no_discordant}
70 ${library.paired_options.dovetail}
71 ${library.paired_options.no_contain}
72 ${library.paired_options.no_overlap}
73 #end if
74 #if str( $library.unaligned_file ) == "true":
75 --un-conc '$output_unaligned_reads_l'
76 #end if 143 #end if
77 #end if 144 #end if
78 145
79 ## Read group information. 146 ## Read group information.
80 @define_read_group_helpers@ 147 @define_read_group_helpers@
207 <option value="paired">Paired-end</option> 274 <option value="paired">Paired-end</option>
208 <option value="paired_collection">Paired-end Dataset Collection</option> 275 <option value="paired_collection">Paired-end Dataset Collection</option>
209 </param> 276 </param>
210 277
211 <when value="single"> 278 <when value="single">
212 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Must be of datatype &quot;fastqsanger&quot;" /> 279 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTQ file" help="Must be of datatype &quot;fastqsanger&quot;" />
213 <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" /> 280 <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" />
214 <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" /> 281 <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" />
215 </when> 282 </when>
216 <when value="paired"> 283 <when value="paired">
217 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file #1" help="Must be of datatype &quot;fastqsanger&quot;" /> 284 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTQ file #1" help="Must be of datatype &quot;fastqsanger&quot;" />
218 <param name="input_2" format="fastqsanger" type="data" label="FASTQ file #2" help="Must be of datatype &quot;fastqsanger&quot;" /> 285 <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTQ file #2" help="Must be of datatype &quot;fastqsanger&quot;" />
219 <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" /> 286 <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" />
220 <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" /> 287 <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" />
221 <conditional name="paired_options"> 288 <conditional name="paired_options">
222 <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information"> 289 <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information">
223 <option value="no" selected="True">No</option> 290 <option value="no" selected="True">No</option>
224 <option value="yes">Yes</option> 291 <option value="yes">Yes</option>
225 </param> 292 </param>
241 <!-- do nothing --> 308 <!-- do nothing -->
242 </when> 309 </when>
243 </conditional> 310 </conditional>
244 </when> 311 </when>
245 <when value="paired_collection"> 312 <when value="paired_collection">
246 <param name="input_1" format="fastqsanger" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype &quot;fastqsanger&quot;" /> 313 <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;" />
247 <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" /> 314 <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" />
248 <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" /> 315 <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" />
249 <conditional name="paired_options"> 316 <conditional name="paired_options">
250 <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information"> 317 <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information">
251 <option value="no" selected="True">No</option> 318 <option value="no" selected="True">No</option>
252 <option value="yes">Yes</option> 319 <option value="yes">Yes</option>
253 </param> 320 </param>
620 <param name="own_file" value="bowtie2-ref.fasta" /> 687 <param name="own_file" value="bowtie2-ref.fasta" />
621 <param name="save_mapping_stats" value="true" /> 688 <param name="save_mapping_stats" value="true" />
622 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> 689 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
623 <output name="mapping_stats" file="bowtie2-stats.out" ftype="txt"/> 690 <output name="mapping_stats" file="bowtie2-stats.out" ftype="txt"/>
624 </test> 691 </test>
692 <test>
693 <!-- test fastqsanger.gz input -->
694 <param name="type" value="paired"/>
695 <param name="selection" value="no"/>
696 <param name="paired_options_selector" value="no"/>
697 <param name="unaligned_file" value="false"/>
698 <param name="analysis_type_selector" value="simple"/>
699 <param name="source" value="history" />
700 <param name="input_1" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz"/>
701 <param name="input_2" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz"/>
702 <param name="own_file" value="bowtie2-ref.fasta" />
703 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
704 </test>
705 <test>
706 <!-- test fastqsanger.bz2 input -->
707 <param name="type" value="paired"/>
708 <param name="selection" value="no"/>
709 <param name="paired_options_selector" value="no"/>
710 <param name="unaligned_file" value="false"/>
711 <param name="analysis_type_selector" value="simple"/>
712 <param name="source" value="history" />
713 <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/>
714 <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/>
715 <param name="own_file" value="bowtie2-ref.fasta" />
716 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
717 </test>
625 </tests> 718 </tests>
626 719
627 <help><![CDATA[ 720 <help><![CDATA[
628 721
629 **Bowtie2 Overview** 722 **Bowtie2 Overview**