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comparison bismark_bowtie2_wrapper.xml @ 17:aa9bf0f29a9f draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
author bgruening
date Wed, 28 Aug 2019 07:08:45 -0400
parents a4504327c890
children 359f8b60d316
comparison
equal deleted inserted replaced
16:a4504327c890 17:aa9bf0f29a9f
1 <tool id="bismark_bowtie2" name="Bismark Mapper" version="0.22.1+galaxy3" profile="18.01"> 1 <tool id="bismark_bowtie2" name="Bismark Mapper" version="0.22.1+galaxy4" profile="18.01">
2 <description>Bisulfite reads mapper</description> 2 <description>Bisulfite reads mapper</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.22.1">bismark</requirement> 4 <requirement type="package" version="0.22.1">bismark</requirement>
5 <requirement type="package" version="1.8">samtools</requirement> 5 <requirement type="package" version="1.8">samtools</requirement>
6 <requirement type="package" version="2.3.5">bowtie2</requirement> 6 <requirement type="package" version="2.3.5">bowtie2</requirement>
10 10
11 #if $singlePaired.sPaired == "single": 11 #if $singlePaired.sPaired == "single":
12 #if $singlePaired.input_singles.ext == "fasta": 12 #if $singlePaired.input_singles.ext == "fasta":
13 #set read1 = 'input_1.fa' 13 #set read1 = 'input_1.fa'
14 #elif $singlePaired.input_singles.ext in ["fastq.gz", "fastqsanger.gz"]: 14 #elif $singlePaired.input_singles.ext in ["fastq.gz", "fastqsanger.gz"]:
15 #set read1 = 'input_1.fq.gz' 15 #if $params.pbat == "--pbat"
16 #set read1 = 'input_1.fq'
17 #else
18 #set read1 = 'input_1.fq.gz'
19 #end if
16 #else 20 #else
17 #set read1 = 'input_1.fq' 21 #set read1 = 'input_1.fq'
18 #end if 22 #end if
19 ln -s '${singlePaired.input_singles}' '${read1}' && 23
24 #if $params.pbat == "--pbat" and $singlePaired.input_singles.ext in ["fastq.gz", "fastqsanger.gz"]:
25 zcat '${singlePaired.input_singles}' > '${read1}' &&
26 #else
27 ln -s '${singlePaired.input_singles}' '${read1}' &&
28 #end if
20 #else: 29 #else:
21 #set $mate1 = list() 30 #set $mate1 = list()
22 #set $mate2 = list() 31 #set $mate2 = list()
23 #for $mate_pair in $singlePaired.mate_list 32 #for $mate_pair in $singlePaired.mate_list
24 33
25 #if $mate_pair.input_mate1.ext == "fasta": 34 #if $mate_pair.input_mate1.ext == "fasta":
26 #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fa' 35 #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fa'
27 #elif $mate_pair.input_mate1.ext in ["fastq.gz", "fastqsanger.gz"]: 36 #elif $mate_pair.input_mate1.ext in ["fastq.gz", "fastqsanger.gz"]:
28 #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq.gz' 37 #if $params.pbat == "--pbat"
38 #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq'
39 #else
40 #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq.gz'
41 #end if
29 #else 42 #else
30 #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq' 43 #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq'
31 #end if 44 #end if
32 ln -s '${mate_pair.input_mate1}' '${read1}' && 45
46 #if $params.pbat == "--pbat" and $mate_pair.input_mate1.ext in ["fastq.gz", "fastqsanger.gz"]:
47 zcat '${mate_pair.input_mate1}' > '${read1}' &&
48 #else
49 ln -s '${mate_pair.input_mate1}' '${read1}' &&
50 #end if
33 51
34 #if $mate_pair.input_mate2.ext == "fasta": 52 #if $mate_pair.input_mate2.ext == "fasta":
35 #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fa' 53 #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fa'
36 #elif $mate_pair.input_mate2.ext in ["fastq.gz", "fastqsanger.gz"]: 54 #elif $mate_pair.input_mate2.ext in ["fastq.gz", "fastqsanger.gz"]:
37 #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq.gz' 55 #if $params.pbat == "--pbat"
56 #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq'
57 #else
58 #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq.gz'
59 #end if
38 #else 60 #else
39 #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq' 61 #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq'
40 #end if 62 #end if
41 ln -s '${mate_pair.input_mate2}' '${read2}' && 63
64 #if $params.pbat == "--pbat" and $mate_pair.input_mate2.ext in ["fastq.gz", "fastqsanger.gz"]:
65 zcat '${mate_pair.input_mate2}' > '${read2}' &&
66 #else
67 ln -s '${mate_pair.input_mate2}' '${read2}' &&
68 #end if
42 69
43 $mate1.append( str($read1) ) 70 $mate1.append( str($read1) )
44 $mate2.append( str($read2) ) 71 $mate2.append( str($read2) )
45 #end for 72 #end for
46 #end if 73 #end if
135 $params.no_mixed 162 $params.no_mixed
136 ## if set, disable the original behaviour 163 ## if set, disable the original behaviour
137 $params.no_discordant 164 $params.no_discordant
138 165
139 $params.non_directional 166 $params.non_directional
167
168 $params.pbat
140 169
141 #if $params.bismark_stdout: 170 #if $params.bismark_stdout:
142 --stdout '$output_stdout' 171 --stdout '$output_stdout'
143 #end if 172 #end if
144 173
287 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="true" 316 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="true"
288 label="Offer all report files concatenated in one file (Mapping Report)"/> 317 label="Offer all report files concatenated in one file (Mapping Report)"/>
289 <param argument="--non-directional" name="non_directional" type="boolean" 318 <param argument="--non-directional" name="non_directional" type="boolean"
290 truevalue="--non-directional" falsevalue="" checked="false" 319 truevalue="--non-directional" falsevalue="" checked="false"
291 label="The sequencing library was constructed in a non strand-specific manner, alignments to all four bisulfite strands will be reported."/> 320 label="The sequencing library was constructed in a non strand-specific manner, alignments to all four bisulfite strands will be reported."/>
321 <param argument="--pbat" name="pbat" type="boolean"
322 truevalue="--pbat" falsevalue="" checked="false"
323 label="Treat input data as PBAT-Seq libraries"
324 help="Use this option only if you are certain that your libraries were constructed following a PBAT protocol. If you don't know what PBAT-Seq is you should not specify this option." />
325
292 326
293 <!--end output options --> 327 <!--end output options -->
294 </when> <!-- full --> 328 </when> <!-- full -->
295 </conditional> <!-- params --> 329 </conditional> <!-- params -->
296 <!-- 330 <!--
542 576
543 <assert_command> 577 <assert_command>
544 <has_text text="--score-min 'L,0,-0.8'" /> 578 <has_text text="--score-min 'L,0,-0.8'" />
545 </assert_command> 579 </assert_command>
546 </test> 580 </test>
581 <test>
582 <param name="genomeSource" value="history"/>
583 <param name="own_file" value="mm10.tiny.fa.gz" />
584 <param name="sPaired" value="single"/>
585 <param name="input_singles" value="input1.fq.gzip" ftype="fastqsanger.gz"/>
586 <param name="sort_bam" value="false"/>
587 <param name="settingsType" value="custom"/>
588 <param name="suppressed_read_file" value="true"/>
589 <param name="unmapped_read_file" value="true"/>
590 <param name="bismark_stdout" value="true"/>
591 <param name="isReportOutput" value="true"/>
592 <conditional name="params">
593 <param name="settingsType" value="custom" />
594 <param name="pbat" value="true" />
595 </conditional>
596
597 <output name="output_stdout" file="summary_pbat.txt" ftype="txt" lines_diff="94">
598 <assert_contents>
599 <has_text text="Sequences analysed in total:" />
600 <has_text text="44115" />
601 <has_text text="Mapping efficiency:" />
602 <has_text text="0.0%" />
603 <has_text text="Bismark run complete" />
604 </assert_contents>
605 </output>
606 <output name="report_file" file="mapping_report_pbat.txt" ftype="txt" lines_diff="6"/>
607 <output name="output" file="mapped_reads_pbat.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
608
609 <assert_command>
610 <has_text text="--pbat" />
611 </assert_command>
612 </test>
547 </tests> 613 </tests>
548 614
549 <help> 615 <help>
550 <![CDATA[ 616 <![CDATA[
551 617