Mercurial > repos > bgruening > bismark

comparison bismark_bowtie2_wrapper.xml @ 14:b6aa3b6ba129 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
author bgruening
date Tue, 30 Jul 2019 10:33:02 -0400
parents f211753166bd
children 0b656f8c5637
comparison
equal deleted inserted replaced
13:f211753166bd 14:b6aa3b6ba129
1 <tool id="bismark_bowtie2" name="Bismark Mapper" version="0.22.1" profile="18.01"> 1 <tool id="bismark_bowtie2" name="Bismark Mapper" version="0.22.1+galaxy1" 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>
7 </requirements> 7 </requirements>
8 <command><![CDATA[ 8 <command><![CDATA[
9 #import re
10
9 #if $singlePaired.sPaired == "single": 11 #if $singlePaired.sPaired == "single":
10 #if $singlePaired.input_singles.ext == "fasta": 12 #if $singlePaired.input_singles.ext == "fasta":
11 #set read1 = 'input_1.fa' 13 #set read1 = 'input_1.fa'
12 #elif $singlePaired.input_singles.ext in ["fastq.gz", "fastqsanger.gz"]: 14 #elif $singlePaired.input_singles.ext in ["fastq.gz", "fastqsanger.gz"]:
13 #set read1 = 'input_1.fq.gz' 15 #set read1 = 'input_1.fq.gz'
17 ln -s '${singlePaired.input_singles}' ${read1} && 19 ln -s '${singlePaired.input_singles}' ${read1} &&
18 #else: 20 #else:
19 #set $mate1 = list() 21 #set $mate1 = list()
20 #set $mate2 = list() 22 #set $mate2 = list()
21 #for $mate_pair in $singlePaired.mate_list 23 #for $mate_pair in $singlePaired.mate_list
22 $mate1.append( str($mate_pair.input_mate1) )
23 $mate2.append( str($mate_pair.input_mate2) )
24 24
25 #if $mate_pair.input_mate1.ext == "fasta": 25 #if $mate_pair.input_mate1.ext == "fasta":
26 #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1)) + '_1.fa' 26 #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fa'
27 #elif $mate_pair.input_mate1.ext in ["fastq.gz", "fastqsanger.gz"]: 27 #elif $mate_pair.input_mate1.ext in ["fastq.gz", "fastqsanger.gz"]:
28 #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1)) + '_1.fq.gz' 28 #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq.gz'
29 #else 29 #else
30 #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1)) + '_1.fq' 30 #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq'
31 #end if 31 #end if
32 ln -s '${mate_pair.input_mate1}' ${read1} && 32 ln -s '${mate_pair.input_mate1}' ${read1} &&
33 33
34 #if $mate_pair.input_mate2.ext == "fasta": 34 #if $mate_pair.input_mate2.ext == "fasta":
35 #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1)) + '_2.fa' 35 #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fa'
36 #elif $mate_pair.input_mate2.ext in ["fastq.gz", "fastqsanger.gz"]: 36 #elif $mate_pair.input_mate2.ext in ["fastq.gz", "fastqsanger.gz"]:
37 #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1)) + '_2.fq.gz' 37 #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq.gz'
38 #else 38 #else
39 #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1)) + '_2.fq' 39 #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq'
40 #end if 40 #end if
41 ln -s '${mate_pair.input_mate2}' ${read2} && 41 ln -s '${mate_pair.input_mate2}' ${read2} &&
42
43 $mate1.append( str($read1) )
44 $mate2.append( str($read2) )
42 #end for 45 #end for
43 #end if 46 #end if
44 47
45 python '$__tool_directory__/bismark_wrapper.py' 48 python '$__tool_directory__/bismark_wrapper.py'
46 49
479 </assert_contents> 482 </assert_contents>
480 </output> 483 </output>
481 <output name="report_file" file="mapping_report_short.txt" ftype="txt" lines_diff="6"/> 484 <output name="report_file" file="mapping_report_short.txt" ftype="txt" lines_diff="6"/>
482 <output name="output" file="mapped_reads_short.bam" ftype="qname_input_sorted.bam" lines_diff="14"/> 485 <output name="output" file="mapped_reads_short.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
483 </test> 486 </test>
487 <test>
488 <param name="genomeSource" value="history"/>
489 <param name="own_file" value="mm10.tiny.fa.gz" />
490 <param name="sPaired" value="paired"/>
491 <repeat name="mate_list">
492 <param name="input_mate1" value="input1.fq" ftype="fastqsanger"/>
493 <param name="input_mate2" value="input1.fq" ftype="fastqsanger"/>
494 </repeat>
495 <param name="sort_bam" value="false"/>
496 <param name="settingsType" value="custom"/>
497 <param name="suppressed_read_file" value="true"/>
498 <param name="unmapped_read_file" value="true"/>
499 <param name="bismark_stdout" value="true"/>
500 <param name="isReportOutput" value="true"/>
501
502 <output name="output_stdout" file="summary_mate.txt" ftype="txt" lines_diff="80">
503 <assert_contents>
504 <has_text text="Sequence pairs analysed in total:" />
505 <has_text text="1000" />
506 <has_text text="Mapping efficiency:" />
507 <has_text text="0.0%" />
508 <has_text text="Bismark run complete" />
509 </assert_contents>
510 </output>
511 <output name="report_file" file="mapping_report_mate.txt" ftype="txt" lines_diff="6"/>
512 <output name="output" file="mapped_reads_mate.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
513 </test>
484 </tests> 514 </tests>
485 515
486 <help> 516 <help>
487 <![CDATA[ 517 <![CDATA[
488 518