Mercurial > repos > bgruening > bismark

comparison bismark_bowtie2_wrapper.xml @ 15:0b656f8c5637 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ec1f38df34e6862abd0b8e7cc0521e25f9933567
author bgruening
date Thu, 01 Aug 2019 10:47:13 -0400
parents b6aa3b6ba129
children a4504327c890
comparison
equal deleted inserted replaced
14:b6aa3b6ba129 15:0b656f8c5637
1 <tool id="bismark_bowtie2" name="Bismark Mapper" version="0.22.1+galaxy1" profile="18.01"> 1 <tool id="bismark_bowtie2" name="Bismark Mapper" version="0.22.1+galaxy2" 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>
14 #elif $singlePaired.input_singles.ext in ["fastq.gz", "fastqsanger.gz"]: 14 #elif $singlePaired.input_singles.ext in ["fastq.gz", "fastqsanger.gz"]:
15 #set read1 = 'input_1.fq.gz' 15 #set read1 = 'input_1.fq.gz'
16 #else 16 #else
17 #set read1 = 'input_1.fq' 17 #set read1 = 'input_1.fq'
18 #end if 18 #end if
19 ln -s '${singlePaired.input_singles}' ${read1} && 19 ln -s '${singlePaired.input_singles}' '${read1}' &&
20 #else: 20 #else:
21 #set $mate1 = list() 21 #set $mate1 = list()
22 #set $mate2 = list() 22 #set $mate2 = list()
23 #for $mate_pair in $singlePaired.mate_list 23 #for $mate_pair in $singlePaired.mate_list
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.element_identifier)) + '_1.fa' 26 #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"]: 27 #elif $mate_pair.input_mate1.ext in ["fastq.gz", "fastqsanger.gz"]:
28 #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq.gz' 28 #set read1 = re.sub('[^\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.element_identifier)) + '_1.fq' 30 #set read1 = re.sub('[^\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.element_identifier)) + '_2.fa' 35 #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"]: 36 #elif $mate_pair.input_mate2.ext in ["fastq.gz", "fastqsanger.gz"]:
37 #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq.gz' 37 #set read2 = re.sub('[^\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.element_identifier)) + '_2.fq' 39 #set read2 = re.sub('[^\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 42
43 $mate1.append( str($read1) ) 43 $mate1.append( str($read1) )
44 $mate2.append( str($read2) ) 44 $mate2.append( str($read2) )
45 #end for 45 #end for
46 #end if 46 #end if
446 <param name="suppressed_read_file" value="true"/> 446 <param name="suppressed_read_file" value="true"/>
447 <param name="unmapped_read_file" value="true"/> 447 <param name="unmapped_read_file" value="true"/>
448 <param name="bismark_stdout" value="true"/> 448 <param name="bismark_stdout" value="true"/>
449 <param name="isReportOutput" value="true"/> 449 <param name="isReportOutput" value="true"/>
450 450
451 <output name="output_stdout" file="summary.txt" ftype="txt" lines_diff="80"> 451 <output name="output_stdout" file="summary.txt" ftype="txt" lines_diff="94">
452 <assert_contents> 452 <assert_contents>
453 <has_text text="Sequences analysed in total:" /> 453 <has_text text="Sequences analysed in total:" />
454 <has_text text="44115" /> 454 <has_text text="44115" />
455 <has_text text="Mapping efficiency:" /> 455 <has_text text="Mapping efficiency:" />
456 <has_text text="1.3%" /> 456 <has_text text="1.3%" />
470 <param name="suppressed_read_file" value="true"/> 470 <param name="suppressed_read_file" value="true"/>
471 <param name="unmapped_read_file" value="true"/> 471 <param name="unmapped_read_file" value="true"/>
472 <param name="bismark_stdout" value="true"/> 472 <param name="bismark_stdout" value="true"/>
473 <param name="isReportOutput" value="true"/> 473 <param name="isReportOutput" value="true"/>
474 474
475 <output name="output_stdout" file="summary_short.txt" ftype="txt" lines_diff="80"> 475 <output name="output_stdout" file="summary_short.txt" ftype="txt" lines_diff="94">
476 <assert_contents> 476 <assert_contents>
477 <has_text text="Sequences analysed in total:" /> 477 <has_text text="Sequences analysed in total:" />
478 <has_text text="1000" /> 478 <has_text text="1000" />
479 <has_text text="Mapping efficiency:" /> 479 <has_text text="Mapping efficiency:" />
480 <has_text text="0.8%" /> 480 <has_text text="0.8%" />
497 <param name="suppressed_read_file" value="true"/> 497 <param name="suppressed_read_file" value="true"/>
498 <param name="unmapped_read_file" value="true"/> 498 <param name="unmapped_read_file" value="true"/>
499 <param name="bismark_stdout" value="true"/> 499 <param name="bismark_stdout" value="true"/>
500 <param name="isReportOutput" value="true"/> 500 <param name="isReportOutput" value="true"/>
501 501
502 <output name="output_stdout" file="summary_mate.txt" ftype="txt" lines_diff="80"> 502 <output name="output_stdout" file="summary_mate.txt" ftype="txt" lines_diff="94">
503 <assert_contents> 503 <assert_contents>
504 <has_text text="Sequence pairs analysed in total:" /> 504 <has_text text="Sequence pairs analysed in total:" />
505 <has_text text="1000" /> 505 <has_text text="1000" />
506 <has_text text="Mapping efficiency:" /> 506 <has_text text="Mapping efficiency:" />
507 <has_text text="0.0%" /> 507 <has_text text="0.0%" />