Mercurial > repos > bgruening > bismark

comparison bismark_bowtie2_wrapper.xml @ 13:f211753166bd draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
author bgruening
date Tue, 30 Jul 2019 06:30:36 -0400
parents 1f15ad5ca867
children b6aa3b6ba129
comparison
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12:78c791a11b4c 13:f211753166bd
1 <tool id="bismark_bowtie2" name="Bismark Mapper" version="0.20.0.3" profile="18.01"> 1 <tool id="bismark_bowtie2" name="Bismark Mapper" version="0.22.1" profile="18.01">
2 <description>Bisulfite reads mapper</description> 2 <description>Bisulfite reads mapper</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.20.0">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="2.3.4.2">bowtie2</requirement> 6 <requirement type="package" version="2.3.5">bowtie2</requirement>
7 </requirements> 7 </requirements>
8 <command><![CDATA[ 8 <command><![CDATA[
9 #if $singlePaired.sPaired == "single":
10 #if $singlePaired.input_singles.ext == "fasta":
11 #set read1 = 'input_1.fa'
12 #elif $singlePaired.input_singles.ext in ["fastq.gz", "fastqsanger.gz"]:
13 #set read1 = 'input_1.fq.gz'
14 #else
15 #set read1 = 'input_1.fq'
16 #end if
17 ln -s '${singlePaired.input_singles}' ${read1} &&
18 #else:
19 #set $mate1 = list()
20 #set $mate2 = list()
21 #for $mate_pair in $singlePaired.mate_list
22 $mate1.append( str($mate_pair.input_mate1) )
23 $mate2.append( str($mate_pair.input_mate2) )
24
25 #if $mate_pair.input_mate1.ext == "fasta":
26 #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1)) + '_1.fa'
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'
29 #else
30 #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1)) + '_1.fq'
31 #end if
32 ln -s '${mate_pair.input_mate1}' ${read1} &&
33
34 #if $mate_pair.input_mate2.ext == "fasta":
35 #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1)) + '_2.fa'
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'
38 #else
39 #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1)) + '_2.fq'
40 #end if
41 ln -s '${mate_pair.input_mate2}' ${read2} &&
42 #end for
43 #end if
44
9 python '$__tool_directory__/bismark_wrapper.py' 45 python '$__tool_directory__/bismark_wrapper.py'
10 46
11 ## Change this to accommodate the number of threads you have available. 47 ## Change this to accommodate the number of threads you have available.
12 --num-threads "\${GALAXY_SLOTS:-4}" 48 --num-threads "\${GALAXY_SLOTS:-4}"
13 49
27 ## 63 ##
28 ## Input parameters 64 ## Input parameters
29 ## 65 ##
30 66
31 #if $singlePaired.sPaired == "single": 67 #if $singlePaired.sPaired == "single":
32 --single-paired '$singlePaired.input_singles' 68 --single-paired '${read1}'
33 69
34 #if $singlePaired.input_singles.ext in ["fastq", "fastq.gz", "fastqillumina"]: 70 #if $singlePaired.input_singles.ext in ["fastq", "fastq.gz", "fastqillumina"]:
35 --phred64-quals 71 --phred64-quals
36 --fastq 72 --fastq
37 #elif $singlePaired.input_singles.ext in ["fastqsanger", "fastqsanger.gz"]: 73 #elif $singlePaired.input_singles.ext in ["fastqsanger", "fastqsanger.gz"]:
39 #elif $singlePaired.input_singles.ext == "fasta": 75 #elif $singlePaired.input_singles.ext == "fasta":
40 --fasta 76 --fasta
41 #end if 77 #end if
42 #else: 78 #else:
43 --mate-paired 79 --mate-paired
44 #set $mate1 = list()
45 #set $mate2 = list()
46 #for $mate_pair in $singlePaired.mate_list
47 $mate1.append( str($mate_pair.input_mate1) )
48 $mate2.append( str($mate_pair.input_mate2) )
49 #end for
50 80
51 --mate1 #echo ','.join($mate1) 81 --mate1 #echo ','.join($mate1)
52 --mate2 #echo ','.join($mate2) 82 --mate2 #echo ','.join($mate2)
53 83
54 #for $mate_pair in $singlePaired.mate_list: 84 #for $mate_pair in $singlePaired.mate_list:
405 <tests> 435 <tests>
406 <test> 436 <test>
407 <param name="genomeSource" value="history"/> 437 <param name="genomeSource" value="history"/>
408 <param name="own_file" value="mm10.tiny.fa.gz" /> 438 <param name="own_file" value="mm10.tiny.fa.gz" />
409 <param name="sPaired" value="single"/> 439 <param name="sPaired" value="single"/>
410 <param name="input_singles" value="input1.fq.gz" ftype="fastqsanger"/> 440 <param name="input_singles" value="input1.fq.gzip" ftype="fastqsanger.gz"/>
411 <param name="sort_bam" value="false"/> 441 <param name="sort_bam" value="false"/>
412 <param name="settingsType" value="custom"/> 442 <param name="settingsType" value="custom"/>
413 <param name="suppressed_read_file" value="true"/> 443 <param name="suppressed_read_file" value="true"/>
414 <param name="unmapped_read_file" value="true"/> 444 <param name="unmapped_read_file" value="true"/>
415 <param name="bismark_stdout" value="true"/> 445 <param name="bismark_stdout" value="true"/>
424 <has_text text="Bismark run complete" /> 454 <has_text text="Bismark run complete" />
425 </assert_contents> 455 </assert_contents>
426 </output> 456 </output>
427 <output name="report_file" file="mapping_report.txt" ftype="txt" lines_diff="6"/> 457 <output name="report_file" file="mapping_report.txt" ftype="txt" lines_diff="6"/>
428 <output name="output" file="mapped_reads.bam" ftype="qname_input_sorted.bam" lines_diff="14"/> 458 <output name="output" file="mapped_reads.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
459 </test>
460 <test>
461 <param name="genomeSource" value="history"/>
462 <param name="own_file" value="mm10.tiny.fa.gz" />
463 <param name="sPaired" value="single"/>
464 <param name="input_singles" value="input1.fq" ftype="fastqsanger"/>
465 <param name="sort_bam" value="false"/>
466 <param name="settingsType" value="custom"/>
467 <param name="suppressed_read_file" value="true"/>
468 <param name="unmapped_read_file" value="true"/>
469 <param name="bismark_stdout" value="true"/>
470 <param name="isReportOutput" value="true"/>
471
472 <output name="output_stdout" file="summary_short.txt" ftype="txt" lines_diff="80">
473 <assert_contents>
474 <has_text text="Sequences analysed in total:" />
475 <has_text text="1000" />
476 <has_text text="Mapping efficiency:" />
477 <has_text text="0.8%" />
478 <has_text text="Bismark run complete" />
479 </assert_contents>
480 </output>
481 <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"/>
429 </test> 483 </test>
430 </tests> 484 </tests>
431 485
432 <help> 486 <help>
433 <![CDATA[ 487 <![CDATA[