Mercurial > repos > bgruening > bismark
comparison bismark_bowtie2_wrapper.xml @ 13:f211753166bd draft
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 |
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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[ |