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Convert tool to use $GALAXY_SLOTS if available.
author Nate Coraor <nate@bx.psu.edu>
date Thu, 16 Jan 2014 13:08:38 -0500
parents e1c59c194b7b
children df86f29bedee
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1:e1c59c194b7b 2:42c4463baaad
4 </requirements> 4 </requirements>
5 <description></description> 5 <description></description>
6 <parallelism method="basic"></parallelism> 6 <parallelism method="basic"></parallelism>
7 <command interpreter="python"> 7 <command interpreter="python">
8 bowtie_wrapper.py 8 bowtie_wrapper.py
9 ## Hackish setting of number of threads 9 ## Set number of threads
10 --threads="4" 10 --threads="\${GALAXY_SLOTS:-4}"
11 ## Outputs 11 ## Outputs
12 --output="${output}" 12 --output="${output}"
13 #if str( $singlePaired.sPaired ) == "single" 13 #if str( $singlePaired.sPaired ) == "single"
14 #if $output_unmapped_reads_l 14 #if $output_unmapped_reads_l
15 --output_unmapped_reads="${output_unmapped_reads_l}" 15 --output_unmapped_reads="${output_unmapped_reads_l}"
447 <test> 447 <test>
448 <!-- 448 <!--
449 Bowtie command: 449 Bowtie command:
450 bowtie -q -p 4 -S +sam-nohead chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out6_u.sam 450 bowtie -q -p 4 -S +sam-nohead chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out6_u.sam
451 sort bowtie_out6_u.sam > bowtie_out6.sam 451 sort bowtie_out6_u.sam > bowtie_out6.sam
452 -p is the number of threads, which is hardcoded above. You need to replace the + with 2 dashes. 452 -p is the number of threads. You need to replace the + with 2 dashes.
453 chrM_base needs to be the base location/name of the index files. 453 chrM_base needs to be the base location/name of the index files.
454 --> 454 -->
455 <param name="genomeSource" value="indexed" /> 455 <param name="genomeSource" value="indexed" />
456 <!-- this is the backwards-compatible "unique value" for this index, not an actual path --> 456 <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
457 <param name="index" value="equCab2chrM" /> 457 <param name="index" value="equCab2chrM" />
468 bowtie -q -X 1000 +ff -p 4 -S +sam-nohead -n 2 -e 70 -l 28 +pairtries 100 +maxbts 800 +best +un bowtie_out8_u.fastq phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out7_u.sam 468 bowtie -q -X 1000 +ff -p 4 -S +sam-nohead -n 2 -e 70 -l 28 +pairtries 100 +maxbts 800 +best +un bowtie_out8_u.fastq phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out7_u.sam
469 sort bowtie_out7_u.sam > bowtie_out7.sam 469 sort bowtie_out7_u.sam > bowtie_out7.sam
470 sort bowtie_out8_u_1.sam > bowtie_out8_1.sam 470 sort bowtie_out8_u_1.sam > bowtie_out8_1.sam
471 sort bowtie_out8_u_2.sam > bowtie_out8_2.sam 471 sort bowtie_out8_u_2.sam > bowtie_out8_2.sam
472 Then also need to modify bowtie_out8_1.sam and bowtie_out8_2.sam so that all @ lines come before sequence lines. 472 Then also need to modify bowtie_out8_1.sam and bowtie_out8_2.sam so that all @ lines come before sequence lines.
473 -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes. 473 -p is the number of threads. You need to replace the + with 2 dashes.
474 The two unmapped output files will be named bowtie_out8_1.fastq and bowtie_out8_2.fastq. 474 The two unmapped output files will be named bowtie_out8_1.fastq and bowtie_out8_2.fastq.
475 chrM_base is the index files' location/base name. 475 chrM_base is the index files' location/base name.
476 --> 476 -->
477 <param name="genomeSource" value="history" /> 477 <param name="genomeSource" value="history" />
478 <param name="ownFile" value="phiX.fasta" /> 478 <param name="ownFile" value="phiX.fasta" />
595 <test> 595 <test>
596 <!-- 596 <!--
597 Bowtie command: 597 Bowtie command:
598 bowtie -q -p 4 -S +sam-nohead -n 2 -e 70 -l 28 +maxbts 125 -y -k 1 chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out9_u.sam 598 bowtie -q -p 4 -S +sam-nohead -n 2 -e 70 -l 28 +maxbts 125 -y -k 1 chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out9_u.sam
599 sort bowtie_out9_u.sam > bowtie_out9.sam 599 sort bowtie_out9_u.sam > bowtie_out9.sam
600 -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes. 600 -p is the number of threads. You need to replace the + with 2 dashes.
601 chrM_base is the index files' location/base name. 601 chrM_base is the index files' location/base name.
602 --> 602 -->
603 <param name="genomeSource" value="indexed" /> 603 <param name="genomeSource" value="indexed" />
604 <!-- this is the backwards-compatible "unique value" for this index, not an actual path --> 604 <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
605 <param name="index" value="equCab2chrM" /> 605 <param name="index" value="equCab2chrM" />
632 <!-- 632 <!--
633 Bowtie command: 633 Bowtie command:
634 bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base 634 bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base
635 bowtie -q -X 1000 +ff -p 4 -S +sam-nohead phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out10_u.sam 635 bowtie -q -X 1000 +ff -p 4 -S +sam-nohead phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out10_u.sam
636 sort bowtie_out10_u.sam > bowtie_out10.sam 636 sort bowtie_out10_u.sam > bowtie_out10.sam
637 -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes. 637 -p is the number of threads. You need to replace the + with 2 dashes.
638 chrM_base is the index files' location/base name. 638 chrM_base is the index files' location/base name.
639 --> 639 -->
640 <param name="genomeSource" value="history" /> 640 <param name="genomeSource" value="history" />
641 <param name="ownFile" value="phiX.fasta" /> 641 <param name="ownFile" value="phiX.fasta" />
642 <param name="indexSettings" value="indexFull" /> 642 <param name="indexSettings" value="indexFull" />