Mercurial > repos > devteam > bowtie_color_wrappers
comparison bowtie_color_wrapper.xml @ 2:393c6829d3c1 draft
Convert tool to use $GALAXY_SLOTS if available.
author | Nate Coraor <nate@bx.psu.edu> |
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date | Thu, 16 Jan 2014 12:48:21 -0500 |
parents | 2506bd84cc54 |
children | a3825c73805c |
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1:2506bd84cc54 | 2:393c6829d3c1 |
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3 <requirement type='package' version="0.12.7">bowtie</requirement> | 3 <requirement type='package' version="0.12.7">bowtie</requirement> |
4 </requirements> | 4 </requirements> |
5 <description></description> | 5 <description></description> |
6 <command interpreter="python"> | 6 <command interpreter="python"> |
7 bowtie_wrapper.py | 7 bowtie_wrapper.py |
8 ## Hackish setting of number of threads | 8 ## Set number of threads |
9 --threads="4" | 9 --threads="\${GALAXY_SLOTS:-4}" |
10 ## Outputs | 10 ## Outputs |
11 --output="${output}" | 11 --output="${output}" |
12 #if str( $singlePaired.sPaired ) == "single" | 12 #if str( $singlePaired.sPaired ) == "single" |
13 #if $output_unmapped_reads_l | 13 #if $output_unmapped_reads_l |
14 --output_unmapped_reads="${output_unmapped_reads_l}" | 14 --output_unmapped_reads="${output_unmapped_reads_l}" |
400 <test> | 400 <test> |
401 <!-- | 401 <!-- |
402 Bowtie command: | 402 Bowtie command: |
403 bowtie -q -p 4 -S +sam-nohead -C chrM_color test-data/bowtie_in1.fastqcssanger > bowtie_out1_u.sam | 403 bowtie -q -p 4 -S +sam-nohead -C chrM_color test-data/bowtie_in1.fastqcssanger > bowtie_out1_u.sam |
404 sort bowtie_out1_u.sam > bowtie_out1.sam | 404 sort bowtie_out1_u.sam > bowtie_out1.sam |
405 -p is the number of threads, which is hardcoded above. You need to replace the + with 2 dashes. | 405 -p is the number of threads. You need to replace the + with 2 dashes. |
406 chrM_color needs to be the base location/name of the index files. | 406 chrM_color needs to be the base location/name of the index files. |
407 --> | 407 --> |
408 <param name="genomeSource" value="indexed" /> | 408 <param name="genomeSource" value="indexed" /> |
409 <param name="index" value="equCab2chrM" /> | 409 <param name="index" value="equCab2chrM" /> |
410 <param name="sPaired" value="single" /> | 410 <param name="sPaired" value="single" /> |
421 sort bowtie_out2_u.sam > bowtie_out2.sam | 421 sort bowtie_out2_u.sam > bowtie_out2.sam |
422 sort bowtie_out3_u_1.sam > bowtie_out3_1.sam | 422 sort bowtie_out3_u_1.sam > bowtie_out3_1.sam |
423 sort bowtie_out3_u_2.sam > bowtie_out3_2.sam | 423 sort bowtie_out3_u_2.sam > bowtie_out3_2.sam |
424 Then also need to modify bowtie_out3_1.sam and bowtie_out3_2.sam so that all @ lines come before sequence lines. | 424 Then also need to modify bowtie_out3_1.sam and bowtie_out3_2.sam so that all @ lines come before sequence lines. |
425 The two unmapped output files will be named bowtie_out4_1.fastq and bowtie_out4_2.fastq | 425 The two unmapped output files will be named bowtie_out4_1.fastq and bowtie_out4_2.fastq |
426 -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes. | 426 -p is the number of threads. You need to replace the + with 2 dashes. |
427 chrM_base is the index files' location/base name. | 427 chrM_base is the index files' location/base name. |
428 --> | 428 --> |
429 <param name="genomeSource" value="history" /> | 429 <param name="genomeSource" value="history" /> |
430 <param name="ownFile" value="chr_m.fasta" /> | 430 <param name="ownFile" value="chr_m.fasta" /> |
431 <param name="indexSettings" value="indexPreSet" /> | 431 <param name="indexSettings" value="indexPreSet" /> |
469 <test> | 469 <test> |
470 <!-- | 470 <!-- |
471 Bowtie command: | 471 Bowtie command: |
472 bowtie -q -p 4 -S +sam-nohead -C -n 2 -e 70 -l 28 +maxbts 125 -k 1 +snpfrac 0.001 +col-keepends chrM_color test-data/bowtie_in1.fastqcssanger > bowtie_out4_u.sam | 472 bowtie -q -p 4 -S +sam-nohead -C -n 2 -e 70 -l 28 +maxbts 125 -k 1 +snpfrac 0.001 +col-keepends chrM_color test-data/bowtie_in1.fastqcssanger > bowtie_out4_u.sam |
473 sort bowtie_out4_u.sam > bowtie_out4.sam | 473 sort bowtie_out4_u.sam > bowtie_out4.sam |
474 -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes. | 474 -p is the number of threads. You need to replace the + with 2 dashes. |
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="indexed" /> | 477 <param name="genomeSource" value="indexed" /> |
478 <param name="index" value="equCab2chrM" /> | 478 <param name="index" value="equCab2chrM" /> |
479 <param name="sPaired" value="single" /> | 479 <param name="sPaired" value="single" /> |
508 <!-- | 508 <!-- |
509 Bowtie command: | 509 Bowtie command: |
510 bowtie-build +noauto +bmaxdivn 4 +dcv 1024 +offrate 5 +ftabchars 10 +little -C -f test-data/chr_m.fasta chrM_color | 510 bowtie-build +noauto +bmaxdivn 4 +dcv 1024 +offrate 5 +ftabchars 10 +little -C -f test-data/chr_m.fasta chrM_color |
511 bowtie -q -X 1000 +ff -p 4 -S +sam-nohead -C chrM_color -1 test-data/bowtie_in3.fastqcssanger -2 test-data/bowtie_in4.fastqcssanger > bowtie_out5_u.sam | 511 bowtie -q -X 1000 +ff -p 4 -S +sam-nohead -C chrM_color -1 test-data/bowtie_in3.fastqcssanger -2 test-data/bowtie_in4.fastqcssanger > bowtie_out5_u.sam |
512 sort bowtie_out5_u.sam > bowtie_out5.sam | 512 sort bowtie_out5_u.sam > bowtie_out5.sam |
513 -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes. | 513 -p is the number of threads. You need to replace the + with 2 dashes. |
514 chrM_base is the index files' location/base name. | 514 chrM_base is the index files' location/base name. |
515 --> | 515 --> |
516 <param name="genomeSource" value="history" /> | 516 <param name="genomeSource" value="history" /> |
517 <param name="ownFile" value="chr_m.fasta" /> | 517 <param name="ownFile" value="chr_m.fasta" /> |
518 <param name="indexSettings" value="indexFull" /> | 518 <param name="indexSettings" value="indexFull" /> |