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comparison bowtie_color_wrapper.xml @ 2:393c6829d3c1 draft

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Convert tool to use $GALAXY_SLOTS if available.
author Nate Coraor <nate@bx.psu.edu>
date Thu, 16 Jan 2014 12:48:21 -0500
parents 2506bd84cc54
children a3825c73805c
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1:2506bd84cc54 2:393c6829d3c1
3 <requirement type='package' version="0.12.7">bowtie</requirement> 3 <requirement type='package' version="0.12.7">bowtie</requirement>
4 </requirements> 4 </requirements>
5 <description></description> 5 <description></description>
6 <command interpreter="python"> 6 <command interpreter="python">
7 bowtie_wrapper.py 7 bowtie_wrapper.py
8 ## Hackish setting of number of threads 8 ## Set number of threads
9 --threads="4" 9 --threads="\${GALAXY_SLOTS:-4}"
10 ## Outputs 10 ## Outputs
11 --output="${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" />