Mercurial > repos > bgruening > bismark

comparison bismark_bowtie2_wrapper.xml @ 16:a4504327c890 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
author bgruening
date Wed, 21 Aug 2019 12:59:48 -0400
parents 0b656f8c5637
children aa9bf0f29a9f
comparison
equal deleted inserted replaced
15:0b656f8c5637 16:a4504327c890
1 <tool id="bismark_bowtie2" name="Bismark Mapper" version="0.22.1+galaxy2" profile="18.01"> 1 <tool id="bismark_bowtie2" name="Bismark Mapper" version="0.22.1+galaxy3" profile="18.01">
2 <description>Bisulfite reads mapper</description> 2 <description>Bisulfite reads mapper</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.22.1">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="2.3.5">bowtie2</requirement> 6 <requirement type="package" version="2.3.5">bowtie2</requirement>
117 ## default 15 117 ## default 15
118 --seed-extention-attempts $params.seed_extention_attempts 118 --seed-extention-attempts $params.seed_extention_attempts
119 ## default 2 119 ## default 2
120 --max-reseed $params.max_reseed 120 --max-reseed $params.max_reseed
121 121
122 ## default 70
123 ##--maqerr $params.maqerr
124
125 ## default unlimited 122 ## default unlimited
126 #if $params.qupto != 0: 123 #if $params.qupto != 0:
127 --qupto $params.qupto 124 --qupto $params.qupto
128 #end if 125 #end if
129 #if $params.skip_reads != 0: 126 #if $params.skip_reads != 0:
130 --skip-reads $params.skip_reads 127 --skip-reads $params.skip_reads
128 #end if
129
130 #if $params.score_min != "":
131 --score-min '${params.score_min}'
131 #end if 132 #end if
132 133
133 ## if set, disable the original behaviour 134 ## if set, disable the original behaviour
134 $params.no_mixed 135 $params.no_mixed
135 ## if set, disable the original behaviour 136 ## if set, disable the original behaviour
250 <param name="seed_mismatches" type="integer" value="0" 251 <param name="seed_mismatches" type="integer" value="0"
251 label="Number of mismatches to be allowed in a seed alignment during multiseed alignment"/> 252 label="Number of mismatches to be allowed in a seed alignment during multiseed alignment"/>
252 <!-- -L --> 253 <!-- -L -->
253 <param name="seed_len" type="integer" value="20" 254 <param name="seed_len" type="integer" value="20"
254 label="Length of the seed substrings to align during multiseed alignment"/> 255 label="Length of the seed substrings to align during multiseed alignment"/>
255 <!-- 256
256 <param name="maqerr" type="integer" value="70" label="Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the 'seed'." />
257 -->
258 <!-- -D --> 257 <!-- -D -->
259 <param name="seed_extention_attempts" type="integer" value="15" 258 <param name="seed_extention_attempts" type="integer" value="15"
260 label="How many consecutive seed extension attempts can fail before Bowtie 2 moves on"/> 259 label="How many consecutive seed extension attempts can fail before Bowtie 2 moves on"/>
261 <!-- -R --> 260 <!-- -R -->
262 <param name="max_reseed" type="integer" value="2" 261 <param name="max_reseed" type="integer" value="2"
265 <param name="qupto" type="integer" value="0" 264 <param name="qupto" type="integer" value="0"
266 label="Only aligns the first N reads or read pairs from the input" 265 label="Only aligns the first N reads or read pairs from the input"
267 help="Default is 0 and means 'no-limit'."/> 266 help="Default is 0 and means 'no-limit'."/>
268 <param name="skip_reads" type="integer" value="0" 267 <param name="skip_reads" type="integer" value="0"
269 label="Skip (i.e. do not align) the first N reads or read pairs from the input"/> 268 label="Skip (i.e. do not align) the first N reads or read pairs from the input"/>
269
270 <param argument="--score-min" name="score_min" type="text" value="" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="This is a function of read length. For instance, specifying `L,0,-0.2` sets the minimum-score function `f` to `f(x) = 0 + -0.2 * x`, where `x` is the read length."/>
270 271
271 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="false" 272 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="false"
272 label="Disable looking for discordant alignments if it cannot find any concordant alignments (only for paired-end reads)" 273 label="Disable looking for discordant alignments if it cannot find any concordant alignments (only for paired-end reads)"
273 help=""/> 274 help=""/>
274 <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="false" 275 <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="false"
509 </assert_contents> 510 </assert_contents>
510 </output> 511 </output>
511 <output name="report_file" file="mapping_report_mate.txt" ftype="txt" lines_diff="6"/> 512 <output name="report_file" file="mapping_report_mate.txt" ftype="txt" lines_diff="6"/>
512 <output name="output" file="mapped_reads_mate.bam" ftype="qname_input_sorted.bam" lines_diff="14"/> 513 <output name="output" file="mapped_reads_mate.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
513 </test> 514 </test>
515 <test>
516 <param name="genomeSource" value="history"/>
517 <param name="own_file" value="mm10.tiny.fa.gz" />
518 <param name="sPaired" value="single"/>
519 <param name="input_singles" value="input1.fq.gzip" ftype="fastqsanger.gz"/>
520 <param name="sort_bam" value="false"/>
521 <param name="settingsType" value="custom"/>
522 <param name="suppressed_read_file" value="true"/>
523 <param name="unmapped_read_file" value="true"/>
524 <param name="bismark_stdout" value="true"/>
525 <param name="isReportOutput" value="true"/>
526 <conditional name="params">
527 <param name="settingsType" value="custom" />
528 <param name="score_min" value="L,0,-0.8" />
529 </conditional>
530
531 <output name="output_stdout" file="summary_custom.txt" ftype="txt" lines_diff="94">
532 <assert_contents>
533 <has_text text="Sequences analysed in total:" />
534 <has_text text="44115" />
535 <has_text text="Mapping efficiency:" />
536 <has_text text="4.5%" />
537 <has_text text="Bismark run complete" />
538 </assert_contents>
539 </output>
540 <output name="report_file" file="mapping_report_custom.txt" ftype="txt" lines_diff="6"/>
541 <output name="output" file="mapped_reads_custom.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
542
543 <assert_command>
544 <has_text text="--score-min 'L,0,-0.8'" />
545 </assert_command>
546 </test>
514 </tests> 547 </tests>
515 548
516 <help> 549 <help>
517 <![CDATA[ 550 <![CDATA[
518 551