Mercurial > repos > bgruening > bismark
comparison bismark_bowtie2_wrapper.xml @ 16:a4504327c890 draft
"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 |
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| 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 |