Mercurial > repos > bgruening > bismark
comparison bismark_bowtie2_wrapper.xml @ 21:120b7b35e442 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
author | bgruening |
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date | Thu, 22 Apr 2021 17:05:46 +0000 |
parents | 359f8b60d316 |
children |
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20:ff6ee551b153 | 21:120b7b35e442 |
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313 <!-- output Options --> | 313 <!-- output Options --> |
314 <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false" | 314 <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false" |
315 label="Write the bismark output and summary information to an extra file"/> | 315 label="Write the bismark output and summary information to an extra file"/> |
316 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="true" | 316 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="true" |
317 label="Offer all report files concatenated in one file (Mapping Report)"/> | 317 label="Offer all report files concatenated in one file (Mapping Report)"/> |
318 <param argument="--non-directional" name="non_directional" type="boolean" | 318 <param argument="--non_directional" name="non_directional" type="boolean" |
319 truevalue="--non-directional" falsevalue="" checked="false" | 319 truevalue="--non_directional" falsevalue="" checked="false" |
320 label="The sequencing library was constructed in a non strand-specific manner, alignments to all four bisulfite strands will be reported."/> | 320 label="The sequencing library was constructed in a non strand-specific manner, alignments to all four bisulfite strands will be reported."/> |
321 <param argument="--pbat" name="pbat" type="boolean" | 321 <param argument="--pbat" name="pbat" type="boolean" |
322 truevalue="--pbat" falsevalue="" checked="false" | 322 truevalue="--pbat" falsevalue="" checked="false" |
323 label="Treat input data as PBAT-Seq libraries" | 323 label="Treat input data as PBAT-Seq libraries" |
324 help="Use this option only if you are certain that your libraries were constructed following a PBAT protocol. If you don't know what PBAT-Seq is you should not specify this option." /> | 324 help="Use this option only if you are certain that your libraries were constructed following a PBAT protocol. If you don't know what PBAT-Seq is you should not specify this option." /> |
547 <output name="output" file="mapped_reads_mate.bam" ftype="qname_input_sorted.bam" lines_diff="14"/> | 547 <output name="output" file="mapped_reads_mate.bam" ftype="qname_input_sorted.bam" lines_diff="14"/> |
548 </test> | 548 </test> |
549 <test> | 549 <test> |
550 <param name="genomeSource" value="history"/> | 550 <param name="genomeSource" value="history"/> |
551 <param name="own_file" value="mm10.tiny.fa.gz" /> | 551 <param name="own_file" value="mm10.tiny.fa.gz" /> |
552 <param name="sPaired" value="paired"/> | |
553 <repeat name="mate_list"> | |
554 <param name="input_mate1" value="input1.fq" ftype="fastqsanger"/> | |
555 <param name="input_mate2" value="input1.fq" ftype="fastqsanger"/> | |
556 </repeat> | |
557 <repeat name="mate_list"> | |
558 <param name="input_mate1" value="input2.fq" ftype="fastqsanger"/> | |
559 <param name="input_mate2" value="input2.fq" ftype="fastqsanger"/> | |
560 </repeat> | |
561 <param name="sort_bam" value="false"/> | |
562 <param name="settingsType" value="custom"/> | |
563 <param name="suppressed_read_file" value="true"/> | |
564 <param name="unmapped_read_file" value="true"/> | |
565 <param name="bismark_stdout" value="true"/> | |
566 <param name="isReportOutput" value="true"/> | |
567 | |
568 <output name="output_stdout" file="summary_mate_two_samples.txt" ftype="txt" lines_diff="94"> | |
569 <assert_contents> | |
570 <has_text text="Sequence pairs analysed in total:" /> | |
571 <has_text text="1000" /> | |
572 <has_text text="Mapping efficiency:" /> | |
573 <has_text text="0.0%" /> | |
574 <has_text text="Bismark run complete" /> | |
575 </assert_contents> | |
576 </output> | |
577 <output name="report_file" file="mapping_report_mate_two_samples.txt" ftype="txt" lines_diff="12"/> | |
578 <output name="output" file="mapped_reads_mate_two_samples.bam" ftype="qname_input_sorted.bam" lines_diff="14"/> | |
579 </test> | |
580 <test> | |
581 <param name="genomeSource" value="history"/> | |
582 <param name="own_file" value="mm10.tiny.fa.gz" /> | |
552 <param name="sPaired" value="single"/> | 583 <param name="sPaired" value="single"/> |
553 <param name="input_singles" value="input1.fq.gzip" ftype="fastqsanger.gz"/> | 584 <param name="input_singles" value="input1.fq.gzip" ftype="fastqsanger.gz"/> |
554 <param name="sort_bam" value="false"/> | 585 <param name="sort_bam" value="false"/> |
555 <param name="settingsType" value="custom"/> | 586 <param name="settingsType" value="custom"/> |
556 <param name="suppressed_read_file" value="true"/> | 587 <param name="suppressed_read_file" value="true"/> |