comparison bismark_bowtie2_wrapper.xml @ 21:120b7b35e442 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
author bgruening
date Thu, 22 Apr 2021 17:05:46 +0000
parents 359f8b60d316
children
comparison
equal deleted inserted replaced
20:ff6ee551b153 21:120b7b35e442
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"/>