Mercurial > repos > lparsons > cutadapt

comparison cutadapt.xml @ 19:49370cb85f0f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 6318c53e772ed592862729f3048ed9bd3a711969
author iuc
date Tue, 18 Dec 2018 14:09:53 -0500
parents 5c7e7d905b33
children e4691e1589d3
comparison
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18:5c7e7d905b33 19:49370cb85f0f
1 <tool id="cutadapt" name="Cutadapt" version="1.16.4" profile="17.09"> 1 <tool id="cutadapt" name="Cutadapt" version="1.16.5" profile="17.09">
2 <description>Remove adapter sequences from Fastq/Fasta</description> 2 <description>Remove adapter sequences from Fastq/Fasta</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
442 <param name="type" value="single" /> 442 <param name="type" value="single" />
443 <param name="input_1" ftype="fastq.gz" value="cutadapt_in_split.fastq.gz" /> 443 <param name="input_1" ftype="fastq.gz" value="cutadapt_in_split.fastq.gz" />
444 <section name="r1" > 444 <section name="r1" >
445 <repeat name="front_adapters"> 445 <repeat name="front_adapters">
446 <conditional name="front_adapter_source"> 446 <conditional name="front_adapter_source">
447 <param name="front_adapter_source_list" value="user"/> 447 <param name="front_adapter_source_list" value="file"/>
448 <param name="front_adapter_name" value="A1" /> 448 <param name="front_adapter_file" ftype="fasta" value="barcodes.fasta" />
449 <param name="front_adapter" value="^GTCGGTAA" />
450 </conditional>
451 </repeat>
452 <repeat name="front_adapters">
453 <conditional name="front_adapter_source">
454 <param name="front_adapter_source_list" value="user"/>
455 <param name="front_adapter_name" value="A2" />
456 <param name="front_adapter" value="^AGGTCACT" />
457 </conditional> 449 </conditional>
458 </repeat> 450 </repeat>
459 </section> 451 </section>
460 </conditional> 452 </conditional>
461 <param name="report" value="False" /> 453 <param name="report" value="False" />
497 489
498 Input files for Cutadapt need to be: 490 Input files for Cutadapt need to be:
499 491
500 - FASTQ.GZ, FASTQ.BZ2, FASTQ or FASTA 492 - FASTQ.GZ, FASTQ.BZ2, FASTQ or FASTA
501 493
502 To trim an adapter, input the ADAPTER sequence e.g. AACCGGTT (with the characters: **$**, **^**, **...**, if anchored or linked). 494 To trim an adapter, input the ADAPTER sequence in plain text or in a FASTA file e.g. AACCGGTT (with the characters: **$**, **^**, **...**, if anchored or linked).
503 495
504 ============================================= =================== 496 ============================================= ===================
505 **Option** **Sequence** 497 **Option** **Sequence**
506 --------------------------------------------- ------------------- 498 --------------------------------------------- -------------------
507 3’ (End) Adapter ADAPTER 499 3’ (End) Adapter ADAPTER