comparison cutadapt.xml @ 19:49370cb85f0f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 6318c53e772ed592862729f3048ed9bd3a711969

18:5c7e7d905b33

<tool id="cutadapt" name="Cutadapt" version="1.16.4" profile="17.09">
    <description>Remove adapter sequences from Fastq/Fasta</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>

                    <param name="type" value="single" />
                    <param name="input_1" ftype="fastq.gz" value="cutadapt_in_split.fastq.gz" />
                    <section name="r1" >
                        <repeat name="front_adapters">
                            <conditional name="front_adapter_source">
                                <param name="front_adapter_source_list" value="user"/>
                                <param name="front_adapter_name" value="A1" />
                                <param name="front_adapter" value="^GTCGGTAA" />
                            </conditional>
                        </repeat>
                        <repeat name="front_adapters">
                            <conditional name="front_adapter_source">
                                <param name="front_adapter_source_list" value="user"/>
                                <param name="front_adapter_name" value="A2" />
                                <param name="front_adapter" value="^AGGTCACT" />
                            </conditional>
                        </repeat>
                    </section>
                </conditional>
                <param name="report" value="False" />

Input files for Cutadapt need to be:

- FASTQ.GZ, FASTQ.BZ2, FASTQ or FASTA

To trim an adapter, input the ADAPTER sequence e.g. AACCGGTT (with the characters: **$**, **^**, **...**, if anchored or linked).

    =============================================   ===================
    **Option**                                      **Sequence**
    ---------------------------------------------   -------------------
    3’ (End) Adapter                                ADAPTER

19:49370cb85f0f

<tool id="cutadapt" name="Cutadapt" version="1.16.5" profile="17.09">
    <description>Remove adapter sequences from Fastq/Fasta</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>

                    <param name="type" value="single" />
                    <param name="input_1" ftype="fastq.gz" value="cutadapt_in_split.fastq.gz" />
                    <section name="r1" >
                        <repeat name="front_adapters">
                            <conditional name="front_adapter_source">
                                <param name="front_adapter_source_list" value="file"/>
                                <param name="front_adapter_file" ftype="fasta"  value="barcodes.fasta" />
                            </conditional>
                        </repeat>
                    </section>
                </conditional>
                <param name="report" value="False" />

Input files for Cutadapt need to be:

- FASTQ.GZ, FASTQ.BZ2, FASTQ or FASTA

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).

    =============================================   ===================
    **Option**                                      **Sequence**
    ---------------------------------------------   -------------------
    3’ (End) Adapter                                ADAPTER