comparison paired_fastq_filtering.xml @ 6:f224513123a1 draft

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5:378565f5a875

<tool id="paired_fastq_filtering" name="Preprocessing of fastq paired-reads">
  <stdio>
     <exit_code range="1:" level="fatal" description="Error" />
  </stdio>
  <description>
    Preprocessing of paired reads fastq files
    including trimming, quality filtering, cutadapt filtering and interlacing. Broken
    pairs are discarded.
  </description>
  <requirements>
    <requirement type="package">blast</requirement>

        
   		  <param name="filter_database" format="fasta" type="data" label="Sequence filter database" help="Provide DNA sequences in fasta format. Sequence reads which has at least 90% similarity over 90% of length to sequence in filter database will be removed. This is suitable option if you want to remove organele DNA or contamination"/>
      </when>
    </conditional>

    <param name="rename" type="boolean" truevalue="-R" falsevalue="" checked="False" label="Rename sequences" help="By default, original sequence ID are used, in case your sequences do not follow proper naming scheme to label paired-end read mate, use this option. All read pairs must be complete!"/>
  </inputs>


  <outputs>
    <data format="fasta" name="paired" label="Interlaced paired reads from datasets ${A.hid} and ${B.hid} "/>

6:f224513123a1

<tool id="paired_fastq_filtering" name="Preprocessing of fastq paired-end reads">
  <stdio>
     <exit_code range="1:" level="fatal" description="Error" />
  </stdio>
  <description>
    Preprocessing of paired-end reads fastq files
    including trimming, quality filtering, cutadapt filtering and interlacing. Broken
    pairs are discarded.
  </description>
  <requirements>
    <requirement type="package">blast</requirement>

        
   		  <param name="filter_database" format="fasta" type="data" label="Sequence filter database" help="Provide DNA sequences in fasta format. Sequence reads which has at least 90% similarity over 90% of length to sequence in filter database will be removed. This is suitable option if you want to remove organele DNA or contamination"/>
      </when>
    </conditional>

    <param name="rename" type="boolean" truevalue="-R" falsevalue="" checked="True" label="Rename sequences" help="By default, original sequence ID are used, in case your sequences do not follow proper naming scheme to label paired-end read mate, use this option. All read pairs must be complete!"/>
  </inputs>


  <outputs>
    <data format="fasta" name="paired" label="Interlaced paired reads from datasets ${A.hid} and ${B.hid} "/>