Mercurial > repos > iuc > bctools_extract_barcodes
view extract_bcs.xml @ 0:ce2477cd3d95 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
author | iuc |
---|---|
date | Tue, 14 Nov 2017 05:53:20 -0500 |
parents | |
children | ceb779d5be5b |
line wrap: on
line source
<tool id="bctools_extract_barcodes" name="Extract barcodes" version="@VERSION@"> <description>according to pattern</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ extract_bcs.py '$reads' #if $barcode_pattern and $barcode_pattern is not None: '$barcode_pattern' #end if --bcs '$extracted_barcodes' > '$reads_cleaned' ]]></command> <inputs> <param name="reads" type="data" format="fastq" label="Barcoded sequences" /> <param name="barcode_pattern" type="text" label="Pattern for extracting barcode nucleotides" help="Starting at 5'-end. X positions will be moved to a separate file, N positions will be kept."> <sanitizer invalid_char="N"> <valid initial="none"> <add value="X"/> <add value="N"/> </valid> </sanitizer> </param> </inputs> <outputs> <data name="reads_cleaned" format="fastq"/> <data name="extracted_barcodes" format="fastq"/> </outputs> <tests> <test> <param name="reads" value="reads.fastq"/> <param name="barcode_pattern" value="XXXNNXXX"/> <output name="reads_cleaned" file="result_original_head.fastq"/> <output name="extracted_barcodes" file="extracted_bcs.fastq"/> </test> </tests> <help><![CDATA[ bctools - Extract barcodes according to pattern =============================================== Exract barcodes from a FASTQ file according to a user-specified pattern and write them to a separate FASTQ file. ]]></help> <expand macro="citations"/> </tool>