Mercurial > repos > rhpvorderman > fast_fastq_filter
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"planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
author | rhpvorderman |
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date | Tue, 28 Dec 2021 14:17:40 +0000 |
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children | 6ee24ca51829 |
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<tool id="fast_fastq_filter" name="fastq-filter" version="0.1.0" python_template_version="3.5" profile="16.04"> <description>filter FASTQ reads fast</description> <requirements> <requirement type="package" version="0.1.0">fastq-filter</requirement> <!-- TODO: Remove this once biocontainer is published --> <container type="docker">quay.io/rhpvorderman/fastq-filter:0.1.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[ #set all_filters = [str(filter['filter']) + ":" + str(filter['filter_threshold']) for filter in $filters] fastq-filter -o '$output1' #echo "'" + "|".join($all_filters) + "'" '$input1' ]]></command> <inputs> <param type="data" name="input1" label="Input FASTQ file" format="fastqsanger,fastqsanger.gz" /> <repeat name="filters" title="Filter" min="1"> <param name="filter" type="select" label="Filter on"> <option value="min_length">minimum length</option> <option value="max_length">maximum length</option> <option value="mean_quality" selected="true">mean quality</option> <option value="median_quality">median quality</option> </param> <param name="filter_threshold" type="integer" label="Filter threshold" value="20"/> </repeat> </inputs> <outputs> <!--Fastqsanger format for now. For conditionally applying fastqsanger.gz the tool needs to be updated. An option is using format auto_detect, so we do not have to conditionally set fastqsanger or fastqsanger.gz--> <data name="output1" format="fastqsanger" /> <!--When the tool is updated for paired input, the optional paired output can probably be found in the cutadapt wrapper --> </outputs> <tests> <test> <param name="input1" value="input.fastq.gz"/> <output name="output1" file="output.fastq.gz"/> </test> </tests> <help><![CDATA[ The following filters are available: + mean_quality:<quality> The mean quality of the FASTQ record is equal or above the given quality value. + median_quality:<quality> The median quality of the FASTQ record is equal or above the given quality value. + min_length:<length> The length of the sequence in the FASTQ record is at least min_length + max_length:<length> The length of the sequence in the FASTQ record is at most max_length ]]></help> <citations> <citation type="bibtex"> @misc{githubfastq-filter, author = {Vorderman, Ruben Harmen Paul}, year = {2021}, title = {fastq-filter}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://github.com/LUMC/fastq-filter}, }</citation> </citations> </tool>