Mercurial > repos > rhpvorderman > fast_fastq_filter
changeset 0:5f0d949db99e draft
"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 |
parents | |
children | 6ee24ca51829 |
files | Dockerfile fast_fastq_filter.xml |
diffstat | 2 files changed, 64 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Dockerfile Tue Dec 28 14:17:40 2021 +0000 @@ -0,0 +1,4 @@ +FROM python:3.10-slim-bullseye + +ENV PYTHONDONTWRITEBYTECODE=true +RUN pip install --no-cache-dir fastq-filter
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fast_fastq_filter.xml Tue Dec 28 14:17:40 2021 +0000 @@ -0,0 +1,60 @@ +<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> \ No newline at end of file