Mercurial > repos > rhpvorderman > fast_fastq_filter
changeset 1:6ee24ca51829 draft default tip
"planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit a4a3ab70c61a5ea14719002eb72a34a02b5d89e3"
| author | rhpvorderman |
|---|---|
| date | Wed, 08 Jun 2022 07:49:43 +0000 |
| parents | 5f0d949db99e |
| children | |
| files | Dockerfile fast_fastq_filter.xml |
| diffstat | 2 files changed, 120 insertions(+), 34 deletions(-) [+] |
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--- a/Dockerfile Tue Dec 28 14:17:40 2021 +0000 +++ b/Dockerfile Wed Jun 08 07:49:43 2022 +0000 @@ -1,4 +1,4 @@ FROM python:3.10-slim-bullseye ENV PYTHONDONTWRITEBYTECODE=true -RUN pip install --no-cache-dir fastq-filter +RUN pip install --no-cache-dir fastq-filter==0.3.0
--- a/fast_fastq_filter.xml Tue Dec 28 14:17:40 2021 +0000 +++ b/fast_fastq_filter.xml Wed Jun 08 07:49:43 2022 +0000 @@ -1,49 +1,135 @@ -<tool id="fast_fastq_filter" name="fastq-filter" version="0.1.0" python_template_version="3.5" profile="16.04"> +<tool id="fast_fastq_filter" name="fastq-filter" version="0.3.0" 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> + <requirement type="package" version="0.3.0">fastq-filter</requirement> <!-- TODO: Remove this once biocontainer is published --> - <container type="docker">quay.io/rhpvorderman/fastq-filter:0.1.0</container> + <container type="docker">quay.io/rhpvorderman/fastq-filter:0.3.0</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' + set -e; + fastq-filter + #if str($filters.minimum_length.enabled) == "true" + --min-length $filters.minimum_length.threshold + #end if + #if str($filters.maximum_length.enabled) == "true" + --max-length $filters.maximum_length.threshold + #end if + #if str($filters.average_error_rate.enabled) == "true" + --average-error-rate $filters.average_error_rate.threshold + #end if + #if str($filters.mean_quality.enabled) == "true" + --mean-quality $filters.mean_quality.threshold + #end if + #if str($filters.median_quality.enabled) == "true" + --median-quality $filters.median_quality.threshold + #end if + --verbose + -o '${output1}.gz' + #if str($library.type) == "paired": + -o ${output2}.gz + #end if + + '$library.input_1' + #if str($library.type) == "paired": + '$library.input_2' + #end if + ; + + mv '${output1}.gz' '$output1'; + #if str($library.type) == "paired": + mv '${output2}.gz' '$output2'; + #end if ]]></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> + <conditional name="library"> + <param name="type" type="select" label="Single-end or Paired-end reads?"> + <option value="single">Single-end</option> + <option value="paired">Paired-end</option> </param> - <param name="filter_threshold" type="integer" label="Filter threshold" value="20"/> - </repeat> + <when value="single"> + <param type="data" name="input_1" label="Input FASTQ file" format="fastqsanger,fastqsanger.gz" /> + </when> + <when value="paired"> + <param type="data" name="input_1" label="Input FASTQ file #1" format="fastqsanger,fastqsanger.gz" /> + <param type="data" name="input_2" label="Input FASTQ file #2" format="fastqsanger,fastqsanger.gz" /> + </when> + </conditional> + <section name="filters" title="Filters" expanded="true"> + <conditional name="minimum_length"> + <param name="enabled" type="boolean" label="Minimum length" + help="The minimum length for a read."/> + <when value="true"> + <param name="threshold" type="integer" label="Threshold" + value="20" min="1"/> + </when> + <when value="false"/> + </conditional> + <conditional name="maximum_length"> + <param name="enabled" type="boolean" label="Maximum length" + help="The maximum length for a read."/> + <when value="true"> + <param name="threshold" type="integer" label="Threshold" + value="1000" min="1"/> + </when> + <when value="false"/> + </conditional> + <conditional name="average_error_rate"> + <param name="enabled" type="boolean" label="Average error rate" + help="The minimum average per base error rate."/> + <when value="true"> + <param name="threshold" type="float" label="Threshold" + value="0.001" min="0"/> + </when> + <when value="false"/> + </conditional> + <conditional name="mean_quality"> + <param name="enabled" type="boolean" label="Mean quality"> + <help> + Average quality. Same as the 'Average error rate' option but + specified with a phred score. I.e a mean quality of 30 is + equivalent to an average error rate of 0.001'. + </help> + </param> + <when value="true"> + <param name="threshold" type="integer" label="Threshold" + value="30" min="0"/> + </when> + <when value="false"/> + </conditional> + <conditional name="median_quality"> + <param name="enabled" type="boolean" label="Median quality"> + <help> + DEPRECATED: The minimum median phred score. This is not as + informative as the average error rate. It is also slower to + calculate. This filter is only included for backwards + compatibility reasons. + </help> + </param> + <when value="true"> + <param name="threshold" type="integer" label="Threshold" + value="30" min="0"/> + </when> + <when value="false"/> + </conditional> + </section> </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 --> + <data name="output1" format="fastqsanger.gz" /> + <data name="output2" format="fastqsanger.gz"> + <filter>library['type'] == 'paired'</filter> + </data> </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: + When paired FASTQ data is given, fastq-filter makes sure the output is in + sync. The filters behave as follows for paired-end data: - + 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 + + average error rate: The average of the combined phred scores is used. + + median quality: The median of the combined phred scores is used. + + Minimum length: at least one of the records of the pair must meet the minimum length. + + Maximum length: None of the records in the pair must exceed the maximum length. + + The rationale for the length filters is that R1 and R2 both sequence the same + molecule and the canonical length is the longest of both. ]]></help> <citations>