Mercurial > repos > rhpvorderman > fast_fastq_filter
comparison fast_fastq_filter.xml @ 0:5f0d949db99e draft
"planemo upload for repository https://github.com/LUMC/fastq-filter/tree/develop/galaxy commit 7c3396382f92bd634b23102351208f8863390cb5"
| author | rhpvorderman |
|---|---|
| date | Tue, 28 Dec 2021 14:17:40 +0000 |
| parents | |
| children | 6ee24ca51829 |
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| -1:000000000000 | 0:5f0d949db99e |
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| 1 <tool id="fast_fastq_filter" name="fastq-filter" version="0.1.0" python_template_version="3.5" profile="16.04"> | |
| 2 <description>filter FASTQ reads fast</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.1.0">fastq-filter</requirement> | |
| 5 <!-- TODO: Remove this once biocontainer is published --> | |
| 6 <container type="docker">quay.io/rhpvorderman/fastq-filter:0.1.0</container> | |
| 7 </requirements> | |
| 8 <command detect_errors="exit_code"><![CDATA[ | |
| 9 #set all_filters = [str(filter['filter']) + ":" + str(filter['filter_threshold']) for filter in $filters] | |
| 10 fastq-filter -o '$output1' | |
| 11 #echo "'" + "|".join($all_filters) + "'" | |
| 12 '$input1' | |
| 13 ]]></command> | |
| 14 <inputs> | |
| 15 <param type="data" name="input1" label="Input FASTQ file" format="fastqsanger,fastqsanger.gz" /> | |
| 16 <repeat name="filters" title="Filter" min="1"> | |
| 17 <param name="filter" type="select" label="Filter on"> | |
| 18 <option value="min_length">minimum length</option> | |
| 19 <option value="max_length">maximum length</option> | |
| 20 <option value="mean_quality" selected="true">mean quality</option> | |
| 21 <option value="median_quality">median quality</option> | |
| 22 </param> | |
| 23 <param name="filter_threshold" type="integer" label="Filter threshold" value="20"/> | |
| 24 </repeat> | |
| 25 </inputs> | |
| 26 <outputs> | |
| 27 <!--Fastqsanger format for now. For conditionally applying fastqsanger.gz the tool needs | |
| 28 to be updated. An option is using format auto_detect, so we do not have to conditionally set | |
| 29 fastqsanger or fastqsanger.gz--> | |
| 30 <data name="output1" format="fastqsanger" /> | |
| 31 <!--When the tool is updated for paired input, the optional paired output can probably be | |
| 32 found in the cutadapt wrapper --> | |
| 33 </outputs> | |
| 34 <tests> | |
| 35 <test> | |
| 36 <param name="input1" value="input.fastq.gz"/> | |
| 37 <output name="output1" file="output.fastq.gz"/> | |
| 38 </test> | |
| 39 </tests> | |
| 40 <help><![CDATA[ | |
| 41 The following filters are available: | |
| 42 | |
| 43 + mean_quality:<quality> The mean quality of the FASTQ record is equal or above the given quality value. | |
| 44 + median_quality:<quality> The median quality of the FASTQ record is equal or above the given quality value. | |
| 45 + min_length:<length> The length of the sequence in the FASTQ record is at least min_length | |
| 46 + max_length:<length> The length of the sequence in the FASTQ record is at most max_length | |
| 47 | |
| 48 ]]></help> | |
| 49 <citations> | |
| 50 <citation type="bibtex"> | |
| 51 @misc{githubfastq-filter, | |
| 52 author = {Vorderman, Ruben Harmen Paul}, | |
| 53 year = {2021}, | |
| 54 title = {fastq-filter}, | |
| 55 publisher = {GitHub}, | |
| 56 journal = {GitHub repository}, | |
| 57 url = {https://github.com/LUMC/fastq-filter}, | |
| 58 }</citation> | |
| 59 </citations> | |
| 60 </tool> |