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 |
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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> |