Mercurial > repos > iuc > artic_guppyplex
comparison artic_guppyplex.xml @ 0:7a82006f7c05 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
| author | iuc |
|---|---|
| date | Fri, 27 Aug 2021 20:34:52 +0000 |
| parents | |
| children | 5ceeb5a5d70f |
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| -1:000000000000 | 0:7a82006f7c05 |
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| 1 <tool id="artic_guppyplex" name="ARTIC guppyplex" version="@PACKAGE_VERSION@+galaxy0" profile="20.09"> | |
| 2 <description>Filter Nanopore reads by read length and (optionally) quality</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <requirements> | |
| 7 <requirement type="package" version="@PACKAGE_VERSION@">artic</requirement> | |
| 8 </requirements> | |
| 9 <command detect_errors="exit_code"> | |
| 10 <![CDATA[ | |
| 11 mkdir inputs && | |
| 12 #for $i, $elem in enumerate($input) | |
| 13 ln -fs '$elem' inputs/fastq${i}.fastq && | |
| 14 #end for | |
| 15 artic guppyplex --min-length $min_length --max-length $max_length | |
| 16 --directory inputs/ | |
| 17 --prefix artic_guppyplex --output '$output1' | |
| 18 ]]> | |
| 19 </command> | |
| 20 <inputs> | |
| 21 <param name="input" multiple="true" type="data" format="fastq" label="Nanopore reads (FASTQ format" /> | |
| 22 <param name="max_length" type="integer" label="Remove reads longer than" value="700" help="remove reads greater than this number of base pairs" /> | |
| 23 <param name="min_length" type="integer" label="Remove reads shorter than" value="400" help="remove reads less than this number of base pairs" /> | |
| 24 <param name="skip_quality_check" argument="--skip-quality-check" type="boolean" truevalue="--skip-quality-check" falsevalue="" checked="False" label="Do not filter on quality score (speeds up processing)" /> | |
| 25 </inputs> | |
| 26 <outputs> | |
| 27 <data name="output1" format="fastq" from_work_dir="run_name_.fastq" /> | |
| 28 </outputs> | |
| 29 <tests> | |
| 30 <test> | |
| 31 <param name="input" value="test.fastq" /> | |
| 32 <output name="output1" file="gupplyplex_output.fastq"/> | |
| 33 </test> | |
| 34 </tests> | |
| 35 <help><![CDATA[ | |
| 36 The ARTIC_ guppyplex tool filters reads by length and (optionally) quality. | |
| 37 This filter is typically used as a pre-processing step in the processing | |
| 38 of amplicon sequencing Nanopore reads, where a size-based filter can | |
| 39 be used to remove possibly-chimeric reads. | |
| 40 | |
| 41 The default paramters of the tool (minimum length of 400 and maximum of 700) | |
| 42 are based on the ARTIC amplicon scheme. If used with a different amplicon | |
| 43 scheme they should be adjusted to use the minimum length of an amplicon as | |
| 44 the minimum length and the maximum length of an amplicon plus 200 as the | |
| 45 maximum length. | |
| 46 | |
| 47 .. _ARTIC: https://artic.readthedocs.io/en/latest/ | |
| 48 ]]></help> | |
| 49 <expand macro="citations" /> | |
| 50 </tool> |