Mercurial > repos > iuc > artic_guppyplex
changeset 2:372def2f8fd6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit e6a1f8250cdcbd279220f1ea9fcc11ac5a90df46"
| author | iuc |
|---|---|
| date | Mon, 31 Jan 2022 10:12:54 +0000 |
| parents | 5ceeb5a5d70f |
| children | 00e20a06ff1e |
| files | artic_guppyplex.xml macros.xml |
| diffstat | 2 files changed, 76 insertions(+), 10 deletions(-) [+] |
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--- a/artic_guppyplex.xml Wed Oct 06 12:04:36 2021 +0000 +++ b/artic_guppyplex.xml Mon Jan 31 10:12:54 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="artic_guppyplex" name="ARTIC guppyplex" version="@PACKAGE_VERSION@+galaxy1" profile="20.09"> +<tool id="artic_guppyplex" name="ARTIC guppyplex" version="@PACKAGE_VERSION@+galaxy2" profile="20.09"> <description>Filter Nanopore reads by read length and (optionally) quality</description> <macros> <import>macros.xml</import> @@ -9,27 +9,89 @@ <command detect_errors="exit_code"> <![CDATA[ mkdir inputs && - #for $i, $elem in enumerate($input) - ln -fs '$elem' inputs/fastq${i}.fastq && - #end for + + ## Note about compression handling in the following: + ## guppyplex use mimetypes.guess_type to guess compression so + ## it's important to get the suffix of the inputs right. + ## Even if it detects compressed input, it will write uncompressed + ## output so we need to handle output compression separately. + + ## symlink input files to appropriate names in the inputs/ directory + bash prepare_inputs.sh && + #if str($input.structure) == 'one_to_one': + #set $compressed = $input.reads.is_of_type("fastq.gz", "fastqsanger.gz") + #else: + #set $compressed = next(iter($input.reads)).is_of_type("fastq.gz", "fastqsanger.gz") + #end if artic guppyplex --min-length $min_length --max-length $max_length + #if $min_quality == 0: + --skip-quality-check + #else: + --quality $min_quality + #end if --directory inputs/ - --prefix artic_guppyplex --output '$output1' + --output guppyplex_out.fastq + #if $compressed: + && gzip guppyplex_out.fastq + #end if ]]> </command> + <configfiles> + <configfile filename="prepare_inputs.sh"><![CDATA[ + #if str($input.structure) == 'one_to_one': +ln -s '$input.reads' inputs/1.${input.reads.ext} + #else: + #for $i, $elem in enumerate($input.reads): +ln -s '$elem' inputs/${i}.${elem.ext} && + #end for +: + #end if + ]]> + </configfile> + </configfiles> <inputs> - <param name="input" multiple="true" type="data" format="fastq" label="Nanopore reads (FASTQ format" /> + <conditional name="input"> + <param name="structure" type="select" + label="Structure of your input data" + help=""> + <option value="one_to_one">One input dataset per sample</option> + <option value="one_to_many">Multiple input datasets per sample</option> + </param> + <when value="one_to_one"> + <param name="reads" type="data" format="@FASTQ_FORMATS@" + label="Sequencing dataset(s) - one per sample" /> + </when> + <when value="one_to_many"> + <param name="reads" multiple="true" type="data" format="@FASTQ_FORMATS@" + label="Partial sequencing datasets for your sample" + help="Multiple datasets selected here will get combined into a single output for a single assumed sample. Select a nested list to have its inner lists interpreted as data from one sample each and to obtain one output per inner list." /> + </when> + </conditional> <param name="max_length" type="integer" label="Remove reads longer than" value="700" help="remove reads greater than this number of base pairs" /> <param name="min_length" type="integer" label="Remove reads shorter than" value="400" help="remove reads less than this number of base pairs" /> - <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)" /> + <param name="min_quality" type="integer" min="0" value="7" + label="Eliminate reads with a mean base quality score of less than" + help="Set to 0 to skip the quality check." /> </inputs> <outputs> - <data name="output1" format="fastq" from_work_dir="run_name_.fastq" /> + <data name="output" format_source="reads" from_work_dir="guppyplex_out.fastq*" /> </outputs> <tests> <test> - <param name="input" value="test.fastq" /> - <output name="output1" file="gupplyplex_output.fastq"/> + <conditional name="input"> + <param name="structure" value="one_to_one" /> + <param name="reads" value="test.fastq" /> + </conditional> + <output name="output" file="gupplyplex_output.fastq"/> + </test> + <test> + <conditional name="input"> + <param name="structure" value="one_to_many" /> + <param name="reads" value="test.fastq,test.fastq" /> + </conditional> + <!-- guppyplex drops duplicate reads so we don't need a new + test file for checking this branch --> + <output name="output" file="gupplyplex_output.fastq"/> </test> </tests> <help><![CDATA[ @@ -44,6 +106,9 @@ the minimum length and the maximum length of an amplicon plus 200 as the maximum length. + The tool can also be used simultaneously to gather partial fastq + datasets into single datasets per sample. + .. _ARTIC: https://artic.readthedocs.io/en/latest/ ]]></help> <expand macro="citations" />
--- a/macros.xml Wed Oct 06 12:04:36 2021 +0000 +++ b/macros.xml Mon Jan 31 10:12:54 2022 +0000 @@ -1,5 +1,6 @@ <macros> <token name="@PACKAGE_VERSION@">1.2.1</token> + <token name="@FASTQ_FORMATS@">fastq,fastq.gz,fastqsanger,fastqsanger.gz</token> <xml name="citations"> <citations> <citation type="bibtex">