Mercurial > repos > iuc > hapog
view hapog.xml @ 1:7d56a813fd24 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit 34255461a89adf6cdd9e781ac1fe47e8c41227ba
author | iuc |
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date | Tue, 10 Oct 2023 17:29:42 +0000 |
parents | c61bc8bb5f1e |
children | ee0d6e789958 |
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<tool id="hapog" name="Hapo-G" profile="21.05" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>genome polishing</description> <macros> <token name="@TOOL_VERSION@">1.3.6</token> <token name="@VERSION_SUFFIX@">0</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">hapog</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ hapog --genome '${genome}' --output output/ ## setting default threads to 2 until ## https://github.com/institut-de-genomique/HAPO-G/issues/34 ## gets addressed, at least --threads \${GALAXY_SLOTS:-2} #if str( $reads.type ) == "short": #for $i in $reads.pe1 --pe1 '${i}' #end for #for $i in $reads.pe2 --pe2 '${i}' #end for #elif str( $reads.type ) == "short_collection": #for $i in $reads.pecol --pe1 '${i.forward}' --pe2 '${i.reverse}' #end for #elif str( $reads.type ) == "long": --single '${single}' #elif str( $reads.type ) == "bam": -b '${bam}' #end if $u ]]></command> <inputs> <param argument="--genome" type="data" format="fasta" label="Genome assembly to polish"/> <conditional name="reads"> <param name="type" type="select" label="Type of data used for polishing"> <option value="short">Short (paired) reads</option> <option value="short_collection">Short (paired) reads collection</option> <option value="long">Long reads</option> <option value="bam">Pre-aligned reads (BAM)</option> </param> <when value="short"> <param argument="--pe1" type="data" format="fastq,fastq.gz" multiple="true" label="First set of short reads"/> <param argument="--pe2" type="data" format="fastq,fastq.gz" multiple="true" label="Second set of short reads"/> </when> <when value="short_collection"> <param name="pecol" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Paired collection of short reads"/> </when> <when value="long"> <param argument="--single" type="data" format="fastq,fastq.gz" label="Long reads"/> </when> <when value="bam"> <param name="bam" type="data" format="bam" label="Pre-aligned reads"/> </when> </conditional> <param argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Include unpolished sequences in final output" /> </inputs> <outputs> <data format="fasta" name="output" label="${tool.name}: polished assembly from ${on_string}" from_work_dir="output/hapog_results/hapog.fasta"/> <data format="tsv" name="changes" label="${tool.name}: report of changes" from_work_dir="output/hapog_results/hapog.changes"/> </outputs> <tests> <test> <param name="genome" value="genome.fa" /> <conditional name="reads"> <param name="type" value="short" /> <param name="pe1" value="fastq1.fq" /> <param name="pe2" value="fastq2.fq" /> </conditional> <output name="output" file="hapog_short.fasta" /> <output name="changes" file="hapog_short.changes" /> </test> <test> <param name="genome" value="genome.fa" /> <conditional name="reads"> <param name="type" value="short" /> <param name="pe1" value="fastq1.fq.gz" /> <param name="pe2" value="fastq2.fq.gz" /> </conditional> <output name="output" file="hapog_short.fasta"/> <output name="changes" file="hapog_short.changes" /> </test> <test> <param name="genome" value="genome.fa" /> <conditional name="reads"> <param name="type" value="long" /> <param name="single" value="fastq1.fq" /> </conditional> <output name="output" file="hapog_long.fasta" /> <output name="changes" file="hapog_long.changes" /> </test> <test> <param name="genome" value="genome.fa" /> <conditional name="reads"> <param name="type" value="long" /> <param name="single" value="fastq1.fq.gz" /> </conditional> <output name="output" file="hapog_long.fasta"/> <output name="changes" file="hapog_long.changes" /> </test> <test> <param name="genome" value="genome.fa" /> <conditional name="reads"> <param name="type" value="bam" /> <param name="bam" value="input.bam" /> </conditional> <output name="output" file="hapog_bam.fasta"/> <output name="changes" file="hapog_bam.changes" /> </test> </tests> <help><![CDATA[ Hapo-G uses alignments produced by BWA (or any other aligner that produces SAM files) to polish the consensus of a genome assembly. ]]></help> <citations> <citation type="doi">10.1093/nargab/lqab034</citation> </citations> </tool>