Mercurial > repos > galaxy-australia > purge_haplotigs
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"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
author | galaxy-australia |
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date | Wed, 20 Apr 2022 06:46:59 +0000 |
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<tool id="purge_haplotigs_purge" name="Purge Haplotigs Purge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" > <description>Purge contigs</description> <xrefs> <xref type='bio.tools'>purgehaplotigs</xref> </xrefs> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> <command><![CDATA[ purge_haplotigs purge #if $adv_options.align_cov: -align_cov '$adv_options.align_cov' #end if #if $adv_options.max_match: -max_match '$adv_options.max_match' #end if #if $adv_options.wind_min: -wind_min '$adv_options.wind_min' #end if #if $adv_options.wind_nmax: -wind_nmax '$adv_options.wind_nmax' #end if #if $additional.optional_selector == "use_additional_options": #if $additional.create_dotplot.include_dotplot =="Yes": -dotplots -bam '$additional.create_dotplot.aligned_bam' #end if #if $additional.with_repeat.has_repeat =="Yes": -repeats '$additional.with_repeat.repeat' #end if #end if -t \${GALAXY_SLOTS:-4} -g $genome -c $coverage 2>&1 ]]></command> <inputs> <param name="genome" type="data" format="fasta" label="Genome Assembly" help="Fasta file indexed with samtools faidx"/> <param name="coverage" type="data" format="csv" label="Contig Coverage" help="Contig Coverage file"/> <section name="adv_options" title="Advance Parameters" expanded="False"> <param argument="-align_cov" type="integer" value="70" label="Cutoff value to identify haplotigs" help="A cutoff value to identify a contig as a haplotigs in percentage: default=70 (-align_cov)"/> <param argument="-max_match" type="integer" value="250" label="Cutoff value to identify repetitive regions" help="A cutoff value to identify repetitive regions: default=250 (-repeats)"/> <param argument="-wind_min" type="integer" value="5000" label="Minimum window size" help="Minimum window size for BED coverage (dotplots): default=5000 (-wind_min)"/> <param argument="-wind_nmax" type="integer" value="200" label="Max windows per contig" help="Max windows per contig for BED coverage plots (dotplots) : default=200 (-wind_nmax)"/> </section> <conditional name="additional"> <param name="optional_selector" type="select" label="Additional Parameters"> <option value="no">No</option> <option value="use_additional_options">Yes</option> </param> <when value="no"/> <when value="use_additional_options"> <conditional name="with_repeat"> <param type="select" name="has_repeat" label="Repetitive region file"> <option value="No">no repetitive region file</option> <option value="Yes">with repetitive region file</option> </param> <when value="No"/> <when value="Yes"> <param name="repeat" argument="-repeats" type="data" format="bed" label="Repetitive region (BED)" help="repetitive regions in BED file format (-repeats)"/> </when> </conditional> <conditional name="create_dotplot"> <param type="select" name="include_dotplot" label="Generate dotplot" help="repetitive regions in BED file format (-repeats)"> <option value="No">No</option> <option value="Yes">Yes</option> </param> <when value="No"/> <when value="Yes"> <param name="aligned_bam" argument="-bam" type="data" format="bam" label="BAM file" help="Alignment file (BAM) to reference genome, required for generating dotplots (-bam)"/> </when> </conditional> </when> </conditional> </inputs> <outputs> <data name="curated_haplotigs" format="fasta" label="${tool.name} on ${on_string}: curated haplotigs" from_work_dir="curated.haplotigs.fasta"/> <data name="curated_sequences" format="fasta" label="${tool.name} on ${on_string}: curated sequences" from_work_dir="curated.fasta"/> <data name="curated_artefacts" format="fasta" label="${tool.name} on ${on_string}: curated artefacts" from_work_dir="curated.artefacts.fasta"/> <data name="curated_reassignment" format="tsv" label="${tool.name} on ${on_string}: curated assignment" from_work_dir="curated.reassignments.tsv"/> <data name="curated_log" format="txt" label="${tool.name} on ${on_string}: curated log" from_work_dir="curated.contig_associations.log"/> <collection name="output_pngs" type="list" label="${tool.name} on ${on_string}: dotplot diagram"> <filter> additional['optional_selector'] == "use_additional_options" and create_dotplot['include_dotplot'] == "Yes"</filter> <discover_datasets pattern="__name_and_ext__" ext="png" directory="dotplots_reassigned_contigs" visible="false"/> </collection> </outputs> <tests> <test> <!-- #1 test with common parameters --> <param name="genome" value="contigs.fa" ftype="fasta"/> <param name="coverage" value="coverage_stats.csv" ftype="csv"/> <param name="align_cov" value="70" /> <param name="max_match" value="250" /> <param name="wind_min" value="5000" /> <param name="wind_nmax" value="200" /> <output name="curated_haplotigs" file="curated.haplotigs.fasta" ftype="fasta"/> <output name="curated_sequences" file="curated.fasta" ftype="fasta"/> <output name="curated_artefacts" file="curated.artefacts.fasta" ftype="fasta"/> <output name="curated_reassignment" file="curated.reassignments.tsv" ftype="tsv"/> <output name="curated_log" file="curated.contig_associations.log" ftype="txt"/> <conditional name="additional"> <param name="optional_selector" value="no"/> </conditional> </test> <test> <!-- #2 test with common parameters --> <param name="genome" value="contigs.fa" ftype="fasta"/> <param name="coverage" value="coverage_stats.csv" ftype="csv"/> <param name="align_cov" value="70" /> <param name="max_match" value="250" /> <param name="wind_min" value="5000" /> <param name="wind_nmax" value="200" /> <output name="curated_haplotigs" file="curated.haplotigs.fasta" ftype="fasta"/> <output name="curated_sequences" file="curated.fasta" ftype="fasta"/> <output name="curated_artefacts" file="curated.artefacts.fasta" ftype="fasta"/> <output name="curated_reassignment" file="curated.reassignments_w_repeats.tsv" ftype="tsv"/> <output name="curated_log" file="curated.contig_associations.log" ftype="txt"/> <conditional name="additional"> <param name="optional_selector" value="use_additional_options"/> <conditional name="with_repeat"> <param name="has_repeat" value="Yes"/> <param name="repeat" value="repeats.bed"/> </conditional> <conditional name="create_dotplot"> <param name="include_dotplot" value="Yes"/> <param name="dotplots" value="-dotplots"/> <param name="aligned_bam" value="aligned.bam"/> </conditional> </conditional> <output_collection name="output_pngs" type="list" count="5"> <element name="000002F" file="dotplots_reassigned_contigs/000002F.png" ftype="png"> <assert_content> <has_size value="59559" delta="100"/> </assert_content> </element> <element name="000000F_001" file="dotplots_reassigned_contigs/000000F_001.png" ftype="png"> <assert_contents> <has_size value="31923" delta="100"/> </assert_contents> </element> <element name="000000F_002" file="dotplots_reassigned_contigs/000000F_002.png" ftype="png"> <assert_contents> <has_size value="42614" delta="100"/> </assert_contents> </element> <element name="000000F_003" file="dotplots_reassigned_contigs/000000F_003.png" ftype="png"> <assert_contents> <has_size value="47498" delta="100"/> </assert_contents> </element> <element name="000000F_004" file="dotplots_reassigned_contigs/000000F_004.png" ftype="png"> <assert_contents> <has_size value="32534" delta="100"/> </assert_contents> </element> </output_collection> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** Running the purging pipeline from the purge_haplotigs tool. **Input** - input file (g) : Genome assembly in fasta format - input file (c) : Contig by contig coverage stats csv file from the previous step. **Parameters** *OPTIONAL* - repeats : BED-format file of repeats to ignore during analysis. - dotplots : Generate dotplots for manual inspection. - bam : Samtools-indexed bam file of aligned and sorted reads/subreads to the reference, required for generating dotplots. *ADVANCED* - align_cov : Percent cutoff for identifying a contig as a haplotig. DEFAULT = 70 - max_match : Percent cutoff for identifying repetitive contigs. Ignored when using repeat annotations (-repeats). DEFAULT = 250 - I : Minimap2 indexing, drop minimisers every N bases, DEFAULT = 4G - wind_min : Min window size for BED coverage plots (for dotplots). DEFAULT = 5000 - wind_nmax : Max windows per contig for BED coverage plots (for dotplots). DEFAULT = 200 **Output** - curated.haplotigs.fasta - curated.contig_associations.log - curated.fasta - curated.reassignments.tsv - curated.artefacts.fasta .. class:: infomark **References** ]]></help> <citations> <citation type="doi">DOI: 10.1186/s12859-018-2485-7</citation> </citations> </tool>