Mercurial > repos > iuc > funannotate_annotate
view funannotate_annotate.xml @ 1:78407487f758 draft
"planemo upload commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
author | iuc |
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date | Thu, 18 Nov 2021 21:57:19 +0000 |
parents | a5baa4ff168d |
children | aa19eaac7d4b |
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<tool id="funannotate_annotate" name="Funannotate functional" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>annotation</description> <macros> <import>macros.xml</import> </macros> <requirements> <expand macro="requirements" /> </requirements> <version_command>funannotate check --show-versions</version_command> <command><![CDATA[ #if $uglyTestingHack == "true": ## funannotate_db contains some hard coded path, need to rewrite one for tests (not in real life when using data manager) ## Need to copy too as the test_data is read only on CI cp -r '${database.fields.path}' './hacked_database' && sed -i.bak 's|/tmp/prout|'`pwd`'/hacked_database|' './hacked_database/trained_species/fly/info.json' && #end if funannotate annotate #if $input.input_type == 'gbk' --genbank '${input.genbank}' #else --gff '${input.gff}' --fasta '${input.fasta}' --species '${input.species}' #end if --out output #if $uglyTestingHack == "true": --database `pwd`'/hacked_database' #else --database '$database.fields.path' #end if #if $sbt: --sbt '${sbt}' #end if #if $annotations: --annotations '${annotations}' #end if #if $eggnog: --eggnog '${eggnog}' #end if #if $antismash: --antismash '${antismash}' #end if #if $iprscan: --iprscan '${iprscan}' #end if #if $phobius: --phobius '${phobius}' #end if --busco_db '${busco_db}' --isolate '${isolate}' --strain '${strain}' #if $rename: --rename '${rename}' #end if #if $fix: --fix '${fix}' #end if #if $remove: --remove '${remove}' #end if --cpus \${GALAXY_SLOTS:-2} && mv output/annotate_results/*.gbk out.gbk && mv output/annotate_results/*.annotations.txt out.annotations.txt && mv output/annotate_results/*.contigs.fsa out.contigs.fsa && mv output/annotate_results/*.agp out.agp && mv output/annotate_results/*.tbl out.tbl && mv output/annotate_results/*.sqn out.sqn && mv output/annotate_results/*.scaffolds.fa out.scaffolds.fa && mv output/annotate_results/*.proteins.fa out.proteins.fa && mv output/annotate_results/*.mrna-transcripts.fa out.mrna-transcripts.fa && mv output/annotate_results/*.cds-transcripts.fa out.cds-transcripts.fa && mv output/annotate_results/*.gff3 out.gff3 && mv output/annotate_results/*.discrepency.report.txt out.discrepency.report.txt && mv output/annotate_results/*.stats.json out.stats.json ]]></command> <inputs> <conditional name="input"> <param name="input_type" type="select" label="Input format"> <option value="gbk" selected="True">GenBank (from 'Funannotate predict annotation' tool)</option> <option value="gff">GFF</option> </param> <when value="gbk"> <param argument="--genbank" type="data" format="genbank" label="Genome annotation in genbank format" help="Output from 'Funannotate predict annotation' tool" /> </when> <when value="gff"> <param argument="--gff" type="data" format="gff3" label="Genome annotation in gff format" /> <param argument="--fasta" type="data" format="fasta" label="Genome sequence" /> <param argument="--species" type="text" optional="false" label="Name of the species to annotate" help="e.g. Genus species"> <validator type="empty_field" /> </param> </when> </conditional> <param name="database" label="Funannotate database" type="select"> <options from_data_table="funannotate"> <column name="value" index="0" /> <column name="name" index="1" /> <column name="path" index="3" /> <filter type="sort_by" column="0" /> <filter type="static_value" column="2" value="1.0" /> </options> </param> <param argument="--sbt" type="data" format="sbt" optional="true" label="NCBI submission template file" help="Create it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/ (or leave empty to use a default one, not suitable for submission at NCBI)" /> <param argument="--eggnog" type="data" format="tabular" optional="true" label="Eggnog-mapper annotations file" help="'annotations' output from 'eggNOG Mapper' tool" /> <param argument="--antismash" type="data" format="genbank" optional="true" label="antiSMASH secondary metabolism results" help="Genbank output from 'Antismash' tool" /> <param argument="--iprscan" type="data" format="xml" optional="true" label="InterProScan5 XML file" help="XML output from InterProScan" /> <param argument="--phobius" type="data" format="tabular" optional="true" label="Phobius pre-computed results" /> <param argument="--busco_db" type="select" label="BUSCO models"> <expand macro="busco_species"/> </param> <param argument="--annotations" type="data" format="tabular" optional="true" label="Custom annotations" help="3 column tsv file" /> <param argument="--isolate" type="text" label="Isolate name" help="If relevant (e.g. Af293)" /> <param argument="--strain" type="text" label="Strain name" help="If relevant (e.g. FGSCA4)" /> <param argument="--rename" type="text" label="locus_tag from NCBI to rename GFF gene models with" /> <param argument="--fix" type="data" format="tabular" optional="true" label="Gene/Product names fixed" help="TSV: GeneID Name Product" /> <param argument="--remove" type="data" format="tabular" optional="true" label="Gene/Product names to remove" help="TSV: Gene Product" /> <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated"> <option value="gbk" selected="true">Annotated genome (genbank)</option> <option value="annotations">TSV file of all annotations added to genome. (i.e. import into excel)</option> <option value="contigs_fsa">Multi-fasta file of contigs, split at gaps (use for NCBI submission)</option> <option value="agp">AGP file; showing linkage/location of contigs (use for NCBI submission)</option> <option value="tbl">NCBI tbl annotation file (use for NCBI submission)</option> <option value="sqn">NCBI Sequin genome file (use for NCBI submission)</option> <option value="scaffolds_fa">Multi-fasta file of scaffolds</option> <option value="proteins_fa">Multi-fasta file of protein coding genes</option> <option value="mrna_transcripts_fa">Multi-fasta file of transcripts (mRNA)</option> <option value="cds_transcripts_fa">Multi-fasta file of transcripts (CDS)</option> <option value="gff3">Annotation in GFF3 format</option> <option value="discrepency">tbl2asn summary report of annotated genome</option> <option value="stats">Statistics</option> <option value="must_fix">TSV file of Gene Name/Product deflines that failed to pass tbl2asn checks and must be fixed</option> <option value="need_curating">TSV file of Gene Name/Product defines that need to be curated</option> <option value="new_names_passed">TSV file of Gene Name/Product deflines that passed tbl2asn but are not in Gene2Products database.</option> </param> <!-- Need this to change path in the test funannotate_db --> <param type="hidden" name="uglyTestingHack" value="" /> </inputs> <outputs> <data name='gbk' format='genbank' label="${tool.name} on ${on_string}: annotated genome (genbank)" from_work_dir="out.gbk"> <filter>outputs and 'gbk' in outputs</filter> </data> <data name='annot' format='tabular' label="${tool.name} on ${on_string}: all annotations" from_work_dir="out.annotations.txt"> <filter>outputs and 'annotations' in outputs</filter> </data> <data name='contigs_fsa' format='fasta' label="${tool.name} on ${on_string}: contigs fasta, split at gaps" from_work_dir="out.contigs.fsa"> <filter>outputs and 'contigs_fsa' in outputs</filter> </data> <data name='agp' format='tabular' label="${tool.name} on ${on_string}: NCBI tbl annotation file" from_work_dir="out.agp"> <filter>outputs and 'agp' in outputs</filter> </data> <data name='tbl' format='txt' label="${tool.name} on ${on_string}: NCBI tbl annotation file" from_work_dir="out.tbl"> <filter>outputs and 'tbl' in outputs</filter> </data> <data name='sqn' format='txt' label="${tool.name} on ${on_string}: NCBI Sequin genome" from_work_dir="out.sqn"> <filter>outputs and 'sqn' in outputs</filter> </data> <data name='fa_scaffolds' format='fasta' label="${tool.name} on ${on_string}: scaffolds sequences" from_work_dir="out.scaffolds.fa"> <filter>outputs and 'scaffolds_fa' in outputs</filter> </data> <data name='fa_proteins' format='fasta' label="${tool.name} on ${on_string}: protein sequences" from_work_dir="out.proteins.fa"> <filter>outputs and 'proteins_fa' in outputs</filter> </data> <data name='fa_transcripts_mrna' format='fasta' label="${tool.name} on ${on_string}: transcript mRNA sequences" from_work_dir="out.mrna-transcripts.fa"> <filter>outputs and 'mrna_transcripts_fa' in outputs</filter> </data> <data name='fa_transcripts_cds' format='fasta' label="${tool.name} on ${on_string}: transcript CDS sequences" from_work_dir="out.cds-transcripts.fa"> <filter>outputs and 'cds_transcripts_fa' in outputs</filter> </data> <data name='gff3' format='gff3' label="${tool.name} on ${on_string}: annotation (GFF3)" from_work_dir="out.gff3"> <filter>outputs and 'gff3' in outputs</filter> </data> <data name='tbl2asn_report' format='txt' label="${tool.name} on ${on_string}: tbl2asn summary report of annotated genome" from_work_dir="out.discrepency.report.txt"> <filter>outputs and 'discrepency' in outputs</filter> </data> <data name='stats' format='json' label="${tool.name} on ${on_string}: stats" from_work_dir="out.stats.json"> <filter>outputs and 'gbk' in outputs</filter> </data> <data name='must_fix' format='json' label="${tool.name} on ${on_string}: Gene Name/Product must-fix" from_work_dir="output/annotate_results/Gene2Products.must-fix.txt"> <filter>outputs and 'must_fix' in outputs</filter> </data> <data name='need_curating' format='json' label="${tool.name} on ${on_string}: Gene Name/Product need-curating" from_work_dir="output/annotate_results/Gene2Products.need-curating.txt"> <filter>outputs and 'need_curating' in outputs</filter> </data> <data name='new_names_passed' format='json' label="${tool.name} on ${on_string}: Gene Name/Product new-names-passed" from_work_dir="output/annotate_results/Gene2Products.new-names-passed.txt"> <filter>outputs and 'new_names_passed' in outputs</filter> </data> </outputs> <tests> <test> <conditional name="input"> <param name="input_type" value="gbk" /> <param name="genbank" value="predict_augustus/Genus_species.gbk" /> </conditional> <param name="database" value="2021-07-20-120000" /> <param name="busco_db" value="insecta" /> <param name="outputs" value="gbk,annotations,contigs_fsa,agp,tbl,sqn,scaffolds_fa,proteins_fa,mrna_transcripts_fa,cds_transcripts_fa,gff3,discrepency,stats,must_fix,need_curating,new_names_passed" /> <output name="gbk"> <assert_contents> <has_text text="DEFINITION Genus species." /> </assert_contents> </output> <output name="annot"> <assert_contents> <has_text text="EC_number" /> <has_text text="EOG090W0T3K" /> </assert_contents> </output> <output name="contigs_fsa"> <assert_contents> <has_text text=">contig_1" /> </assert_contents> </output> <output name="agp"> <assert_contents> <has_text text="contig_1" /> </assert_contents> </output> <output name="tbl"> <assert_contents> <has_text text="locus_tag" /> </assert_contents> </output> <output name="sqn"> <assert_contents> <has_text text="Seq-submit" /> </assert_contents> </output> <output name="fa_scaffolds"> <assert_contents> <has_text text=">sample" /> </assert_contents> </output> <output name="fa_proteins"> <assert_contents> <has_text text=">FUN_000001-T1 FUN_000001" /> </assert_contents> </output> <output name="fa_transcripts_mrna"> <assert_contents> <has_text text=">FUN_000001-T1 FUN_000001" /> </assert_contents> </output> <output name="fa_transcripts_cds"> <assert_contents> <has_text text=">FUN_000001-T1 FUN_000001" /> </assert_contents> </output> <output name="gff3"> <assert_contents> <has_text text="ID=FUN_000001;" /> </assert_contents> </output> <output name="tbl2asn_report"> <assert_contents> <has_text text="Discrepancy Report Results" /> </assert_contents> </output> <output name="stats"> <assert_contents> <has_text text="avg_gene_length" /> </assert_contents> </output> <output name="must_fix"> <assert_contents> <has_text text="tbl2asn Error" /> </assert_contents> </output> <output name="need_curating"> <assert_contents> <has_text text="Original Description" /> </assert_contents> </output> <output name="new_names_passed"> <assert_contents> <has_text text="Passed Description" /> </assert_contents> </output> </test> <test> <conditional name="input"> <param name="input_type" value="gff" /> <param name="gff" value="predict_augustus/Genus_species.gff3" /> <param name="fasta" value="genome.fa" /> <param name="species" value="Genus species" /> </conditional> <param name="database" value="2021-07-20-120000" /> <param name="busco_db" value="insecta" /> <param name="outputs" value="gbk,annotations,contigs_fsa,agp,tbl,sqn,scaffolds_fa,proteins_fa,mrna_transcripts_fa,cds_transcripts_fa,gff3,discrepency,stats,must_fix,need_curating,new_names_passed" /> <output name="gbk"> <assert_contents> <has_text text="DEFINITION Genus species." /> </assert_contents> </output> <output name="annot"> <assert_contents> <has_text text="EC_number" /> <has_text text="EOG090W0T3K" /> </assert_contents> </output> <output name="contigs_fsa"> <assert_contents> <has_text text=">contig_1" /> </assert_contents> </output> <output name="agp"> <assert_contents> <has_text text="contig_1" /> </assert_contents> </output> <output name="tbl"> <assert_contents> <has_text text="locus_tag" /> </assert_contents> </output> <output name="sqn"> <assert_contents> <has_text text="Seq-submit" /> </assert_contents> </output> <output name="fa_scaffolds"> <assert_contents> <has_text text=">sample" /> </assert_contents> </output> <output name="fa_proteins"> <assert_contents> <has_text text=">FUN_000001-T1 FUN_000001" /> </assert_contents> </output> <output name="fa_transcripts_mrna"> <assert_contents> <has_text text=">FUN_000001-T1 FUN_000001" /> </assert_contents> </output> <output name="fa_transcripts_cds"> <assert_contents> <has_text text=">FUN_000001-T1 FUN_000001" /> </assert_contents> </output> <output name="gff3"> <assert_contents> <has_text text="ID=FUN_000001;" /> </assert_contents> </output> <output name="tbl2asn_report"> <assert_contents> <has_text text="Discrepancy Report Results" /> </assert_contents> </output> <output name="stats"> <assert_contents> <has_text text="avg_gene_length" /> </assert_contents> </output> <output name="must_fix"> <assert_contents> <has_text text="tbl2asn Error" /> </assert_contents> </output> <output name="need_curating"> <assert_contents> <has_text text="Original Description" /> </assert_contents> </output> <output name="new_names_passed"> <assert_contents> <has_text text="Passed Description" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ Funannotate_ annotate --------------------- Funannotate_ is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). This script functionally annotates the results from funannotate predict. It pulls annotation from PFAM, InterPro, EggNog, UniProtKB, MEROPS, CAZyme, and GO ontology. .. _Funannotate: http://funannotate.readthedocs.io ]]></help> <expand macro="citations" /> </tool>