Mercurial > repos > richard-burhans > ncbi_egapx
changeset 40:b095c69eab5b draft
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 69aca8290c162e4bce52ff788553a3676b0a7be6
author | richard-burhans |
---|---|
date | Fri, 18 Jul 2025 00:58:39 +0000 |
parents | 4f85da43b40c |
children | d129c3d0e920 |
files | macros.xml ncbi_egapx.xml test-data/input.yaml |
diffstat | 3 files changed, 59 insertions(+), 47 deletions(-) [+] |
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--- a/macros.xml Mon Jun 30 23:21:01 2025 +0000 +++ b/macros.xml Fri Jul 18 00:58:39 2025 +0000 @@ -4,7 +4,7 @@ <container type="docker">quay.io/galaxy/egapx:@TOOL_VERSION@-alpha</container> </requirements> </xml> - <token name="@TOOL_VERSION@">0.4.0</token> + <token name="@TOOL_VERSION@">0.4.1</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">23.0</token> <xml name="edam_ontology"> @@ -44,17 +44,7 @@ <has_size min="1"/> </assert_contents> </element> - <element name="annotation_data" ftype="tabular"> - <assert_contents> - <has_size min="1"/> - </assert_contents> - </element> - <element name="gnomon_accepted" ftype="txt"> - <assert_contents> - <has_size min="1"/> - </assert_contents> - </element> - <element name="complete_cds" ftype="fasta"> + <element name="complete_genomic_gtf" ftype="gtf"> <assert_contents> <has_size min="1"/> </assert_contents> @@ -64,12 +54,7 @@ <has_size min="1"/> </assert_contents> </element> - <element name="complete_genomic_gtf" ftype="gtf"> - <assert_contents> - <has_size min="1"/> - </assert_contents> - </element> - <element name="complete_proteins" ftype="fasta"> + <element name="complete_cds" ftype="fasta"> <assert_contents> <has_size min="1"/> </assert_contents> @@ -79,12 +64,27 @@ <has_size min="1"/> </assert_contents> </element> - <element name="gnomon_contam_report" ftype="fasta"> + <element name="complete_proteins" ftype="fasta"> + <assert_contents> + <has_size min="1"/> + </assert_contents> + </element> + <element name="annotation_data" ftype="tabular"> <assert_contents> <has_size min="1"/> </assert_contents> </element> - <element name="gnomon_quality_report" ftype="fasta"> + <element name="sra_metadata" ftype="tabular"> + <assert_contents> + <has_size min="1"/> + </assert_contents> + </element> + <element name="gnomon_accept_ftable_annot" ftype="txt"> + <assert_contents> + <has_size min="0"/> + </assert_contents> + </element> + <element name="gnomon_contam_rpt" ftype="tabular"> <assert_contents> <has_size min="1"/> </assert_contents> @@ -94,27 +94,37 @@ <has_size min="1"/> </assert_contents> </element> - <element name="sra_metadata" ftype="binary"> + <element name="gnomon_quality_report" ftype="tabular"> <assert_contents> <has_size min="1"/> </assert_contents> </element> - <element name="feature_counts" ftype="xml"> + <element name="busco_report" ftype="txt"> + <assert_contents> + <has_size min="1"/> + </assert_contents> + </element> + <element name="busco_report_json" ftype="json"> + <assert_contents> + <has_size min="1"/> + </assert_contents> + </element> + <element name="stats_feature_counts" ftype="xml"> <assert_contents> <is_valid_xml/> </assert_contents> </element> - <element name="feature_stats" ftype="xml"> + <element name="stats_feature_stats" ftype="xml"> <assert_contents> <is_valid_xml/> </assert_contents> </element> - <element name="all_unannotated_val" ftype="xml"> + <element name="validated_all_unannotated" ftype="xml"> <assert_contents> - <is_valid_xml/> + <has_size min="0"/> </assert_contents> </element> - <element name="genome_val" ftype="xml"> + <element name="validated_genome" ftype="xml"> <assert_contents> <is_valid_xml/> </assert_contents> @@ -126,11 +136,6 @@ <has_size min="1"/> </assert_contents> </element> - <element name="run_params" ftype="yaml"> - <assert_contents> - <has_size min="1"/> - </assert_contents> - </element> <element name="run_report" ftype="html"> <assert_contents> <has_size min="1"/> @@ -146,6 +151,11 @@ <has_size min="1"/> </assert_contents> </element> + <element name="run_params" ftype="yaml"> + <assert_contents> + <has_size min="1"/> + </assert_contents> + </element> </output_collection> </xml> </macros>
--- a/ncbi_egapx.xml Mon Jun 30 23:21:01 2025 +0000 +++ b/ncbi_egapx.xml Fri Jul 18 00:58:39 2025 +0000 @@ -268,28 +268,30 @@ <data name="complete_genomic_gff" format="gff" label="Final annotation for ${on_string}" from_work_dir="egapx_out/complete.genomic.gff"/> <collection name="output_files" type="list" label="EGAPx output for ${on_string}"> <data name="annotated_genome" format="asn1" label="Final annotation" from_work_dir="egapx_out/annotated_genome.asn"/> - <data name="annotation_data" format="tabular" label="Annotation structured comment" from_work_dir="egapx_out/annotation_data.cmt"/> - <data name="gnomon_accepted" format="txt" label="Gnomon accepted annotation models" from_work_dir="egapx_out/annot_builder_output/accept.ftable_annot"/> + <data name="complete_genomic_gtf" format="gtf" label="Final annotation" from_work_dir="egapx_out/complete.genomic.gtf"/> + <data name="complete_genomic_fna" format="fasta" label="Full genome sequences" from_work_dir="egapx_out/complete.genomic.fna"/> <data name="complete_cds" format="fasta" label="Annotated CDS" from_work_dir="egapx_out/complete.cds.fna"/> - <data name="complete_genomic_fna" format="fasta" label="Full genome sequences" from_work_dir="egapx_out/complete.genomic.fna"/> - <data name="complete_genomic_gtf" format="gtf" label="Final annotation" from_work_dir="egapx_out/complete.genomic.gtf"/> - <data name="complete_proteins" format="fasta" label="Annotated protein products" from_work_dir="egapx_out/complete.proteins.faa"/> <data name="complete_transcripts" format="fasta" label="Annotated transcripts" from_work_dir="egapx_out/complete.transcripts.fna"/> - <data name="gnomon_contam_report" format="tabular" label="Gnomon contamination report" from_work_dir="egapx_out/GNOMON/contam_rpt.tsv"/> - <data name="gnomon_quality_report" format="tabular" label="Gnomon quality report" from_work_dir="egapx_out/GNOMON/new.gnomon_quality_report.txt"/> - <data name="gnomon_report" format="txt" label="Gnomon report" from_work_dir="egapx_out/GNOMON/new.gnomon_report.txt"/> + <data name="complete_proteins" format="fasta" label="Annotated protein products" from_work_dir="egapx_out/complete.proteins.faa"/> + <data name="annotation_data" format="tabular" label="Annotation structured comment" from_work_dir="egapx_out/annotation_data.cmt"/> <data name="sra_metadata" format="tabular" label="SRA run metadata" from_work_dir="egapx_out/sra_metadata.dat"/> - <data name="feature_counts" format="xml" label="Feature counts" from_work_dir="egapx_out/stats/feature_counts.xml"/> - <data name="feature_stats" format="xml" label="Feature stats" from_work_dir="egapx_out/stats/feature_stats.xml"/> - <data name="all_unannotated_val" format="xml" label="all_unannotated" from_work_dir="egapx_out/validated/all_unannotated.val"/> - <data name="genome_val" format="xml" label="all_unannotated" from_work_dir="egapx_out/validated/genome.val"/> + <data name="gnomon_accept_ftable_annot" format="txt" label="Gnomon accepted annotation models" from_work_dir="egapx_out/annot_builder_output/accept.ftable_annot"/> + <data name="gnomon_contam_rpt" format="tabular" label="Gnomon contamination report" from_work_dir="egapx_out/GNOMON/contam_rpt.tsv"/> + <data name="gnomon_report" format="txt" label="Gnomon report" from_work_dir="egapx_out/GNOMON/new.gnomon_report.txt"/> + <data name="gnomon_quality_report" format="tabular" label="Gnomon quality report" from_work_dir="egapx_out/GNOMON/new.gnomon_quality_report.txt"/> + <data name="busco_report" format="txt" label="BUSCO report" from_work_dir="egapx_out/busco/short_summary*.txt"/> + <data name="busco_report_json" format="json" label="BUSCO report (json)" from_work_dir="egapx_out/busco/short_summary*.json"/> + <data name="stats_feature_counts" format="xml" label="Feature counts" from_work_dir="egapx_out/stats/feature_counts.xml"/> + <data name="stats_feature_stats" format="xml" label="Feature stats" from_work_dir="egapx_out/stats/feature_stats.xml"/> + <data name="validated_all_unannotated" format="xml" label="validation all_unannotated" from_work_dir="egapx_out/validated/all_unannotated.val"/> + <data name="validated_genome" format="xml" label="valudation genome" from_work_dir="egapx_out/validated/genome.val"/> </collection> <collection name="nextflow_stats" type="list" label="EGAPx nextflow stats for ${on_string}"> <data name="nextflow_log" format="txt" label="Nextflow execution log" from_work_dir="egapx_out/nextflow/nextflow.log"/> - <data name="run_params" format="yaml" label="Nextflow run parameters" from_work_dir="egapx_out/nextflow/run_params.yaml"/> <data name="run_report" format="html" label="Nextflow execution report" from_work_dir="egapx_out/nextflow/run.report.html"/> <data name="run_timeline" format="html" label="Nextflow execution timeline" from_work_dir="egapx_out/nextflow/run.timeline.html"/> <data name="run_trace" format="tabular" label="Nextflow trace file" from_work_dir="egapx_out/nextflow/run.trace.txt"/> + <data name="run_params" format="yaml" label="Nextflow run parameters" from_work_dir="egapx_out/nextflow/run_params.yaml"/> </collection> <collection name="star_alignments" type="list" label="EGAPx STAR alignments for ${on_string}"> <discover_datasets pattern="(?:.+/)?bam\.[0-9A-Za-z]{10}/(?P<designation>.+)\.bam" format="bam" directory="egapx_out" recurse="true" match_relative_path="true"/> @@ -297,7 +299,7 @@ </collection> </outputs> <tests> - <test expect_num_outputs="20" expect_test_failure="true"> + <test expect_num_outputs="27" expect_test_failure="true"> <conditional name="cond_input_style"> <param name="input_style" value="fillform"/> <conditional name="cond_genome_style"> @@ -315,7 +317,7 @@ </section> <expand macro="test_outputs"/> </test> - <test expect_num_outputs="21" expect_test_failure="true"> + <test expect_num_outputs="27" expect_test_failure="true"> <conditional name="cond_input_style"> <param name="input_style" value="history"/> <param name="yamlin" value="input.yaml"/>
--- a/test-data/input.yaml Mon Jun 30 23:21:01 2025 +0000 +++ b/test-data/input.yaml Fri Jul 18 00:58:39 2025 +0000 @@ -1,6 +1,6 @@ genome: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/020/809/275/GCF_020809275.1_ASM2080927v1/GCF_020809275.1_ASM2080927v1_genomic.fna.gz taxid: 6954 -reads: +short_reads: - https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572_1.gz - https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572_2.gz - https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248_1.gz