Mercurial > repos > richard-burhans > ncbi_egapx
changeset 29:8ada50a892fa draft default tip
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit f2b75ca7f0f40a117d37ec27c1fc48047c014823
| author | richard-burhans |
|---|---|
| date | Thu, 23 Jan 2025 21:23:14 +0000 |
| parents | 27b73b9f84c0 |
| children | |
| files | macros.xml ncbi_egapx.xml test-data/input.yaml |
| diffstat | 3 files changed, 117 insertions(+), 74 deletions(-) [+] |
line wrap: on
line diff
--- a/macros.xml Thu Jan 16 18:30:47 2025 +0000 +++ b/macros.xml Thu Jan 23 21:23:14 2025 +0000 @@ -5,7 +5,7 @@ </requirements> </xml> <token name="@TOOL_VERSION@">0.3.2-alpha</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@VERSION_SUFFIX@">3</token> <token name="@PROFILE@">23.0</token> <xml name="edam_ontology"> <edam_operations> @@ -32,4 +32,95 @@ <person givenName="Richard" familyName="Burhans" url="https://science.psu.edu/bmb/people/rcb112"/> </creator> </xml> + <xml name="test_outputs"> + <output name="complete_genomic_gff" ftype="gff"> + <assert_contents> + <has_size min="1"/> + </assert_contents> + </output> + <output_collection name="output_files" type="list"> + <element name="complete_genomic_gtf" ftype="gtf"> + <assert_contents> + <has_size min="1"/> + </assert_contents> + </element> + <element name="complete_genomic_fna" ftype="fasta"> + <assert_contents> + <has_size min="1"/> + </assert_contents> + </element> + <element name="complete_cds" ftype="fasta"> + <assert_contents> + <has_size min="1"/> + </assert_contents> + </element> + <element name="complete_transcripts" ftype="fasta"> + <assert_contents> + <has_size min="1"/> + </assert_contents> + </element> + <element name="complete_proteins" ftype="fasta"> + <assert_contents> + <has_size min="1"/> + </assert_contents> + </element> + <element name="annotated_genome" ftype="asn1"> + <assert_contents> + <has_size min="1"/> + </assert_contents> + </element> + <element name="accept_ftable_annot" ftype="txt"> + <assert_contents> + <has_size min="1"/> + </assert_contents> + </element> + <element name="annotation_data_cmt" ftype="tabular"> + <assert_contents> + <has_size min="1"/> + </assert_contents> + </element> + <element name="feature_counts" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </element> + <element name="feature_stats" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </element> + <element name="genome_val" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </element> + </output_collection> + <output_collection name="nextflow_stats" type="list"> + <element name="run_report" ftype="html"> + <assert_contents> + <has_size min="1"/> + </assert_contents> + </element> + <element name="run_timeline" ftype="html"> + <assert_contents> + <has_size min="1"/> + </assert_contents> + </element> + <element name="nextflow_log" ftype="txt"> + <assert_contents> + <has_size min="1"/> + </assert_contents> + </element> + <element name="run_trace" ftype="tabular"> + <assert_contents> + <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 Thu Jan 16 18:30:47 2025 +0000 +++ b/ncbi_egapx.xml Thu Jan 23 21:23:14 2025 +0000 @@ -99,6 +99,7 @@ #if $cond_input_style.cond_rnaseq_style.rnaseq_style == "history" reads: $reads_config #else +reads: #set reads_values = $rnaseq.split() #for $read in [str(rv).strip() for rv in $reads_values] - $read @@ -179,13 +180,27 @@ </conditional> </inputs> <outputs> - <data name="output" format="gff" label="EGAPx annotation for ${on_string}" from_work_dir="egapx_out/complete.genomic.gff"/> + <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="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_transcripts" format="fasta" label="Annotated transcripts" from_work_dir="egapx_out/complete.transcripts.fna"/> + <data name="complete_proteins" format="fasta" label="Annotated proteins" from_work_dir="egapx_out/complete.proteins.faa"/> + <data name="annotated_genome" format="asn1" label="Final annotation" from_work_dir="egapx_out/annotated_genome.asn"/> + <data name="accept_ftable_annot" format="txt" label="Accepted annotation models" from_work_dir="egapx_out/annot_builder_output/accept.ftable_annot"/> + <data name="annotation_data_cmt" format="tabular" label="Structured Comment" from_work_dir="egapx_out/annotation_data.cmt"/> + <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="" from_work_dir="egapx_out/validated/all_unannotated.val"/> + <data name="genome_val" format="xml" label="" from_work_dir="egapx_out/validated/genome.val"/> + </collection> <collection name="nextflow_stats" type="list" label="EGAPx nextflow stats for ${on_string}"> - <data name="nf_report" format="html" label="Nextflow execution report" from_work_dir="egapx_out/run.report.html"/> - <data name="nf_timeline" format="html" label="Nextflow execution timeline" from_work_dir="egapx_out/run.timeline.html"/> - <data name="nf_log" format="txt" label="Nextflow execution log" from_work_dir="egapx_out/nextflow.log"/> - <data name="nf_trace" format="tabular" label="Nextflow trace file" from_work_dir="egapx_out/run.trace.txt"/> - <data name="nf_params" format="yaml" label="Nextflow run parameters" from_work_dir="egapx_out/run_params.yaml"/> + <data name="run_report" format="html" label="Nextflow execution report" from_work_dir="egapx_out/run.report.html"/> + <data name="run_timeline" format="html" label="Nextflow execution timeline" from_work_dir="egapx_out/run.timeline.html"/> + <data name="nextflow_log" format="txt" label="Nextflow execution log" from_work_dir="egapx_out/nextflow.log"/> + <data name="run_trace" format="tabular" label="Nextflow trace file" from_work_dir="egapx_out/run.trace.txt"/> + <data name="run_params" format="yaml" label="Nextflow run parameters" from_work_dir="egapx_out/run_params.yaml"/> </collection> </outputs> <tests> @@ -195,76 +210,13 @@ <param name="genome_style" value="uri"/> <param name="uri" value="https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/020/809/275/GCF_020809275.1_ASM2080927v1/GCF_020809275.1_ASM2080927v1_genomic.fna.gz"/> <param name="rnaseq_style" value="list"/> - <param name="rnaseq" value="https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572.1 https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572.2 https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248.1 https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248.2"/> - <param name="extra" value="hmm: https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/gnomon/hmm_parameters/6956.params tasks: star_wnode: star_wnode: -cpus-per-worker 4"/> - <output name="output"> - <assert_contents> - <has_size min="1"/> - </assert_contents> - </output> - <output_collection name="nextflow_stats" type="list"> - <element name="nf_log"> - <assert_contents> - <has_size min="1"/> - </assert_contents> - </element> - <element name="nf_report"> - <assert_contents> - <has_size min="1"/> - </assert_contents> - </element> - <element name="nf_trace"> - <assert_contents> - <has_size min="1"/> - </assert_contents> - </element> - <element name="nf_timeline"> - <assert_contents> - <has_size min="1"/> - </assert_contents> - </element> - <element name="nf_params"> - <assert_contents> - <has_size min="1"/> - </assert_contents> - </element> - </output_collection> + <param name="rnaseq" value="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 https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248_2.gz"/> + <expand macro="test_outputs"/> </test> <test expect_test_failure="true"> <param name="input_style" value="history"/> <param name="yamlin" value="input.yaml"/> - <output name="output"> - <assert_contents> - <has_size min="1"/> - </assert_contents> - </output> - <output_collection name="nextflow_stats" type="list"> - <element name="nf_log"> - <assert_contents> - <has_size min="1"/> - </assert_contents> - </element> - <element name="nf_report"> - <assert_contents> - <has_size min="1"/> - </assert_contents> - </element> - <element name="nf_trace"> - <assert_contents> - <has_size min="1"/> - </assert_contents> - </element> - <element name="nf_timeline"> - <assert_contents> - <has_size min="1"/> - </assert_contents> - </element> - <element name="nf_params"> - <assert_contents> - <has_size min="1"/> - </assert_contents> - </element> - </output_collection> + <expand macro="test_outputs"/> </test> </tests> <help><![CDATA[
--- a/test-data/input.yaml Thu Jan 16 18:30:47 2025 +0000 +++ b/test-data/input.yaml Thu Jan 23 21:23:14 2025 +0000 @@ -1,4 +1,4 @@ -genome: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/020/809/275/GCA_020809275.1_ASM2080927v1/GCA_020809275.1_ASM2080927v1_genomic.fna.gz +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: - https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572_1.gz