Mercurial > repos > richard-burhans > ncbi_egapx
changeset 7:42734f3397cd draft
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 6ae533b0ae510a4a856c14c79219e31a2837daab
| author | richard-burhans |
|---|---|
| date | Fri, 11 Oct 2024 19:54:09 +0000 |
| parents | 3a8a37414e56 |
| children | 908c494fa84e |
| files | ncbi_egapx.xml |
| diffstat | 1 files changed, 23 insertions(+), 4 deletions(-) [+] |
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--- a/ncbi_egapx.xml Wed Sep 11 15:06:07 2024 +0000 +++ b/ncbi_egapx.xml Fri Oct 11 19:54:09 2024 +0000 @@ -109,15 +109,27 @@ </conditional> </inputs> <outputs> - <collection name="egapx_out" type="list" label="Outputs from egapx"> - <discover_datasets pattern="__name_and_ext__" directory="egapx_out" visible="false"/> + <data name="output" format="gff" label="EGAPx annotation for ${on_string}" from_work_dir="egapx_out/accept.gff"/> + <collection name="nextflow_stats" label="EGAPx nextflow stats for ${on_string}" type="list"> + <data name="nf_log" format="txt" label="Nextflow execution log" from_work_dir="egapx_out/nextflow.log"/> + <data name="nf_report" format="html" label="Nextflow execution report" from_work_dir="egapx_out/run.report.html"/> + <data name="nf_trace" format="tabular" label="Nextflow trace file" from_work_dir="egapx_out/run.trace.txt"/> + <data name="nf_timeline" format="html" label="Nextflow execution timeline" from_work_dir="egapx_out/run.timeline.html"/> + <data name="nf_params" format="yaml" label="Nextflow run parameters" from_work_dir="egapx_out/run_params.yaml"/> </collection> </outputs> <tests> <test expect_test_failure="true"> <param name="input_style" value="history"/> <param name="yamlin" value="input.yaml"/> - <output_collection name="egapx_out" type="list" count="8"/> + <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> </test> <test expect_test_failure="true"> <param name="input_style" value="fillform"/> @@ -127,7 +139,14 @@ <param name="rna_type_select" 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="xtra" value="proteins: [] 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_collection name="egapx_out" type="list" count="8"/> + <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> </test> </tests> <help><![CDATA[