| Previous changeset 9:3bbe70fef6df (2023-12-11) Next changeset 11:9c15ca7e764e (2024-06-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 737d7e9a31c9d340a38ddfef3ac20847989718e0 |
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modified:
funannotate_annotate.xml |
| b |
| diff -r 3bbe70fef6df -r d0336d67702b funannotate_annotate.xml --- a/funannotate_annotate.xml Mon Dec 11 19:18:59 2023 +0000 +++ b/funannotate_annotate.xml Sun Feb 11 00:08:00 2024 +0000 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="funannotate_annotate" name="Funannotate functional" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n+<tool id="funannotate_annotate" name="Funannotate functional" profile="20.01" version="@TOOL_VERSION@+galaxy5">\n <description>annotation</description>\n <macros>\n <import>macros.xml</import>\n@@ -72,27 +72,14 @@\n \n &&\n \n-## funannotate sometimes leaves multiple *part.tbl and *part.sqn files\n+## Funannotate sometimes leaves multiple *part.tbl and *part.sqn files:\n ## https://github.com/nextgenusfs/funannotate/issues/777\n+## The partial tbl files are combined by funannotate and are deleted below.\n+## The sqn files are discrete and are collected with discover_datasets.\n find output/annotate_results \n--regex ".*part_[0-9]+\\.\\(sqn\\|tbl\\)$"\n+-regex ".*part_[0-9]+\\.\\(tbl\\)$"\n -delete\n \n-&&\n-\n-mv output/annotate_results/*.gbk out.gbk &&\n-mv output/annotate_results/*.annotations.txt out.annotations.txt &&\n-mv output/annotate_results/*.contigs.fsa out.contigs.fsa &&\n-mv output/annotate_results/*.agp out.agp &&\n-mv output/annotate_results/*.tbl out.tbl &&\n-mv output/annotate_results/*.sqn out.sqn &&\n-mv output/annotate_results/*.scaffolds.fa out.scaffolds.fa &&\n-mv output/annotate_results/*.proteins.fa out.proteins.fa &&\n-mv output/annotate_results/*.mrna-transcripts.fa out.mrna-transcripts.fa &&\n-mv output/annotate_results/*.cds-transcripts.fa out.cds-transcripts.fa &&\n-mv output/annotate_results/*.gff3 out.gff3 &&\n-mv output/annotate_results/*.discrepency.report.txt out.discrepency.report.txt &&\n-mv output/annotate_results/*.stats.json out.stats.json\n ]]></command>\n <inputs>\n \n@@ -164,43 +151,44 @@\n </param>\n </inputs>\n <outputs>\n- <data name=\'gbk\' format=\'genbank\' label="${tool.name} on ${on_string}: annotated genome (genbank)" from_work_dir="out.gbk">\n+ <data name=\'gbk\' format=\'genbank\' label="${tool.name} on ${on_string}: annotated genome (genbank)" from_work_dir="output/annotate_results/*.gbk">\n <filter>outputs and \'gbk\' in outputs</filter>\n </data>\n- <data name=\'annot\' format=\'tabular\' label="${tool.name} on ${on_string}: all annotations" from_work_dir="out.annotations.txt">\n+ <data name=\'annot\' format=\'tabular\' label="${tool.name} on ${on_string}: all annotations" from_work_dir="output/annotate_results/*.annotations.txt">\n <filter>outputs and \'annotations\' in outputs</filter>\n </data>\n- <data name=\'contigs_fsa\' format=\'fasta\' label="${tool.name} on ${on_string}: contigs fasta, split at gaps" from_work_dir="out.contigs.fsa">\n+ <data name=\'contigs_fsa\' format=\'fasta\' label="${tool.name} on ${on_string}: contigs fasta, split at gaps" from_work_dir="output/annotate_results/*.contigs.fsa">\n <filter>outputs and \'contigs_fsa\' in outputs</filter>\n </data>\n- <data name=\'agp\' format=\'tabular\' label="${tool.name} on ${on_string}: AGP file" from_work_dir="out.agp">\n+ <data name=\'agp\' format=\'tabular\' label="${tool.name} on ${on_string}: AGP file" from_work_dir="output/annotate_results/*.agp">\n <filter>outputs and \'agp\' in outputs</filter>\n </data>\n- <data name=\'tbl\' format=\'txt\' label="${tool.name} on ${on_string}: NCBI tbl annotation file" from_work_dir="out.tbl">\n+ <data name=\'tbl\' format=\'txt\' label="${tool.name} on ${on_string}: NCBI tbl annotation file" from_work_dir="output/annotate_results/*.tbl">\n <filter>outputs and \'tbl\' in outputs</filter>\n </data>\n- <data name=\'sqn\' format=\'txt\' label="${tool.name} on ${on_string}: NCBI Sequin genome" from_work_dir="out.sqn">\n+ <collection name="sqn" type="list" label="${tool.name} on ${on_string}: NCBI Sequin genome files">\n+ <discover_datasets pattern="(?P<designation>.+)\\.sqn" directory="output/annotate_results" format="txt" recurse="false"/>\n <filter>outputs and \'sqn\' in outputs</filter>\n- </data'..b'\' label="${tool.name} on ${on_string}: protein sequences" from_work_dir="out.proteins.fa">\n+ <data name=\'fa_proteins\' format=\'fasta\' label="${tool.name} on ${on_string}: protein sequences" from_work_dir="output/annotate_results/*.proteins.fa">\n <filter>outputs and \'proteins_fa\' in outputs</filter>\n </data>\n- <data name=\'fa_transcripts_mrna\' format=\'fasta\' label="${tool.name} on ${on_string}: transcript mRNA sequences" from_work_dir="out.mrna-transcripts.fa">\n+ <data name=\'fa_transcripts_mrna\' format=\'fasta\' label="${tool.name} on ${on_string}: transcript mRNA sequences" from_work_dir="output/annotate_results/*.mrna-transcripts.fa">\n <filter>outputs and \'mrna_transcripts_fa\' in outputs</filter>\n </data>\n- <data name=\'fa_transcripts_cds\' format=\'fasta\' label="${tool.name} on ${on_string}: transcript CDS sequences" from_work_dir="out.cds-transcripts.fa">\n+ <data name=\'fa_transcripts_cds\' format=\'fasta\' label="${tool.name} on ${on_string}: transcript CDS sequences" from_work_dir="output/annotate_results/*.cds-transcripts.fa">\n <filter>outputs and \'cds_transcripts_fa\' in outputs</filter>\n </data>\n- <data name=\'gff3\' format=\'gff3\' label="${tool.name} on ${on_string}: annotation (GFF3)" from_work_dir="out.gff3">\n+ <data name=\'gff3\' format=\'gff3\' label="${tool.name} on ${on_string}: annotation (GFF3)" from_work_dir="output/annotate_results/*.gff3">\n <filter>outputs and \'gff3\' in outputs</filter>\n </data>\n- <data name=\'tbl2asn_report\' format=\'txt\' label="${tool.name} on ${on_string}: tbl2asn summary report of annotated genome" from_work_dir="out.discrepency.report.txt">\n+ <data name=\'tbl2asn_report\' format=\'txt\' label="${tool.name} on ${on_string}: tbl2asn summary report of annotated genome" from_work_dir="output/annotate_results/*.discrepency.report.txt">\n <filter>outputs and \'discrepency\' in outputs</filter>\n </data>\n- <data name=\'stats\' format=\'json\' label="${tool.name} on ${on_string}: stats" from_work_dir="out.stats.json">\n+ <data name=\'stats\' format=\'json\' label="${tool.name} on ${on_string}: stats" from_work_dir="output/annotate_results/*.stats.json">\n <filter>outputs and \'gbk\' in outputs</filter>\n </data>\n <data name=\'must_fix\' format=\'json\' label="${tool.name} on ${on_string}: Gene Name/Product must-fix" from_work_dir="output/annotate_results/Gene2Products.must-fix.txt">\n@@ -248,11 +236,13 @@\n <has_text text="locus_tag" />\n </assert_contents>\n </output>\n- <output name="sqn">\n- <assert_contents>\n- <has_text text="Seq-submit" />\n- </assert_contents>\n- </output>\n+ <output_collection name="sqn" type="list">\n+ <element name="Genus_species">\n+ <assert_contents>\n+ <has_text text="Seq-submit" />\n+ </assert_contents>\n+ </element> \n+ </output_collection>\n <output name="fa_scaffolds">\n <assert_contents>\n <has_text text=">sample" />\n@@ -340,11 +330,13 @@\n <has_text text="locus_tag" />\n </assert_contents>\n </output>\n- <output name="sqn">\n- <assert_contents>\n- <has_text text="Seq-submit" />\n- </assert_contents>\n- </output>\n+ <output_collection name="sqn" type="list">\n+ <element name="Genus_species">\n+ <assert_contents>\n+ <has_text text="Seq-submit" />\n+ </assert_contents>\n+ </element> \n+ </output_collection>\n <output name="fa_scaffolds">\n <assert_contents>\n <has_text text=">sample" />\n' |