| Previous changeset 1:2c1cb37a3ffe (2019-05-08) |
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Commit message:
"planemo upload for repository https://github.com/phac-nml/refseq_masher commit 7176dbde2cafbf0858e806923a9f0bd3b2ebf7c0" |
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modified:
contains.xml matches.xml |
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removed:
test-data/SRR1203042_1-head4000-contains.tab test-data/SRR1203042_1-head4000-refseq_masher-matches-m2.tab |
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| diff -r 2c1cb37a3ffe -r 1ec42f033bb4 contains.xml --- a/contains.xml Wed May 08 09:15:56 2019 -0400 +++ b/contains.xml Fri Jun 25 23:38:54 2021 +0000 |
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| @@ -3,7 +3,7 @@ Find NCBI RefSeq Genomes contained in your sequences </description> <requirements> - <requirement type="package" version="0.1.1">refseq_masher</requirement> + <requirement type="package" version="0.1.2">refseq_masher</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[ @@ -157,10 +157,11 @@ <param name="min_identity" value="0.9"/> <param name="max_pvalue" value="0.01"/> </section> - <output name="output_path_tab" - value="SRR1203042_1-head4000-contains.tab" - ftype="tabular" - lines_diff="0"> + <output name="output_path_tab" ftype="tabular"> + <assert_contents> + <has_n_columns n="24" /> + <has_n_lines n="6" /> + </assert_contents> </output> </test> </tests> |
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| diff -r 2c1cb37a3ffe -r 1ec42f033bb4 matches.xml --- a/matches.xml Wed May 08 09:15:56 2019 -0400 +++ b/matches.xml Fri Jun 25 23:38:54 2021 +0000 |
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| @@ -3,7 +3,7 @@ Find closest matching NCBI RefSeq Genomes to your sequences </description> <requirements> - <requirement type="package" version="0.1.1">refseq_masher</requirement> + <requirement type="package" version="0.1.2">refseq_masher</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[ @@ -168,10 +168,11 @@ <param name="output_type" value="tab"/> <param name="min_kmer_threshold" value="2"/> </section> - <output name="output_path_tab" - value="SRR1203042_1-head4000-refseq_masher-matches-m2.tab" - ftype="tabular" - lines_diff="0"> + <output name="output_path_tab" ftype="tabular"> + <assert_contents> + <has_n_columns n="22" /> + <has_n_lines n="2" /> + </assert_contents> </output> </test> </tests> |
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| diff -r 2c1cb37a3ffe -r 1ec42f033bb4 test-data/SRR1203042_1-head4000-contains.tab --- a/test-data/SRR1203042_1-head4000-contains.tab Wed May 08 09:15:56 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -sample top_taxonomy_name identity shared_hashes median_multiplicity pvalue full_taxonomy taxonomic_subspecies taxonomic_species taxonomic_genus taxonomic_family taxonomic_order taxonomic_class taxonomic_phylum taxonomic_superkingdom subspecies serovar plasmid bioproject biosample taxid assembly_accession match_id match_comment -SRR1203042-head4000 Salmonella enterica subsp. enterica serovar Typhimurium 0.934797 136/400 1 0.0 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella; enterica; subsp. enterica; serovar Typhimurium Salmonella enterica subsp. enterica Salmonella enterica Salmonella Enterobacteriaceae Enterobacterales Gammaproteobacteria Proteobacteria Bacteria enterica Typhimurium PRJNA188943 90371 ./rcn/refseq-NG-90371-PRJNA188943-.-.-.-Salmonella_enterica_subsp._enterica_serovar_Typhimurium.fna -SRR1203042-head4000 Salmonella enterica subsp. enterica serovar Typhimurium 0.934797 136/400 1 0.0 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella; enterica; subsp. enterica; serovar Typhimurium Salmonella enterica subsp. enterica Salmonella enterica Salmonella Enterobacteriaceae Enterobacterales Gammaproteobacteria Proteobacteria Bacteria enterica Typhimurium PRJNA188943 90371 ./rcn/refseq-NR-90371-PRJNA188943-.-.-.-Salmonella_enterica_subsp._enterica_serovar_Typhimurium.fna -SRR1203042-head4000 Salmonella enterica subsp. enterica serovar Choleraesuis 0.9326110000000001 131/400 1 0.0 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella; enterica; subsp. enterica; serovar Choleraesuis Salmonella enterica subsp. enterica Salmonella enterica Salmonella Enterobacteriaceae Enterobacterales Gammaproteobacteria Proteobacteria Bacteria enterica Choleraesuis PRJNA188943 119912 ./rcn/refseq-NG-119912-PRJNA188943-.-.-.-Salmonella_enterica_subsp._enterica_serovar_Choleraesuis.fna -SRR1203042-head4000 Salmonella enterica subsp. enterica serovar Choleraesuis 0.9326110000000001 131/400 1 0.0 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella; enterica; subsp. enterica; serovar Choleraesuis Salmonella enterica subsp. enterica Salmonella enterica Salmonella Enterobacteriaceae Enterobacterales Gammaproteobacteria Proteobacteria Bacteria enterica Choleraesuis PRJNA188943 119912 ./rcn/refseq-NR-119912-PRJNA188943-.-.-.-Salmonella_enterica_subsp._enterica_serovar_Choleraesuis.fna -SRR1203042-head4000 Atlantibacter hermannii 0.9224829999999999 110/400 1 0.0 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Atlantibacter; hermannii Atlantibacter hermannii Atlantibacter Enterobacteriaceae Enterobacterales Gammaproteobacteria Proteobacteria Bacteria PRJNA33175 565 ./rcn/refseq-NR-565-PRJNA33175-.-.-.-Escherichia_hermannii.fna |
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| diff -r 2c1cb37a3ffe -r 1ec42f033bb4 test-data/SRR1203042_1-head4000-refseq_masher-matches-m2.tab --- a/test-data/SRR1203042_1-head4000-refseq_masher-matches-m2.tab Wed May 08 09:15:56 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -sample top_taxonomy_name distance pvalue matching full_taxonomy taxonomic_subspecies taxonomic_species taxonomic_genus taxonomic_family taxonomic_order taxonomic_class taxonomic_phylum taxonomic_superkingdom subspecies serovar plasmid bioproject biosample taxid assembly_accession match_id -SRR1203042-head4000 Salmonella enterica subsp. enterica serovar Typhimurium 0.141301 7.688639999999999e-108 22/400 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella; enterica; subsp. enterica; serovar Typhimurium Salmonella enterica subsp. enterica Salmonella enterica Salmonella Enterobacteriaceae Enterobacterales Gammaproteobacteria Proteobacteria Bacteria enterica Typhimurium PRJNA188943 90371 ./rcn/refseq-NR-90371-PRJNA188943-.-.-.-Salmonella_enterica_subsp._enterica_serovar_Typhimurium.fna |