Mercurial > repos > dfornika > mob_suite
changeset 49:1e4197d25ef6 draft
"planemo upload for repository https://github.com/phac-nml/mob-suite commit e7f174176bcd08b8b4abce84e12262c840bc0db2-dirty"
| author | dfornika |
|---|---|
| date | Wed, 11 Dec 2019 18:04:06 +0000 |
| parents | 20dc7e1d2f4c |
| children | 82e55a181434 |
| files | mob_typer.xml test-data/mobtyper_plasmid_476.fasta_report.txt test-data/plasmid_476.fasta_literature_report.txt test-data/plasmid_476.fasta_literaturehostrange_asci_tree.txt test-data/plasmid_476.fasta_literaturehostrange_phylogeny_tree.nwk test-data/plasmid_476.fasta_refseqhostrange_asci_tree.txt test-data/plasmid_476.fasta_refseqhostrange_phylostats.txt test-data/plasmid_476.fasta_refseqhostrange_report.txt test-data/plasmid_476_refseqhostrange_phylogeny_tree.nwk |
| diffstat | 9 files changed, 127 insertions(+), 10 deletions(-) [+] |
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--- a/mob_typer.xml Wed Dec 11 00:10:21 2019 +0000 +++ b/mob_typer.xml Wed Dec 11 18:04:06 2019 +0000 @@ -8,9 +8,7 @@ <![CDATA[ ln -s '${input}' '${input.name}' && mob_typer --num_threads \${GALAXY_SLOTS:-4} --infile '${input.name}' - #if str($host_range_detailed) == "True": - --host_range_detailed - #end if + ${host_range_detailed} --min_rep_evalue '$adv_param.min_rep_evalue_value' --min_mob_evalue '$adv_param.min_mob_evalue_value' --min_con_evalue '$adv_param.min_con_evalue_value' @@ -25,7 +23,7 @@ </command> <inputs> <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/> - <param name="host_range_detailed" type="boolean" checked="true" label="Perform detailed host range analysis" /> + <param name="host_range_detailed" type="boolean" truevalue="--host_range_detailed" falsevalue="" checked="true" label="Perform detailed host range analysis" /> <section name="adv_param" title="Advanced parameters" expanded="False"> <param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn"/> <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn"/> @@ -36,7 +34,7 @@ <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer" min="0" max="100" value="80"/> <param name="min_ori_ident" label="Minimum sequence identity for oriT elements" type="integer" min="0" max="100" value="90"/> <param name="min_mpf_ident" label="Minimum sequence identity for mpf elements" type="integer" min="0" max="100" value="80"/> - </section> + </section> </inputs> <outputs> <data name="plasmid_report" label="${tool.name}: Plasmid report on ${input.name}" format="tabular"> @@ -44,15 +42,27 @@ </data> <data name="refseq_hostrange_phylogeny_tree" label="${tool.name} on ${on_string}: RefSeq Host Range Phylogeny Tree" format="newick"> <discover_datasets directory="outdir" pattern=".+_refseqhostrange_phylogeny_tree\.nwk" format="newick" /> - <filter>str(host_range_detailed)=='True'</filter> + <!-- <filter>host_range_detailed</filter> --> </data> </outputs> <tests> <test> - <param name="input" value="plasmid_476.fasta" ftype="fasta"/> - <assert_stderr> - <has_text text="CP015838"/> - </assert_stderr> + <param name="input" value="plasmid_476.fasta" ftype="fasta" /> + <param name="host_range_detailed" value="False" /> + <output name="plasmid_report"> + <assert_contents> + <has_text text="000145__HE610900_00001"/> + </assert_contents> + </output> + </test> + <test> + <param name="input" value="plasmid_476.fasta" ftype="fasta" /> + <param name="host_range_detailed" value="True" /> + <output name="refseq_hostrange_phylogeny_tree"> + <assert_contents> + <has_text text="(624:1,984897:1)"/> + </assert_contents> + </output> </test> </tests> <help>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mobtyper_plasmid_476.fasta_report.txt Wed Dec 11 18:04:06 2019 +0000 @@ -0,0 +1,2 @@ +file_id num_contigs total_length gc rep_type(s) rep_type_accession(s) relaxase_type(s) relaxase_type_accession(s) mpf_type mpf_type_accession(s) orit_type(s) orit_accession(s) PredictedMobility mash_nearest_neighbor mash_neighbor_distance mash_neighbor_cluster NCBI-HR-rank NCBI-HR-Name LitRepHRPlasmClass LitPredDBHRRank LitPredDBHRRankSciName LitRepHRRankInPubs LitRepHRNameInPubs LitMeanTransferRate LitClosestRefAcc LitClosestRefDonorStrain LitClosestRefRecipientStrain LitClosestRefTransferRate LitClosestConjugTemp LitPMIDs LitPMIDsNumber LitClosestMashDist +plasmid_476 1 91194 49.86183301532996 IncI1 000145__HE610900_00001 MOBP NC_019097 MPF_I NC_019097_00085,NZ_CM001473_00069,NC_022267_00069,NC_019097_00075,NC_015965_00072,NC_023290_00086,NC_019111_00038,NC_022267_00057,NC_019097_00056 MOBP JN253636 Conjugative CP016520 0.000508006 476 order Enterobacterales NarrowHostRange family Enterobacteriaceae order Enterobacteriales 0.03025255 KJ484639 - - - - 20851899;23333216;25987637;29899511;30761100 5 0.00228199
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plasmid_476.fasta_literature_report.txt Wed Dec 11 18:04:06 2019 +0000 @@ -0,0 +1,2 @@ +LiteratureQueryReplicon LiteratureSearchReplicon LiteratureFoundPlasmidsNames LiteratureFoundPlasmidsNumber LiteratureReportedHostRangePlasmidClass LiteratureReportedHostPlasmidSpecies LiteratureReportedPlasmidHostSpeciesNumber LiteraturePredictedHostRangeTreeRank LiteraturePredictedHostRangeTreeRankSciName LiteratureReportedHostRangeRankInPubs LiteratureReportedHostRangeNameInPubs LiteratureMinTransferRateRange LiteratureMaxTransferRateRange LiteratureMeanTransferRateRange LiteraturePMIDs LiteraturePublicationsNumber LiteratureClosestRefrencePlasmidAcc LiteratureClosestReferencePlasmidName LiteratureClosestReferencePlasmidSize LiteratureClosestReferenceMashDistance LiteratureClosestReferenceDonorStrain LiteratureClosestReferenceRecipientStrain LiteratureClosestReferenceTransferRate LiteratureClosestReferenceConjugationTemperature +IncI1 IncI1 pCMY2,pSD107,pEK204,pKHSB1,pSH1148,p628-CTXM,R64,pHNRD174,pPWD4_103,pND11_107,pEC545_1,pCTXM1-MU2 12 NarrowHostRange Salmonella enterica ,Escherichia coli ,Shigella sonnei,Klebsiella pneumoniae,Escherichia coli,Salmonella enterica 6 family Enterobacteriaceae order Enterobacteriales 5e-06 0.087 0.03025255 20851899;23333216;25987637;29899511;30761100 5 KJ484639 pC23-89 89513 0.00228199 - - - -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plasmid_476.fasta_literaturehostrange_asci_tree.txt Wed Dec 11 18:04:06 2019 +0000 @@ -0,0 +1,12 @@ + + /-species, Shigella sonnei + | + |--species, Escherichia coli + | +-family, Enterobacteriaceae-species, Klebsiella pneumoniae + | + | /-no rank, Salmonella enterica subsp. enterica serovar Typhimurium + | | + \subspecies, Salmonella enterica subsp. enterica-no rank, Salmonella enterica subsp. enterica serovar Heidelberg + | + \-no rank, Salmonella enterica subsp. enterica serovar Derby \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plasmid_476.fasta_literaturehostrange_phylogeny_tree.nwk Wed Dec 11 18:04:06 2019 +0000 @@ -0,0 +1,1 @@ +(624:1,562:1,573:1,(90371:1,611:1,28144:1)1:1); \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plasmid_476.fasta_refseqhostrange_asci_tree.txt Wed Dec 11 18:04:06 2019 +0000 @@ -0,0 +1,68 @@ + + /-species, Shigella sonnei + /genus, Shigella + | \-no rank, Shigella dysenteriae 1 + | + | /-no rank, Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 + | | + | |--no rank, Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1898 + | /no rank, Salmonella enterica subsp. enterica serovar Typhimurium + | | |--no rank, Salmonella enterica subsp. enterica serovar Typhimurium str. CDC 2010K-1587 + | | | + | | \-no rank, Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74 + | | + | | /-no rank, Salmonella enterica subsp. enterica serovar Anatum str. USDA-ARS-USMARC-1781 + | | | + | |-no rank, Salmonella enterica subsp. enterica serovar Anatum-no rank, Salmonella enterica subsp. enterica serovar Anatum str. USDA-ARS-USMARC-1783 + | | | + | | \-no rank, Salmonella enterica subsp. enterica serovar Anatum str. USDA-ARS-USMARC-1727 + | | + | | /-no rank, Salmonella enterica subsp. enterica serovar Heidelberg str. SL476 + | | | + |-species, Salmonella entericasubspecies, Salmonella enterica subsp. entericano rank, Salmonella enterica subsp. enterica serovar Heidelberg-no rank, Salmonella enterica subsp. enterica serovar Heidelberg str. CFSAN002069 + | | | + | | \-no rank, Salmonella enterica subsp. enterica serovar Heidelberg str. 41578 + | | + | |-no rank, Salmonella enterica subsp. enterica serovar Kentucky-no rank, Salmonella enterica subsp. enterica serovar Kentucky str. CVM29188 + | | + | |--no rank, Salmonella enterica subsp. enterica serovar Enteritidis + | | + | |--no rank, Salmonella enterica subsp. enterica serovar Ouakam + | | + | |--no rank, Salmonella enterica subsp. enterica serovar Saintpaul + /family, Enterobacteriaceae | + | | |--no rank, Salmonella enterica subsp. enterica serovar Newport str. CVM 22462 + | | | + | | \-no rank, Salmonella enterica subsp. enterica serovar Cerro str. CFSAN001588 + | | + | | /-no rank, Escherichia coli W + | | | + | | | /-no rank, Escherichia coli O104:H4 str. 2011C-3493 + | | |-no rank, Escherichia coli O104:H4 + | | | \-no rank, Escherichia coli O104:H4 str. C227-11 + | | | + | | |--no rank, Escherichia coli KO11FL + | | | + | | |--no rank, Escherichia coli O25:NM + | | | + | | |--no rank, Escherichia coli UMNK88 + | | | +-order, Enterobacterales |-species, Escherichia coli-no rank, Escherichia coli PCN061 + | | | + | | |--no rank, Escherichia coli B7A + | | | + | | |--no rank, Escherichia coli SE11 + | | | + | | |--no rank, Escherichia coli NCCP15648 + | | | + | | |--no rank, Escherichia coli ETEC 1392/75 + | | | + | | |--no rank, Escherichia coli O119:H6 + | | | + | | \-no rank, Escherichia coli O139:H28 str. E24377A + | | + | \-species, Klebsiella pneumoniae + | + | /-species, Serratia marcescens + \genus, Serratia + \-species, Serratia sp. SCBI \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plasmid_476.fasta_refseqhostrange_phylostats.txt Wed Dec 11 18:04:06 2019 +0000 @@ -0,0 +1,19 @@ +rank sci_name db_hits convergance_rank convergance_sci_name +superkingdom Bacteria 354 +phylum Proteobacteria 354 +class Gammaproteobacteria 354 +order Enterobacterales 354 +family Enterobacteriaceae 351 +family Yersiniaceae 3 +genus Shigella 14 +genus Salmonella 113 +genus Escherichia 221 +genus Serratia 3 +genus Klebsiella 3 +species Shigella sonnei 10 +species Salmonella enterica 113 +species Escherichia coli 221 +species Serratia sp. SCBI 1 +species Klebsiella pneumoniae 3 +species Serratia marcescens 2 +species Shigella dysenteriae 4
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plasmid_476.fasta_refseqhostrange_report.txt Wed Dec 11 18:04:06 2019 +0000 @@ -0,0 +1,2 @@ +filename query_replicons query_mob_cluster_ids query_relaxase_names query_relaxase_name_accs convergance_refseq_rank convergance_refseq_sci_name +plasmid_476.fasta IncI1 476 None None order Enterobacterales
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plasmid_476_refseqhostrange_phylogeny_tree.nwk Wed Dec 11 18:04:06 2019 +0000 @@ -0,0 +1,1 @@ +(((624:1,984897:1)1:1,(((216597:1,1454638:1,1454641:1,909946:1)1:1,(1454596:1,1454583:1,1454584:1)1:1,(454169:1,1271864:1,1124936:1)1:1,(439842:1)1:1,149539:1,1243585:1,90105:1,858305:1,1410916:1)1:1)1:1,(566546:1,(1133852:1,1048254:1)1:1,595495:1,1446707:1,696406:1,1358422:1,340184:1,409438:1,1200752:1,762608:1,397448:1,331111:1)1:1,573:1)1:1,(615:1,488142:1)1:1); \ No newline at end of file