# HG changeset patch
# User dfornika
# Date 1576087446 0
# Node ID 1e4197d25ef6ebff10ed19724ea85a0625daab39
# Parent  20dc7e1d2f4ccf4624388b86156863096c2d8c3d
"planemo upload for repository https://github.com/phac-nml/mob-suite commit e7f174176bcd08b8b4abce84e12262c840bc0db2-dirty"

diff -r 20dc7e1d2f4c -r 1e4197d25ef6 mob_typer.xml
--- 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>
diff -r 20dc7e1d2f4c -r 1e4197d25ef6 test-data/mobtyper_plasmid_476.fasta_report.txt
--- /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
diff -r 20dc7e1d2f4c -r 1e4197d25ef6 test-data/plasmid_476.fasta_literature_report.txt
--- /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	-	-	-	-
diff -r 20dc7e1d2f4c -r 1e4197d25ef6 test-data/plasmid_476.fasta_literaturehostrange_asci_tree.txt
--- /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
diff -r 20dc7e1d2f4c -r 1e4197d25ef6 test-data/plasmid_476.fasta_literaturehostrange_phylogeny_tree.nwk
--- /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
diff -r 20dc7e1d2f4c -r 1e4197d25ef6 test-data/plasmid_476.fasta_refseqhostrange_asci_tree.txt
--- /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
diff -r 20dc7e1d2f4c -r 1e4197d25ef6 test-data/plasmid_476.fasta_refseqhostrange_phylostats.txt
--- /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
diff -r 20dc7e1d2f4c -r 1e4197d25ef6 test-data/plasmid_476.fasta_refseqhostrange_report.txt
--- /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
diff -r 20dc7e1d2f4c -r 1e4197d25ef6 test-data/plasmid_476_refseqhostrange_phylogeny_tree.nwk
--- /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