--- a/mob_typer.xml	Wed Dec 11 19:17:11 2019 -0500
+++ b/mob_typer.xml	Fri Jun 05 13:02:15 2020 -0400
@@ -1,153 +1,110 @@
-<tool id="mob_typer" name="MOB-Typer" version="2.0.5+galaxy0">
+<tool id="mob_typer" name="MOB-Typer" version="3.0.0">
   <description>Get the plasmid type and mobility given its sequence</description>
   <requirements>
-     <requirement type="package" version="2.0.5">mob_suite</requirement>
+     <requirement type="package" version="3.0.0">mob_suite</requirement>
   </requirements>
   <version_command>mob_typer --version</version_command>
   <command detect_errors="exit_code">
   <![CDATA[
     ln -s '${input}' '${input.name}' &&
     mob_typer  --num_threads \${GALAXY_SLOTS:-4} --infile '${input.name}'
-    ${host_range_detailed}
+
+
+   #if $adv_param.multi
+    --multi
+   #end if 
+
    --min_rep_evalue '$adv_param.min_rep_evalue_value'
    --min_mob_evalue '$adv_param.min_mob_evalue_value'
    --min_con_evalue '$adv_param.min_con_evalue_value'
-   --min_ori_evalue '$adv_param.min_ori_evalue_value'
-   --min_mpf_evalue '$adv_param.min_mpf_evalue'
+   --min_length '$adv_param.min_length'
    --min_rep_ident '$adv_param.min_rep_ident'
    --min_mob_ident '$adv_param.min_mob_ident'
-   --min_ori_ident '$adv_param.min_ori_ident'
-   --min_mpf_ident '$adv_param.min_mpf_ident'
-    --outdir 'outdir';
+
+   --min_con_ident '$adv_param.min_con_ident'
+   --min_rep_cov '$adv_param.min_rep_cov'
+   --min_mob_cov '$adv_param.min_mob_cov'
+   --min_con_cov '$adv_param.min_con_cov'
+   --min_overlap '$adv_param.min_overlap'
+   
+   #if $adv_param.plasmid_db
+   --plasmid_db '$adv_param.plasmid_db'
+   #end if
+
+
+   #if $adv_param.plasmid_mash_db
+   --plasmid_mash_db '$adv_param.plasmid_mash_db'
+   #end if
+
+   #if $adv_param.plasmid_meta
+   --plasmid_meta '$adv_param.plasmid_meta'
+   #end if
+
+   #if $adv_param.repetitive_mask
+   --repetitive_mask '$adv_param.repetitive_mask'
+   #end if
+
+   #if $adv_param.plasmid_mob
+   --plasmid_mob '$adv_param.plasmid_mob'
+   #end if
+   
+   #if $adv_param.plasmid_mpf
+   --plasmid_mpf '$adv_param.plasmid_mpf'
+   #end if
+
+   #if $adv_param.plasmid_orit
+   --plasmid_orit '$adv_param.plasmid_orit'
+   #end if
+
+   #if $adv_param.debug
+   --debug
+   #end if
+
+   --out_file plasmid_report.txt;
+
   ]]>
   </command>
   <inputs>
     <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
-    <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="multi" type="boolean" truevalue="true" falsevalue="" checked="false" label="Treat each input sequence as an independant plasmid?" />
       <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"/> 
       <param name="min_con_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for contig blastn"/> 
-      <param name="min_ori_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for oriT elements blastn"/>
-      <param name="min_mpf_evalue" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for mpf elements blastn"/>
+      <param name="min_length" type="integer" value="1000" label="Minimum length of contigs to classify"/> 
       <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer"  min="0" max="100" value="80"/>
       <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"/>
+      <param name="min_con_ident" label="Minimum sequence identity for contigs" type="integer"  min="0" max="100" value="80"/>
+      <param name="min_rep_cov" label="Minimum percentage coverage of replicon query by input assembly" type="integer"  min="0" max="100" value="80"/>
+      <param name="min_mob_cov" label="Minimum percentage coverage of relaxase query by input assembly" type="integer"  min="0" max="100" value="80"/>
+      <param name="min_con_cov" label="Minimum percentage coverage of assembly contig by the plasmid reference database to be considered" type="integer"  min="0" max="100" value="70"/>
+      <param name="min_overlap" label="Minimum overlap of fragments" type="integer"  min="0" max="100" value="10"/>
+      <param name="debug" type="boolean" truevalue="true" falsevalue="" checked="false" label="Provide debug information?" />
+      <param name="plasmid_db" optional="true" type="data" format="fasta" label="Reference Database of complete plasmids" help=""/>
+      <param name="plasmid_mash_db" optional="true" type="data" format="binary" label="Custom MASH database of plasmids" help="Companion MASH database of reference database"/>
+      <param name="plasmid_meta" type="data" optional="true" format="text" label="Plasmid cluster metadata file" help="MOB-cluster plasmid cluster formatted metadata file matched to the reference plasmid db"/>
+      <param name="plasmid_replicons" type="data" optional="true" format="fasta" label="FASTA file with plasmid replicons" help="FASTA of plasmid replicons"/>
+      <param name="repetitive_mask" type="data" optional="true" format="fasta" label="FASTA of known repetitive elements" help="FASTA of known repetitive elements"/>
+      <param name="plasmid_mob" type="data" optional="true" format="fasta" label="FASTA of plasmid relaxases" help="FASTA of plasmid relaxases"/>
+      <param name="plasmid_mpf" type="data" optional="true" format="fasta" label="FASTA of known plasmid mate-pair proteins" help="FASTA of known plasmid mate-pair proteins"/>
+      <param name="plasmid_orit" type="data" optional="true" format="fasta" label="FASTA of known plasmid oriT dna sequences" help="FASTA of known plasmid oriT dna sequences"/>
     </section>
   </inputs>
   <outputs>
-    <data name="plasmid_report" from_work_dir="outdir/mobtyper*_report.txt" label="${tool.name}: Plasmid report on ${input.element_identifier}"  format="tabular" />
-    <data name="refseq_hostrange_phylogeny_tree" from_work_dir="outdir/*_refseqhostrange_phylogeny_tree.nwk" label="${tool.name} on ${input.element_identifier}: RefSeq Host Range Phylogeny Tree" format="newick">
-      <filter>host_range_detailed</filter>
-    </data>
-    <data name="literature_hostrange_phylogeny_tree" from_work_dir="outdir/*_literaturehostrange_phylogeny_tree.nwk" label="${tool.name} on ${input.element_identifier}: Literature Host Range Phylogeny Tree" format="newick">
-      <filter>host_range_detailed</filter>
-    </data>
-    <data name="refseq_hostrange_ascii_tree" from_work_dir="outdir/*_refseqhostrange_asci_tree.txt" label="${tool.name} on ${input.element_identifier}: RefSeq Host Range ASCII Tree" format="txt">
-      <filter>host_range_detailed</filter>
-    </data>
-    <data name="literature_hostrange_ascii_tree" from_work_dir="outdir/*_literaturehostrange_asci_tree.txt" label="${tool.name} on ${input.element_identifier}: Literature Host Range ASCII Tree" format="txt">
-      <filter>host_range_detailed</filter>
-    </data>
-    <data name="literature_report" from_work_dir="outdir/*_literature_report.txt" label="${tool.name} on ${input.element_identifier}: Literature Report" format="tabular">
-      <filter>host_range_detailed</filter>
-    </data>
-    <data name="refseq_hostrange_report" from_work_dir="outdir/*_refseqhostrange_report.txt" label="${tool.name} on ${input.element_identifier}: RefSeq Host Range Report" format="tabular">
-      <filter>host_range_detailed</filter>
-    </data>
-    <data name="refseq_hostrange_phylostats" from_work_dir="outdir/*_refseqhostrange_phylostats.txt" label="${tool.name} on ${input.element_identifier}: RefSeq Host Range Phylogeny Stats" format="tabular">
-      <filter>host_range_detailed</filter>
-    </data>
+    <data name="plasmid_report" from_work_dir="plasmid_report.txt" label="${tool.name}: Plasmid report on ${input.element_identifier}"  format="tabular" />
   </outputs>
   <tests>
     <test>
-      <param name="input" value="plasmid_476.fasta" ftype="fasta" />
-      <param name="host_range_detailed" value="False" />
+      <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
       <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>
-    <test>
-      <param name="input" value="plasmid_476.fasta" ftype="fasta" />
-      <param name="host_range_detailed" value="True" />
-      <output name="literature_hostrange_phylogeny_tree">
-        <assert_contents>
-          <has_text text="(90371:1,611:1,28144:1)"/> 
-        </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_ascii_tree">
-        <assert_contents>
-          <has_text text="order, Enterobacterales"/>
-          <has_text text="family, Enterobacteriaceae"/>
-          <has_text text="genus, Shigella"/>
-          <has_text text="species, Escherichia coli"/>
-          <has_text text="genus, Serratia"/>
-          <has_text text="species, Serratia marcescens"/>
-          <has_text text="species, Klebsiella pneumoniae"/>
-        </assert_contents>
-      </output>
-    </test>
-    <test>
-      <param name="input" value="plasmid_476.fasta" ftype="fasta" />
-      <param name="host_range_detailed" value="True" />
-      <output name="literature_hostrange_ascii_tree">
-        <assert_contents>
-          <has_text text="family, Enterobacteriaceae"/>
-          <has_text text="species, Escherichia coli"/>
-          <has_text text="species, Klebsiella pneumoniae"/>
-          <has_text text="subspecies, Salmonella enterica subsp. enterica"/>
-        </assert_contents>
-      </output>
-    </test>
-    <test>
-      <param name="input" value="plasmid_476.fasta" ftype="fasta" />
-      <param name="host_range_detailed" value="True" />
-      <output name="literature_report">
-        <assert_contents>
-          <has_text text="IncI1"/>
-          <has_text text="R64"/>
-          <has_text text="pHNRD174"/>
-          <has_text text="pKHSB1"/>
-          <has_text text="pCTXM1-MU2"/>
+          <has_text text="KJ484639"/>
+          <has_text text="MOBP"/>
+          <has_text text="NC_019097"/>
+          <has_text text="conjugative"/>
+          <has_text text="AA474"/>
+          <has_text text="AI614"/>
           <has_text_matching expression="family\tEnterobacteriaceae"/>
-          <has_text_matching expression="order\tEnterobacteriales"/>
-        </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_report">
-        <assert_contents>
-          <has_text text="IncI1"/>
-          <has_text text="Enterobacterales"/> 
-        </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_phylostats">
-        <assert_contents>
-          <has_line_matching expression="rank\tsci_name\tdb_hits\tconvergance_rank\tconvergance_sci_name"/>
-          <has_line_matching expression="family\tEnterobacteriaceae\t351"/>
-          <has_line_matching expression="genus\tSalmonella\t113"/> 
         </assert_contents>
       </output>
     </test>