# HG changeset patch
# User dfornika
# Date 1576023021 0
# Node ID 20dc7e1d2f4ccf4624388b86156863096c2d8c3d
# Parent  f286c91a0b92cdb0abea3b959433007aad406d5b
"planemo upload for repository https://github.com/phac-nml/mob-suite commit d6d757cdcd6e012b1cfa9514b8b7157448a2c029-dirty"

diff -r f286c91a0b92 -r 20dc7e1d2f4c mob_hostrange.xml
--- a/mob_hostrange.xml	Thu Nov 21 23:36:10 2019 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,89 +0,0 @@
-<tool id="mob_hostrange" name="MOB-Hostrange" version="2.0.2+galaxy0">
-    <description>
-        Provides information on plasmid reproductive host range and transfer rate using both sequencing
-        and experimental data from public databases (NCBI) and publications (PubMED).
-    </description>
-    <requirements>
-        <requirement type="package" version="2.0.2">mob_suite</requirement>
-    </requirements>   
-    <command detect_errors="exit_code">
-        <![CDATA[
-            mob_hostrange
-              ${exact_match}
-              ${loose_match}
-              ${host_range_detailed}
-              #if str(${replicon_name}) != '':
-                --replicon_name '${replicon_name}'
-              #end if
-              #if str(${relaxase_name}) != '':
-                --relaxase_name '${relaxase_name}'
-              #end if
-              #if str(${relaxase_accession}) != '':
-                --relaxase_accession '${relaxase_accession}'
-              #end if
-              #if str(${cluster_id}) != '':
-                --cluster_id '${cluster_id}'
-              #end if
-              --inputseq '${inputseq}'
-              --outdir '.'
-        ]]>
-    </command>
-    <inputs>
-        <param name="inputseq" type="data" format="fasta" label="Input plasmid" help="plasmid FASTA file"/>
-        <param name="exact_match" type="boolean" truevalue="--exact_match" falsevalue="" checked="false"/>
-        <param name="loose_match" type="boolean" truevalue="--loose_match" falsevalue="" checked="false"/>
-        <param name="host_range_detailed" type="boolean" truevalue="--host_range_detailed" falsevalue="" checked="false"/>
-        <param name="replicon_name" type="text" />
-        <param name="relaxase_name" type="text" />
-        <param name="relaxase_accession" type="text" />
-        <param name="cluster_id" type="text" />
-    </inputs>
-    <outputs>
-        <data name="hostrange_phylostats" label="${tool.name}: Phylostats report on ${input.name}" format="tabular">
-            <discover_datasets pattern=".+hostrange_phylostats\.txt" visible="true" format="tabular" />
-        </data>
-        <data name="hostrange_report" label="${tool.name}: Hostrange report on ${input.name}" format="tabular">
-            <discover_datasets pattern=".+hostrange_report\.txt" visible="true" format="tabular" />
-        </data>
-    </outputs>
-    <tests>
-        <test>
-            <param name="inputseq" value="plasmid_476.fasta" ftype="fasta"/>
-            <assert_stderr>
-                <has_text text="RefSeq Plasmid database found no hits"/> 
-            </assert_stderr>
-        </test>
-    </tests>
-    <help>
-
-        **Syntax**
-
-        This tool provides information on plasmid reproductive host range and transfer rate using both sequencing and experimental data from public databases (NCBI) and publications (PubMED). The predicted host range represents a range of putative hosts where a given plasmid can stably replicate and be maintained by the host. The host range module makes no source attribution predictions of a plasmid.
-
-        For more information please visit https://github.com/phac-nml/mob-suite/. 
-
-        -----
-
-        **Input:**
-
-        A FASTA file with a single or multiple contigs (e.g. plasmid.fasta):
-
-
-        **Output:**
-
-        Tab-delimited reports listing predicted hostrange information. Refer to https://github.com/phac-nml/mob-suite#mob-hostrange-report-file-format for the description of each column.
-
-
-    </help>
-    <citations>
-        <citation type="bibtex">
-            @misc{githubmob-suite,
-            author = {Robertson J, Nash J},
-            title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
-            publisher = {GitHub},
-            journal = {GitHub repository},
-            doi = {10.1099/mgen.0.000206},
-            url = {https://github.com/phac-nml/mob-suite}
-        }</citation>
-    </citations>
-</tool>
diff -r f286c91a0b92 -r 20dc7e1d2f4c mob_recon.xml
--- a/mob_recon.xml	Thu Nov 21 23:36:10 2019 +0000
+++ b/mob_recon.xml	Wed Dec 11 00:10:21 2019 +0000
@@ -1,17 +1,18 @@
-<tool id="mob_recon" name="MOB-Recon" version="2.0.2+galaxy0">
+<tool id="mob_recon" name="MOB-Recon" version="2.0.5+galaxy0">
   <description>Type contigs and extract plasmid sequences</description>
   <requirements>
-     <requirement type="package" version="2.0.2">mob_suite</requirement>
-  </requirements>   
+     <requirement type="package" version="2.0.5">mob_suite</requirement>
+  </requirements>
+  <version_command>mob_recon --version</version_command>
   <command detect_errors="exit_code">
   <![CDATA[  
     #import re
     #import os.path
     
-    #set $named_input = re.sub(r'(\s|\(|\)|:|!)', '_', str($input.element_identifier)+".fasta")
-    ln -s "$input" $named_input && 
+    #set $named_input = re.sub(r'(\s|\(|\)|:|!)', '_', str($input.element_identifier)+'.fasta')
+    ln -s '$input' '$named_input' &&
     
-    mob_recon  --num_threads \${GALAXY_SLOTS:-4}  --infile "${named_input}" 
+    mob_recon  --num_threads \${GALAXY_SLOTS:-4}  --infile '${named_input}'
     #if str($adv_param.unicycler_contigs) == "True":
       --unicycler_contigs 
     #end if   
@@ -19,7 +20,7 @@
       --run_circlator 
     #end if 
     #if str($adv_param.min_length_condition.min_length_param) == "True":
-      --min_length ${adv_param.min_length_condition.min_length_value}
+      --min_length '${adv_param.min_length_condition.min_length_value}'
     #end if 
     --run_typer --min_rep_evalue '${adv_param.min_rep_evalue}'
     --min_rep_evalue '${adv_param.min_rep_evalue}'
@@ -68,7 +69,7 @@
     <data name="contig_report" format="tabular" from_work_dir="outdir/contig_report.txt" label="${tool.name} on ${on_string}: Overall contig MOB-recon report"/> 
     <data name="repetitive_blast_report" format="tabular" from_work_dir="outdir/repetitive_blast_report.txt" label="${tool.name} on ${on_string}: Repetitive elements BLAST report"/>
     <data name="mobtyper_aggregate_report" format="tabular" from_work_dir="outdir/mobtyper_aggregate_report.txt" label="${tool.name} on ${on_string}: Aggregate MOB-typer report for all contigs"/>
-    <data name="chromosome" format="fasta" from_work_dir="outdir/chromosome.fasta" label="${tool.name} on ${on_string}: Chromosome"/>
+    <data name="chromosome" format="fasta" from_work_dir="outdir/chromosome.fasta" label="${tool.name} on ${on_string}: Chromosomal sequences"/>
     <collection name="plasmids" type="list" label="${tool.name} on ${on_string}: Plasmids">
       <discover_datasets pattern="__name_and_ext__" directory="outdir/plasmids" />
     </collection>
diff -r f286c91a0b92 -r 20dc7e1d2f4c mob_typer.xml
--- a/mob_typer.xml	Thu Nov 21 23:36:10 2019 +0000
+++ b/mob_typer.xml	Wed Dec 11 00:10:21 2019 +0000
@@ -1,12 +1,16 @@
-<tool id="mob_typer" name="MOB-Typer" version="2.0.2+galaxy0">
+<tool id="mob_typer" name="MOB-Typer" version="2.0.5+galaxy0">
   <description>Get the plasmid type and mobility given its sequence</description>
   <requirements>
-     <requirement type="package" version="2.0.2">mob_suite</requirement>
-  </requirements>   
+     <requirement type="package" version="2.0.5">mob_suite</requirement>
+  </requirements>
+  <version_command>mob_typer --version</version_command>
   <command detect_errors="exit_code">
   <![CDATA[
-    ln -s "${input}" "${input.name}";
-    mob_typer  --num_threads \${GALAXY_SLOTS:-4} --infile "${input.name}" 
+    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
    --min_rep_evalue '$adv_param.min_rep_evalue_value'
    --min_mob_evalue '$adv_param.min_mob_evalue_value'
    --min_con_evalue '$adv_param.min_con_evalue_value'
@@ -21,6 +25,7 @@
   </command>
   <inputs>
     <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
+    <param name="host_range_detailed" type="boolean" checked="true" label="Perform detailed host range analysis" />
     <section name="adv_param" title="Advanced parameters" expanded="False">
       <param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn"/> 
       <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn"/> 
@@ -35,8 +40,12 @@
   </inputs>
   <outputs>
     <data name="plasmid_report" label="${tool.name}: Plasmid report on ${input.name}" format="tabular">
-      <discover_datasets directory="outdir" pattern=".+_report\.txt" visible="true" format="tabular" assign_primary_output="true"/>
-    </data>  
+      <discover_datasets directory="outdir" pattern="mobtyper.+_report\.txt" visible="true" format="tabular" assign_primary_output="true"/>
+    </data>
+    <data name="refseq_hostrange_phylogeny_tree" label="${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>
+    </data>
   </outputs>
   <tests>
     <test>
diff -r f286c91a0b92 -r 20dc7e1d2f4c test-data/mob_hostrange_._refseqhostrange_phylostats.txt
--- a/test-data/mob_hostrange_._refseqhostrange_phylostats.txt	Thu Nov 21 23:36:10 2019 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-rank	sci_name	db_hits	convergance_rank	convergance_sci_name
diff -r f286c91a0b92 -r 20dc7e1d2f4c test-data/mob_hostrange_._refseqhostrange_report.txt
--- a/test-data/mob_hostrange_._refseqhostrange_report.txt	Thu Nov 21 23:36:10 2019 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-filename	query_replicons	query_mob_cluster_ids	query_relaxase_names	query_relaxase_name_accs	convergance_refseq_rank	convergance_refseq_sci_name
--	None	None	None	None	NA	NA