# HG changeset patch
# User dfornika
# Date 1569431332 14400
# Node ID 0c31aadddc8d84ed5ca65391186c59700ef146c9
# Parent  72c998d3052b208c4163eba47f6a24f7ce8ff81f
planemo upload for repository https://github.com/phac-nml/mob-suite commit 0dd60ac52b9d34ee1f446182eda78cb8c01de6d1-dirty

diff -r 72c998d3052b -r 0c31aadddc8d mob_recon.xml
--- a/mob_recon.xml	Tue Sep 24 19:23:38 2019 -0400
+++ b/mob_recon.xml	Wed Sep 25 13:08:52 2019 -0400
@@ -33,8 +33,6 @@
     --min_con_ident '${adv_param.min_con_ident}'
     --min_rpp_ident '${adv_param.min_rpp_ident}'
     --outdir '.' && 
-    mkdir ./plasmids && (cp plasmid*.fasta ./plasmids 2> /dev/null || true) &&
-    tar -czf plasmids.tar.gz plasmids
   ]]>  
   </command>
   <inputs>
@@ -77,11 +75,9 @@
     <data name="repetitive_element_report" format="tabular" from_work_dir="repetitive_blast_report.txt" label="${tool.name} on ${on_string}: Repetitive elements BLAST report"/>
     <data name="mobtyper_aggregate_report" format="tabular" from_work_dir="mobtyper_aggregate_report.txt" label="${tool.name} on ${on_string}: Aggregate MOB-typer report for all contigs"/>
     <data name="chromosome" format="fasta" from_work_dir="chromosome.fasta" label="${tool.name} on ${on_string}: Chromosome" />
-    <data name="plasmids_zipped" format="zip" from_work_dir="plasmids.zip" label="${tool.name} on ${on_string}: Plasmids (zipped)" />
-    <collection name="plasmids_collection" type="list" label="${tool.name} on ${on_string}: Plasmids (Collection)">
+    <collection name="plasmids_collection" type="list" label="${tool.name} on ${on_string}: Plasmids">
         <discover_datasets pattern="__name_and_ext__" directory="plasmids" />
-    </collection>
-    
+    </collection>    
   </outputs>
   <tests>
     <test>
diff -r 72c998d3052b -r 0c31aadddc8d mob_typer.xml
--- a/mob_typer.xml	Tue Sep 24 19:23:38 2019 -0400
+++ b/mob_typer.xml	Wed Sep 25 13:08:52 2019 -0400
@@ -34,7 +34,7 @@
     </section>  
   </inputs>
   <outputs>
-    <data name="outfile1" label="${tool.name}: Plasmid report on ${input.name}" format="tabular">
+    <data name="mob_typer_report" label="${tool.name}: Plasmid report on ${input.name}" format="tabular">
       <discover_datasets pattern=".+_report\.txt" visible="true" format="tabular" assign_primary_output="true"/>
     </data>  
   </outputs>
diff -r 72c998d3052b -r 0c31aadddc8d mob_typer_zipped.xml
--- a/mob_typer_zipped.xml	Tue Sep 24 19:23:38 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,83 +0,0 @@
-<tool id="mob_typer_zipped" name="MOB-Typer (zipped input)" version="2.0.0">
-  <description>Get the plasmid type and mobility given its sequence</description>
-  <requirements>
-     <requirement type="package" version="2.0.0">mob_suite</requirement>
-  </requirements>   
-  <command detect_errors="exit_code">
-  <![CDATA[
-    tar -xzf "${input}" &&
-    for plasmid in plasmids/*.fasta; do
-      mob_typer  --num_threads \${GALAXY_SLOTS:-4} --infile $plasmid 
-        --min_rep_evalue '$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_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 '.';
-    done
-  ]]>
-  </command>
-  <inputs>
-    <param name="input" type="data" format="zip" label="Input" help="Zipped directory of FASTA fils with contig(s)"/>
-    <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"/> 
-      <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_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"/>
-    </section>  
-  </inputs>
-  <outputs>
-    <data name="mob_typer_report" label="${tool.name}: Plasmid report on ${input.name}" format="tabular">
-      <discover_datasets pattern=".+_report\.txt" visible="true" format="tabular" assign_primary_output="true"/>
-    </data>  
-  </outputs>
-  <tests>
-    <test>
-        <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
-        <assert_stdout>
-            <has_text text="JN253636"/> 
-         </assert_stdout>
-    </test>
-  </tests>
-  <help>
-
-**Syntax**
-
-This tool provides *in-silico* predictions on plasmid typing including identification of replicon, relaxase and mate-pair formation protein types. MOB-typer also predicts mobility of a plasmid (Conjugative, Mobilizable, Non-mobilizable). Do not include multiple unrelated plasmids in the input FASTA file as they will be treated as a single 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 report listing identified plasmid(s) and their predicted mobility. Refer to https://github.com/phac-nml/mob-suite#mob-typer-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>