diff mobsuite_cpo.xml @ 0:917a05a03ac9 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mobsuite_cpo.xml	Tue Aug 14 17:18:49 2018 -0400
@@ -0,0 +1,104 @@
+<tool id="mob_recon" name="MOB-Recon" version="1.4.8">
+  <description>Type contigs and extract plasmid sequences</description>
+  <requirements>
+     <requirement type="package" version="1.4.8">mob_suite</requirement>
+  </requirements>   
+  <command detect_errors="exit_code">
+  <![CDATA[  
+    ln -s "${input}" "${input.name}"; 
+    
+    mob_recon  --num_threads \${GALAXY_SLOTS:-4} --infile "${input.name}" 
+    #if str($adv_param.unicycler_contigs) == "True":
+      --unicycler_contigs 
+    #end if   
+    #if str($adv_param.run_circlator) == "True":
+      --run_circlator 
+    #end if 
+    #if str($adv_param.min_length_condition.min_length_param) == "True":
+      --min_length ${adv_param.min_length_condition.min_length_value}
+    #end if 
+    --run_typer --outdir '.';
+  ]]>  
+  </command>
+  <inputs>
+    <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
+    <section name="adv_param" title="Advanced parameters" expanded="False">
+      <param name="unicycler_contigs" label="Check for circularity flag generated by unicycler in contigs fasta headers" type="select" value="True">
+        <option value="True">Yes</option>
+        <option value="False">No</option>
+      </param>
+      <param name="run_circlator" label="Run circlator minums2 pipeline to check for circular contigs" type="select" value="True">
+        <option value="True">Yes</option>
+        <option value="False">No</option>
+      </param>
+      <conditional name="min_length_condition">
+        <param name="min_length_param" label="Minimum length of contigs to classify" type="select" value="False">
+          <option value="False">No</option>
+          <option value="True">Yes</option>
+       </param>   
+        <when value="True">
+          <param name="min_length_value" type="integer" value="500" min="50"/> 
+        </when>  
+        <when value="False"/>
+      </conditional> 
+    </section>  
+  </inputs>
+  <outputs>
+    <data name="outfile1" format="tabular" from_work_dir="contig_report.txt" label="${tool.name}: Overall contig MOB-recon report"/> 
+    <data name="outfile2" format="tabular" from_work_dir="repetitive_blast_report.txt" label="${tool.name}: Repetitive elements BLAST report"/>
+    <data name="outfile3" format="fasta" from_work_dir="chromosome.fasta" label="${tool.name}: Chromosomal sequences"/>
+    <data name="outfile4" format="tabular" from_work_dir="mobtyper_aggregate_report.txt" label="${tool.name}: Aggregate MOB-typer report for all contigs"/>
+    <data name="outfile5" format="fasta" label="${tool.name}: Plasmid sequence"  hidden="true">
+        <discover_datasets pattern="plasmid_.+\.(?P&lt;ext&gt;.+)" ext="fasta" visible="true" assign_primary_output="false"/>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+        <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
+        <section name="adv_param">
+         <param name="evalue" value="0.00001"/>
+         <param name="unicycler_contigs" value="True"/>
+         <param name="run_circlator"  value="True"/>
+        </section>
+        <output name="outfile1">
+          <assert_contents>
+            <has_text text="NC_019097"/>
+          </assert_contents>  
+        </output> 
+    </test>
+  </tests>
+  <help>
+
+**Syntax**
+
+This tool reconstructs individual plasmid sequences from draft genome assemblies using the plasmid reference databases.
+
+For more information please visit https://github.com/phac-nml/mob-suite/. 
+
+-----
+
+**Input:**
+
+A FASTA file with a single or multiple contigs (e.g. a draft genome assembly):
+
+
+**Output:**
+
+Tab-delimited report listing information for each input contig on its cluster number, possible replicon, relaxase, and repetitive elements types, etc. Refer to https://github.com/phac-nml/mob-suite#mob-recon-contig-report-format for the description of each column.
+
+Note: Plasmid sequences will not be output if none are found. Some plasmid could be intergrated into a chromosome.
+
+
+  </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>