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diff mob_typer.xml @ 6:9424de64bfa8 draft

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"planemo upload for repository https://github.com/phac-nml/mob-suite commit dc6eaf2675bf842ab7a52c3fdf16d01028cddc9a"
author nml
date Wed, 11 Dec 2019 19:17:11 -0500
parents 09424ec94e80
children 822575bf359f
line wrap: on
line diff
--- a/mob_typer.xml	Wed Nov 13 14:09:11 2019 -0500
+++ b/mob_typer.xml	Wed Dec 11 19:17:11 2019 -0500
@@ -1,12 +1,14 @@
-<tool id="mob_typer" name="MOB-Typer" version="1.4.9.1+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="1.4.9.1">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}'
+    ${host_range_detailed}
    --min_rep_evalue '$adv_param.min_rep_evalue_value'
    --min_mob_evalue '$adv_param.min_mob_evalue_value'
    --min_con_evalue '$adv_param.min_con_evalue_value'
@@ -16,11 +18,12 @@
    --min_mob_ident '$adv_param.min_mob_ident'
    --min_ori_ident '$adv_param.min_ori_ident'
    --min_mpf_ident '$adv_param.min_mpf_ident'
-    --outdir '.';
+    --outdir 'outdir';
   ]]>
   </command>
   <inputs>
     <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
+    <param name="host_range_detailed" type="boolean" truevalue="--host_range_detailed" falsevalue="" checked="true" label="Perform detailed host range analysis" />
     <section name="adv_param" title="Advanced parameters" expanded="False">
       <param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn"/> 
       <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn"/> 
@@ -31,19 +34,122 @@
       <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer"  min="0" max="100" value="80"/>
       <param name="min_ori_ident" label="Minimum sequence identity for oriT elements" type="integer"  min="0" max="100" value="90"/>
       <param name="min_mpf_ident" label="Minimum sequence identity for mpf elements" type="integer"  min="0" max="100" value="80"/>
-    </section>  
+    </section>
   </inputs>
   <outputs>
-    <data name="outfile1" label="${tool.name}: Plasmid report on ${input.name}" format="tabular">
-      <discover_datasets pattern=".+_report\.txt" visible="true" format="tabular" assign_primary_output="true"/>
-    </data>  
+    <data name="plasmid_report" from_work_dir="outdir/mobtyper*_report.txt" label="${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>
   </outputs>
   <tests>
     <test>
-        <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
-        <assert_stdout>
-            <has_text text="JN253636"/> 
-         </assert_stdout>
+      <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>
+    <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_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>
   </tests>
   <help>