Mercurial > repos > dfornika > mob_suite

changeset 51:4e818dfe0f23 draft default tip

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"planemo upload for repository https://github.com/phac-nml/mob-suite commit ab13ec30d5f68d86e535356ce452230617d4d7d1-dirty"
author dfornika
date Wed, 11 Dec 2019 22:19:55 +0000
parents 82e55a181434
children
files mob_recon.xml mob_typer.xml
diffstat 2 files changed, 86 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/mob_recon.xml	Wed Dec 11 18:41:50 2019 +0000
+++ b/mob_recon.xml	Wed Dec 11 22:19:55 2019 +0000
@@ -66,11 +66,11 @@
     </section>  
   </inputs>
   <outputs>
-    <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 ${on_string}: Chromosomal sequences"/>
-    <collection name="plasmids" type="list" label="${tool.name} on ${on_string}: Plasmids">
+    <data name="contig_report" format="tabular" from_work_dir="outdir/contig_report.txt" label="${tool.name} on ${input.element_identifier}: Overall contig MOB-recon report"/> 
+    <data name="repetitive_blast_report" format="tabular" from_work_dir="outdir/repetitive_blast_report.txt" label="${tool.name} on ${input.element_identifier}: Repetitive elements BLAST report"/>
+    <data name="mobtyper_aggregate_report" format="tabular" from_work_dir="outdir/mobtyper_aggregate_report.txt" label="${tool.name} on ${input.element_identifier}: Aggregate MOB-typer report for all contigs"/>
+    <data name="chromosome" format="fasta" from_work_dir="outdir/chromosome.fasta" label="${tool.name} on ${input.element_identifier}: Chromosomal sequences"/>
+    <collection name="plasmids" type="list" label="${tool.name} on ${input.element_identifier}: Plasmids">
       <discover_datasets pattern="__name_and_ext__" directory="outdir/plasmids" />
     </collection>
   </outputs>
--- a/mob_typer.xml	Wed Dec 11 18:41:50 2019 +0000
+++ b/mob_typer.xml	Wed Dec 11 22:19:55 2019 +0000
@@ -37,11 +37,26 @@
     </section>
   </inputs>
   <outputs>
-    <data name="plasmid_report" from_work_dir="outdir/mobtyper*_report.txt" label="${tool.name}: Plasmid report on ${input.name}"  format="tabular" />
-    <data name="refseq_hostrange_phylogeny_tree" from_work_dir="outdir/*_refseqhostrange_phylogeny_tree.nwk" label="${tool.name} on ${on_string}: RefSeq Host Range Phylogeny Tree" format="newick">
+    <data name="plasmid_report" from_work_dir="outdir/mobtyper*_report.txt" label="${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 ${input.element_identifier}: RefSeq Host Range ASCII Tree" format="txt">
       <filter>host_range_detailed</filter>
     </data>
-    <data name="literature_hostrange_phylogeny_tree" from_work_dir="outdir/*_literaturehostrange_phylogeny_tree.nwk" label="${tool.name} on ${on_string}: Literature Host Range Phylogeny Tree" format="newick">
+    <data name="literature_hostrange_ascii_tree" from_work_dir="outdir/*_literaturehostrange_asci_tree.txt" label="${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>
@@ -73,6 +88,69 @@
         </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>