diff mob_typer.xml @ 0:f081459f2a15 draft

planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob-suite commit 8bd2d0ff4101e7e7e6a45247d616929593a03cd4

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mob_typer.xml	Fri Feb 21 18:41:02 2025 +0000
@@ -0,0 +1,154 @@
+<tool id="mob_typer" name="MOB-Typer" version="@VERSION@+galaxy0">
+  <description>Get the plasmid type and mobility given its sequence</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="bio_tools"/>
+  <expand macro="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}'
+
+
+   #if $adv_param.multi
+    --multi
+   #end if 
+
+   --min_rep_evalue '$adv_param.min_rep_evalue_value'
+   --min_mob_evalue '$adv_param.min_mob_evalue_value'
+   --min_con_evalue '$adv_param.min_con_evalue_value'
+   --min_length '$adv_param.min_length'
+   --min_rep_ident '$adv_param.min_rep_ident'
+   --min_mob_ident '$adv_param.min_mob_ident'
+
+   --min_con_ident '$adv_param.min_con_ident'
+   --min_rep_cov '$adv_param.min_rep_cov'
+   --min_mob_cov '$adv_param.min_mob_cov'
+   --min_con_cov '$adv_param.min_con_cov'
+   --min_overlap '$adv_param.min_overlap'
+   
+   #if $adv_param.plasmid_db
+   --plasmid_db '$adv_param.plasmid_db'
+   #end if
+
+
+   #if $adv_param.plasmid_mash_db
+   --plasmid_mash_db '$adv_param.plasmid_mash_db'
+   #end if
+
+   #if $adv_param.plasmid_meta
+   --plasmid_meta '$adv_param.plasmid_meta'
+   #end if
+
+   #if $adv_param.repetitive_mask
+   --repetitive_mask '$adv_param.repetitive_mask'
+   #end if
+
+   #if $adv_param.plasmid_mob
+   --plasmid_mob '$adv_param.plasmid_mob'
+   #end if
+   
+   #if $adv_param.plasmid_mpf
+   --plasmid_mpf '$adv_param.plasmid_mpf'
+   #end if
+
+   #if $adv_param.plasmid_orit
+   --plasmid_orit '$adv_param.plasmid_orit'
+   #end if
+
+   #if $adv_param.debug
+   --debug
+   #end if
+   
+   #if $adv_param.biomarker_report_file
+   --biomarker_report_file biomarker_report.txt
+   #end if
+   
+
+   --out_file plasmid_report.txt;
+
+  ]]>
+  </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="multi" type="boolean" truevalue="true" falsevalue="" checked="false" label="Treat each input sequence as an independent plasmid?" help="Treat each sequence in the FASTA file as a separate input (--multi)" />
+      <param name="biomarker_report_file" type="boolean" truevalue="true" falsevalue="" checked="false" label="Output BLAST biomarker report?" help="The report will report all biomarkers identified in a given query plasmid (--biomarker_report_file)" />
+
+      <param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn" help="(--min_rep_evalue)"/> 
+      <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn" help="(--min_mob_evalue)"/> 
+      <param name="min_con_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for contig blastn" help="(--min_con_evalue)"/> 
+      <param name="min_length" type="integer" value="1000" label="Minimum length of contigs to classify (bp)" help="(--min_length)"/> 
+      <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer"  min="0" max="100" value="80" help="(--min_rep_ident)"/>
+      <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer"  min="0" max="100" value="80" help="(--min_mob_ident)"/>
+      <param name="min_con_ident" label="Minimum sequence identity for contigs" type="integer"  min="0" max="100" value="80" help="(--min_con_ident)"/>
+      <param name="min_rep_cov" label="Minimum percentage coverage of replicon query by input assembly" type="integer"  min="0" max="100" value="80" help="(--min_rep_ident)"/>
+      <param name="min_mob_cov" label="Minimum percentage coverage of relaxase query by input assembly" type="integer"  min="0" max="100" value="80" help="(--min_mob_cov)"/>
+      <param name="min_con_cov" label="Minimum percentage coverage of assembly contig by the plasmid reference database to be considered" type="integer"  min="0" max="100" value="70" help="(--min_con_cov)"/>
+      <param name="min_overlap" label="Minimum overlap of fragments (bp)" type="integer"  min="0" max="100" value="10" help="(--min_overlap)"/>
+      <param name="debug" type="boolean" truevalue="true" falsevalue="" checked="false" label="Provide debug information?" help="(--debug)"/>
+      <param name="plasmid_db" optional="true" type="data" format="fasta" label="Reference Database of complete plasmids" help="(--plasmid_db)"/>
+      <param name="plasmid_mash_db" optional="true" type="data" format="binary" label="Custom MASH database of plasmids" help="Custom MASH plasmid reference database (--plasmid_mash_db)"/>
+      <param name="plasmid_meta" type="data" optional="true" format="text" label="Plasmid cluster metadata file" help="MOB-cluster plasmid cluster formatted metadata file matched to the reference plasmid database (--plasmid_meta)"/>
+      <param name="plasmid_replicons" type="data" optional="true" format="fasta" label="FASTA file with plasmid replicons" help="FASTA of plasmid replicons custom database (--plasmid_replicons)"/>
+      <param name="repetitive_mask" type="data" optional="true" format="fasta" label="FASTA of known repetitive elements" help="FASTA of known repetitive elements custom database (--repetitive_mask)"/>
+      <param name="plasmid_mob" type="data" optional="true" format="fasta" label="FASTA of plasmid relaxases" help="FASTA of plasmid relaxases custom database (--plasmid_mob)"/>
+      <param name="plasmid_mpf" type="data" optional="true" format="fasta" label="FASTA of known plasmid mate-pair proteins" help="FASTA of known plasmid mate-pair proteins custom database (--plasmid_mpf)"/>
+      <param name="plasmid_orit" type="data" optional="true" format="fasta" label="FASTA of known plasmid oriT dna sequences" help="FASTA of known plasmid oriT DNA sequences custom database (--plasmid_orit)"/>
+    </section>
+  </inputs>
+  <outputs>
+    <data name="plasmid_report" from_work_dir="plasmid_report.txt" label="${tool.name}: Plasmid report on ${input.element_identifier}"  format="tabular" />
+    <data name="biomarker_report" from_work_dir="biomarker_report.txt" label="${tool.name}: Biomarker report on ${input.element_identifier}"  format="tabular" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
+      <output name="plasmid_report">
+        <assert_contents>
+          <has_text text="KJ484639"/>
+          <has_text text="MOBP"/>
+          <has_text text="NC_019097"/>
+          <has_text text="conjugative"/>
+          <has_text text="AA474"/>
+          <has_text text="AI614"/>
+          <has_text_matching expression="family\tEnterobacteriaceae"/>
+        </assert_contents>
+      </output>
+    </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) and potential host range. 
+
+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 and host range and optionally a biomarker report (if selected). Refer to https://github.com/phac-nml/mob-suite#mob-typer-report-file-format for the description of each column.
+
+**Note:** Do not include multiple unrelated plasmids in the input FASTA file as they will be treated as a single plasmid or turn on the **--multi** parameter (i.e. *Treat each input sequence as an independent plasmid?*).
+  </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>