Mercurial > repos > dfornika > mob_suite

changeset 42:bcf6aa9dbc77 draft

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"planemo upload for repository https://github.com/phac-nml/mob-suite commit d5db17429118cd74a85986c49b917caec6f952bd-dirty"
author dfornika
date Thu, 14 Nov 2019 00:47:00 +0000
parents cd69d25ce451
children 21ccebc96bd9
files 1.4/mob_recon.xml 1.4/mob_typer.xml
diffstat 2 files changed, 0 insertions(+), 208 deletions(-) [+]
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--- a/1.4/mob_recon.xml	Thu Nov 14 00:43:21 2019 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,127 +0,0 @@
-<tool id="mob_recon" name="MOB-Recon" version="1.4.9.1+galaxy0">
-  <description>Type contigs and extract plasmid sequences</description>
-  <requirements>
-     <requirement type="package" version="1.4.9.1">mob_suite</requirement>
-  </requirements>   
-  <command detect_errors="exit_code">
-  <![CDATA[  
-    #import re
-    #import os.path
-    
-    #set $named_input = re.sub(r'(\s|\(|\)|:|!)', '_', str($input.element_identifier)+".fasta")
-    ln -s "$input" $named_input && 
-    
-    mob_recon  --num_threads \${GALAXY_SLOTS:-4}  --infile "${named_input}" 
-    #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 ${adv_param.min_length_condition.min_length_value}
-    #end if 
-    --run_typer --min_rep_evalue '${adv_param.min_rep_evalue}'
-    --min_rep_evalue '${adv_param.min_rep_evalue}'
-    --min_mob_evalue '${adv_param.min_mob_evalue}'
-    --min_con_evalue '${adv_param.min_con_evalue}'
-    --min_rep_ident '${adv_param.min_rep_ident}'
-    --min_mob_ident '${adv_param.min_mob_ident}'
-    --min_con_ident  '${adv_param.min_con_ident}'
-    --min_rpp_ident   '${adv_param.min_rpp_ident}'
-    --outdir '.' && 
-    mkdir ./sequences && (cp plasmid*.fasta chromosome.fasta ./sequences 2> /dev/null || true)
-  ]]>  
-  </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 process" 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> 
-      <param name="min_rep_evalue" label="Minimum evalue threshold for replicon blastn" type="float"  min="0.00001" max="1" value="0.00001"/>
-      <param name="min_mob_evalue" label="Minimum evalue threshold for relaxase tblastn" type="float"  min="0.00001" max="1" value="0.00001"/>
-      <param name="min_con_evalue" label="Minimum evalue threshold for contig blastn" type="float"  min="0.00001" max="1" value="0.00001"/>
-      <param name="min_rpp_evalue" label="Minimum evalue threshold for repetitve elements blastn" type="float"  min="0.00001" max="1" value="0.00001"/>
-      <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_con_ident" label="Minimum sequence identity for contigs" type="integer"  min="0" max="100" value="80"/>
-      <param name="min_rpp_ident" label="Minimum sequence identity for repetitive elements" type="integer"  min="0" max="100" value="80"/>
-    </section>  
-  </inputs>
-  <outputs>
-    <data name="outfile1" format="tabular" from_work_dir="contig_report.txt" label="${tool.name} on ${on_string}: Overall contig MOB-recon report"/> 
-    <data name="outfile2" format="tabular" from_work_dir="repetitive_blast_report.txt" label="${tool.name} on ${on_string}: Repetitive elements BLAST report"/>
-    <data name="outfile3" format="tabular" from_work_dir="mobtyper_aggregate_report.txt" label="${tool.name} on ${on_string}: Aggregate MOB-typer report for all contigs"/>
-    <collection name="seqhits" type="list" label="${tool.name} on ${on_string}: Extracted sequences (plasmids,chromosome(s))">
-            <discover_datasets pattern="__name_and_ext__" directory="sequences" />
-    </collection>
-  </outputs>
-  <tests>
-    <test>
-        <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
-        <section name="adv_param">
-         <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/. 
-
-**Workflow**
-
-This preliminary \"Mobilome and Resistome Analysis Workflow\" linking mob_recon with staramr provides reports on mobilome and resistome for a given isolate given a draft genome assembly. The workflow is located in Shared Data --> Workflows --> Mobilome and Resistome Analysis Workflow (MOB-Recon and STARAMR). The workflow file can also be manually downloaded from https://raw.githubusercontent.com/phac-nml/galaxy_tools/master/tools/mob_suite/workflows/AMRworkflow_STARAMR.ga.
-
------
-
-**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>
--- a/1.4/mob_typer.xml	Thu Nov 14 00:43:21 2019 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,81 +0,0 @@
-<tool id="mob_typer" name="MOB-Typer" version="1.4.9.1+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>   
-  <command detect_errors="exit_code">
-  <![CDATA[
-    ln -s "${input}" "${input.name}";
-    mob_typer  --num_threads \${GALAXY_SLOTS:-4} --infile "${input.name}" 
-   --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 '$adv_param.min_mpf_ident'
-    --outdir '.';
-  ]]>
-  </command>
-  <inputs>
-    <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
-    <section name="adv_param" title="Advanced parameters" expanded="False">
-      <param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn"/> 
-      <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn"/> 
-      <param name="min_con_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for contig blastn"/> 
-      <param name="min_ori_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for oriT elements blastn"/>
-      <param name="min_mpf_evalue" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for mpf elements blastn"/>
-      <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer"  min="0" max="100" value="80"/>
-      <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer"  min="0" max="100" value="80"/>
-      <param name="min_ori_ident" label="Minimum sequence identity for oriT elements" type="integer"  min="0" max="100" value="90"/>
-      <param name="min_mpf_ident" label="Minimum sequence identity for mpf elements" type="integer"  min="0" max="100" value="80"/>
-    </section>  
-  </inputs>
-  <outputs>
-    <data name="outfile1" label="${tool.name}: Plasmid report on ${input.name}" format="tabular">
-      <discover_datasets pattern=".+_report\.txt" visible="true" format="tabular" assign_primary_output="true"/>
-    </data>  
-  </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>