comparison mob_recon.xml @ 6:9424de64bfa8 draft

"planemo upload for repository https://github.com/phac-nml/mob-suite commit dc6eaf2675bf842ab7a52c3fdf16d01028cddc9a"

5:09424ec94e80

<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="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**

6:9424de64bfa8

<tool id="mob_recon" name="MOB-Recon" version="2.0.5+galaxy0">
  <description>Type contigs and extract plasmid sequences</description>
  <requirements>
     <requirement type="package" version="2.0.5">mob_suite</requirement>
  </requirements>
  <version_command>mob_recon --version</version_command>
  <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 'outdir' &&
    mkdir ./outdir/plasmids && (mv outdir/plasmid*.fasta ./outdir/plasmids 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="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="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>
  <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="contig_report">
        <assert_contents>
          <has_text text="NC_019097"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help>

**Syntax**