comparison biohansel.xml @ 7:3360158bb0c5 draft

planemo upload for repository https://github.com/phac-nml/biohansel commit e3553c3c89db60cd285a401bc1c06fdd32665dd2

6:ba6a0af656a6

<tool id="biohansel" name="biohansel" version="2.1.5">
  <description>SNP subtyping of genome sequence reads or assemblies</description>
  <requirements>
    <requirement type="package" version="2.1.1">bio_hansel</requirement>
  </requirements>
  <command detect_errors="exit_code">

  ln -s "$input.paired_collection.forward" $forward_filename &&
  ln -s "$input.paired_collection.reverse" $reverse_filename &&
#end if

## Checking for custom scheme.
#if $type_of_scheme.scheme_type == "custom":
  #if $type_of_scheme.scheme_input.is_of_type('fasta'):
    ln -s '$type_of_scheme.scheme_input' '$type_of_scheme.scheme_input.name' &&
  #end if
#end if

  -O match_results.tab
  -S tech_results.tab
  $dev_args.use_json
  $input_files
  --scheme
#if $type_of_scheme.scheme_type == "custom":
  '$type_of_scheme.scheme_input.name'
#else:
  $type_of_scheme.scheme_type
#end if
#if $subtype_metadata_filename

          label="Paired-end reads collection (FASTQ)"
          />
      </when>
    </conditional>
    <conditional name="type_of_scheme">
      <param name="scheme_type" type="select"
        label="SNP Subtyping Scheme"
        help="Select the SNP subtyping scheme you wish to subtype with">
        <option value="heidelberg">Salmonella Heidelberg subtyping scheme</option>
        <option value="enteritidis">Salmonella Enteritidis subtyping scheme</option>
        <option value="custom">Specify your own custom scheme</option>
      </param>
      <when value="heidelberg"/>
      <when value="enteritidis"/>
      <when value="custom">
        <param name="scheme_input" 
          type="data" format="fasta" 
          label="Your biohansel SNP Subtyping Scheme"/>
      </when>
    </conditional>
    <param name="subtype_metadata"
      type="data" format="tabular,csv"
      optional="true"

7:3360158bb0c5

<tool id="biohansel" name="biohansel" version="2.1.6">
  <description>SNP subtyping of genome sequence reads or assemblies</description>
  <requirements>
    <requirement type="package" version="2.1.1">bio_hansel</requirement>
  </requirements>
  <command detect_errors="exit_code">

  ln -s "$input.paired_collection.forward" $forward_filename &&
  ln -s "$input.paired_collection.reverse" $reverse_filename &&
#end if

## Checking for custom scheme.
#if $type_of_scheme.scheme_check == "custom":
  #if $type_of_scheme.scheme_input.is_of_type('fasta'):
    ln -s '$type_of_scheme.scheme_input' '$type_of_scheme.scheme_input.name' &&
  #end if
#end if

  -O match_results.tab
  -S tech_results.tab
  $dev_args.use_json
  $input_files
  --scheme
#if $type_of_scheme.scheme_check == "custom":
  '$type_of_scheme.scheme_input.name'
#else:
  $type_of_scheme.scheme_type
#end if
#if $subtype_metadata_filename

          label="Paired-end reads collection (FASTQ)"
          />
      </when>
    </conditional>
    <conditional name="type_of_scheme">
      <param name="scheme_check" type="select"
        label="Subtyping Schemes"
        help="Use included scheme or custom">
        <option value="standard">Included Biohansel Schemes</option>
        <option value="custom">Select User Custom Scheme</option>
      </param>
      <when value="standard">
        <param name="scheme_type" type="select"
          label="Included SNP Subtyping Scheme">
          <option value="heidelberg">Salmonella Heidelberg subtyping scheme</option>
          <option value="enteritidis">Salmonella Enteritidis subtyping scheme</option>
        </param>
      </when>
      <when value="custom">
        <param name="scheme_input" 
          type="data" format="fasta" 
          label="Your Custom Biohansel SNP Subtyping Scheme"/>
      </when>
    </conditional>
    <param name="subtype_metadata"
      type="data" format="tabular,csv"
      optional="true"