view seqtk_nml.xml @ 1:f49992c79fe4 draft default tip

planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 969557932bff35913d93068d16facb8da4d64123

<tool id="seqtk_nml_sample" name="seqTK Sample NML" version="1.0.1">
  <description>Runs seqTK sample if raw coverage is above user defined threshold </description>
  <requirements>
    <requirement type="package" version="1.2">seqtk</requirement>
    <requirement type="package" version="1.6.924">perl-bioperl</requirement>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[
    perl  '$__tool_directory__/seqtk_nml.pl'

    --ref '$fastar' 

    #if $single_or_paired.type == "single"
    --type single
    --forward '$input_se'
    --out_forward '$output'

    #elif $single_or_paired.type == "paired"
    --type paired
    --forward '$single_or_paired.forward_pe'
    --reverse '$single_or_paired.reverse_pe'
    --out_forward '$output' 
    --out_reverse '$output_rev'
    
    #else
    --type paired
    --forward '$single_or_paired.fastq_collection.forward' 
    --reverse '$single_or_paired.fastq_collection.reverse'
    --out_forward '$output_collection.forward' 
    --out_reverse '$output_collection.reverse'
    #end if

    --cov '$coverage'
    --log '$log'

    ]]></command>
  <inputs>
    <conditional name="single_or_paired">
      <param name="type" type="select" label="Read type">
       <option value="single">Single-end</option>
       <option value="paired">Paired-end</option>
       <option value="collection">Collection Paired-end</option>
     </param>
     <when value="single">
       <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/>
     </when>
     <when value="paired">
       <param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/>
       <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/>
     </when>
     <when value="collection">
      <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="txt" collection_type="paired" />
    </when>
  </conditional>
  <param name="fastar" type="data" label="Fasta Reference File" format="fasta" />
  <param name="coverage" type="integer" label="Desired Coverage" value="50" />
</inputs>
<outputs>
  <data format="fastqsanger" name="output" label="SubSampled Fastq" >
    <filter>single_or_paired['type']!="collection"</filter>
  </data>
  <data format="fastqsanger" name="output_rev" label="SubSampled Fastq Reverse">
    <filter>single_or_paired['type']=="paired"</filter>
  </data>
  <collection name="output_collection" type="paired" label="SubSampled Fastqs">
    <data name="forward" format="fastqsanger"/>
    <data name="reverse" format="fastqsanger"/>
    <filter>single_or_paired['type']=="collection"</filter>
  </collection>
  <data format="txt" name="log" label="Log file"/>
</outputs>

<tests>
  <test>
    <param name="type" value="paired" />
    <param name="forward_pe" value="inputforward.fastq" />
    <param name="reverse_pe" value="inputreverse.fastq" />
    <param name="fastar" value="testref.fasta"/>
    <param name="coverage" value="50" />
    <output name="output" file="outputforward.fastq" />
    <output name="output_rev" file="outputreverse.fastq" />
    <output name="log" file="lognosample.log" />
  </test>
  <test>
    <param name="type" value="paired" />
    <param name="forward_pe" value="inputforward.fastq" />
    <param name="reverse_pe" value="inputreverse.fastq" />
    <param name="fastar" value="testref.fasta"/>
    <param name="coverage" value="25" />
    <output name="output" file="outputdownsamepleforward.fastq" />
    <output name="output_rev" file="outputdownsameplereverse.fastq" />
    <output name="log" file="logdownsample.log" />
  </test>
</tests>
<help><![CDATA[
============
What it does
============
Calculates raw coverage. If the raw coverage is greater than desired coverage, runs seqTK sample to generate downsampled reads. 

=====
Usage
=====

**Parameters**
- Fastq reads (single end, paired end, or paired end collection)
- Fasta reference file

**Options**
- Desired coverage (50)
]]></help>
<citations>
  <citation type="doi">10.1371/journal.pone.0163962</citation>
</citations>
</tool>