annotate fastq_paired_end_interlacer.xml @ 1:ec6ddf449651 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit a5821127c24ed3bf1e9d5ba4fb8b9f3eceb0f3f3

<tool id="fastq_paired_end_interlacer" name="FASTQ interlacer" version="1.2">
  <description>on paired end reads</description>
  <requirements>
    <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>
  </requirements>
  <command>
python $__tool_directory__/fastq_paired_end_interlacer.py
#if $reads.reads_selector == 'paired'
    '${reads.input1_file}' ${reads.input1_file.extension[len('fastq'):]} '${reads.input2_file}' ${reads.input2_file.extension[len('fastq'):]}
#else
    '${reads.reads_coll.forward}' ${reads.reads_coll.forward.extension[len('fastq'):]} '${reads.reads_coll.reverse}' ${reads.reads_coll.reverse.extension[len('fastq'):]}
#end if
'$outfile_pairs' '$outfile_singles'
  </command>
  <inputs>
    <conditional name="reads">
      <param name="reads_selector" type="select" label="Type of paired-end datasets">
        <option value="paired">2 separate datasets</option>
        <option value="paired_collection">1 paired dataset collection</option>
      </param>
      <when value="paired">
        <param name="input1_file" type="data" format="fastqsanger,fastqcssanger" label="Left-hand mates" />
        <param name="input2_file" type="data" format="fastqsanger,fastqcssanger" label="Right-hand mates" />
      </when>
      <when value="paired_collection">
        <param name="reads_coll" type="data_collection" collection_type="paired" format="fastqsanger,fastqcssanger" label="Paired-end reads collection" />
      </when>
    </conditional>
  </inputs>
  <outputs>
    <!-- $input1_file.name = filename  , e.g. paired_end_2_errors.fastqsanger -->
    <!-- $input1_file.id   = ID        , e.g. 10 -->
    <!-- $input1_file.hid  = history ID, e.g. 5  -->
    <data name="outfile_pairs" format="input" label="FASTQ interlacer pairs from ${on_string}"/>
    <data name="outfile_singles" format="input" label="FASTQ interlacer singles from ${on_string}"/>
  </outputs>
  <tests>
    <test>
      <param name="reads_selector" value="paired" />
      <param name="input1_file" value="paired_end_1.fastqsanger" ftype="fastqsanger" />
      <param name="input2_file" value="paired_end_2.fastqsanger" ftype="fastqsanger" />
      <output name="outfile_pairs" file="paired_end_merged.fastqsanger" ftype="fastqsanger" />
      <output name="outfile_singles" file="paired_end_merged_singles.fastqsanger" ftype="fastqsanger" />
    </test>
    <test>
      <param name="reads_selector" value="paired" />
      <param name="input1_file" value="paired_end_1_errors.fastqsanger" ftype="fastqsanger" />
      <param name="input2_file" value="paired_end_2_errors.fastqsanger" ftype="fastqsanger" />
      <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger" />
      <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger" />
    </test>
    <test>
      <param name="reads_selector" value="paired_collection" />
      <param name="reads_coll">
        <collection type="paired">
          <element name="forward" value="paired_end_1.fastqsanger" ftype="fastqsanger" />
          <element name="reverse" value="paired_end_2.fastqsanger" ftype="fastqsanger" />
        </collection>
      </param>
      <output name="outfile_pairs" file="paired_end_merged.fastqsanger" ftype="fastqsanger" />
      <output name="outfile_singles" file="paired_end_merged_singles.fastqsanger" ftype="fastqsanger" />
    </test>
  </tests>
  <help>
**What it does**

This tool joins paired end FASTQ reads from two separate files, one with the left mates and one with the right mates, into a single files where left mates alternate with their right mates. The join is performed using sequence identifiers, allowing the two files to contain differing ordering. If a sequence identifier does not appear in both files, it is included in a separate file.

Sequence identifiers with /1 and /2 appended override the left-hand and right-hand designation; i.e. if the reads end with /1 and /2, the read containing /1 will be used as the left-hand read and the read containing /2 will be used as the right-hand read. Sequences without this designation will follow the left-hand and right-hand settings set by the user.

-----

**Input**

Left-hand mates, for example::

    @1539:931/1
    ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
    +1539:931/1
    BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

Right-hand mates, for example::

    @1539:931/2
    CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
    +1539:931/2
    WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

-----

**Output**

A multiple-fastq file containing interlaced left and right paired reads::

    @1539:931/1
    ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
    +1539:931/1
    BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
    @1539:931/2
    CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
    +1539:931/2
    WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

A multiple-fastq file containing reads that have no mate is also produced.
  </help>
  <citations>
    <citation doi="10.1093/bioinformatics/btq281" />
  </citations>
</tool>