comparison fastq_paired_end_deinterlacer.xml @ 1:462abc5618ba draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a

0:f0949bc49926

<tool id="fastq_paired_end_deinterlacer" name="FASTQ de-interlacer" version="1.1">
  <description>on paired end reads</description>
  <requirements>
    <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
  </requirements>
  <command interpreter="python">fastq_paired_end_deinterlacer.py '$input_file' '${input_file.extension[len( 'fastq' ):]}' '$output1_pairs_file' '$output2_pairs_file' '$output1_singles_file' '$output2_singles_file'</command>
  <inputs>
    <param name="input_file" type="data" format="fastqsanger,fastqcssanger" label="FASTQ reads" />
  </inputs>
  <outputs>
    <data name="output1_pairs_file" format="input" label="FASTQ de-interlacer left mates from data ${input_file.hid}" />
    <data name="output2_pairs_file" format="input" label="FASTQ de-interlacer right mates from data ${input_file.hid}"/>
    <data name="output1_singles_file" format="input" label="FASTQ de-interlacer left singles from data ${input_file.hid}"/>
    <data name="output2_singles_file" format="input" label="FASTQ de-interlacer right singles from data ${input_file.hid}"/>
  </outputs>
  <tests>
    <test>
      <param name="input_file" value="paired_end_merged.fastqsanger" ftype="fastqsanger" />
      <output name="output1_pairs_file" file="paired_end_1.fastqsanger" />
      <output name="output2_pairs_file" file="paired_end_2.fastqsanger" />
      <output name="output1_singles_file" file="paired_end_1_singles.fastqsanger" />
      <output name="output2_singles_file" file="paired_end_2_singles.fastqsanger" />
    </test>
    <test>
      <param name="input_file" value="paired_end_merged_errors.fastqsanger" ftype="fastqsanger" />
      <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" />
      <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" />
      <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" />
      <output name="output2_singles_file" file="paired_end_2_cleaned_singles.fastqsanger" />
    </test>
  </tests>
  <help>
**What it does**

De-interlaces a single fastq dataset representing paired-end run into two fastq datasets containing only the first or second mate read. Reads without mate are saved in separate output files.

Sequence identifiers for paired-end reads must follow the /1 and /2 convention.

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

  </help>
</tool>

1:462abc5618ba

<tool id="fastq_paired_end_deinterlacer" name="FASTQ de-interlacer" version="1.1.1">
    <description>on paired end reads</description>
    <requirements>
        <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement>
    </requirements>
    <command><![CDATA[
gx-fastq-paired-end-deinterlacer '$input_file' '${input_file.extension[len('fastq'):]}' '$output1_pairs_file' '$output2_pairs_file' '$output1_singles_file' '$output2_singles_file'
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ reads" />
    </inputs>
    <outputs>
        <data name="output1_pairs_file" format_source="input_file" label="FASTQ de-interlacer left mates from data ${input_file.hid}" />
        <data name="output2_pairs_file" format_source="input_file" label="FASTQ de-interlacer right mates from data ${input_file.hid}"/>
        <data name="output1_singles_file" format_source="input_file" label="FASTQ de-interlacer left singles from data ${input_file.hid}"/>
        <data name="output2_singles_file" format_source="input_file" label="FASTQ de-interlacer right singles from data ${input_file.hid}"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="paired_end_merged.fastqsanger" ftype="fastqsanger" />
            <output name="output1_pairs_file" file="paired_end_1.fastqsanger" ftype="fastqsanger" />
            <output name="output2_pairs_file" file="paired_end_2.fastqsanger" ftype="fastqsanger" />
            <output name="output1_singles_file" file="paired_end_1_singles.fastqsanger" ftype="fastqsanger" />
            <output name="output2_singles_file" file="paired_end_2_singles.fastqsanger" ftype="fastqsanger" />
        </test>
        <test>
            <param name="input_file" value="paired_end_merged_errors.fastqsanger" ftype="fastqsanger" />
            <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" ftype="fastqsanger" />
            <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" ftype="fastqsanger" />
            <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" ftype="fastqsanger" />
            <output name="output2_singles_file" file="paired_end_2_cleaned_singles.fastqsanger" ftype="fastqsanger" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

De-interlaces a single fastq dataset representing paired-end run into two fastq datasets containing only the first or second mate read. Reads without mate are saved in separate output files.

Sequence identifiers for paired-end reads must follow the /1 and /2 convention.

    @1539:931/2
    CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
    +1539:931/2
    WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btq281</citation>
    </citations>
</tool>