comparison tabular_to_fastq.xml @ 3:643018aa1435 draft

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

2:6e9c13e70d45

<tool id="tabular_to_fastq" name="Tabular to FASTQ" version="1.0.0">
  <description>converter</description>
  <requirements>
    <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
  </requirements>
  <command interpreter="python">tabular_to_fastq.py '$input_file' '$output_file' '$identifier' '$sequence' '$quality'</command>
  <inputs>
    <param name="input_file" type="data" format="tabular" label="Tabular file to convert" />
    <param name="identifier" label="Identifier column" type="data_column" data_ref="input_file" />
    <param name="sequence" label="Sequence column" type="data_column" data_ref="input_file" />
    <param name="quality" label="Quality column" type="data_column" data_ref="input_file" />
  </inputs>
  <outputs>
    <data name="output_file" format="fastq" />
  </outputs>
  <tests>
    <!-- basic test -->
    <test>
      <param name="input_file" value="fastq_to_tabular_out_1.tabular" ftype="tabular" />
      <param name="identifier" value="1" />
      <param name="sequence" value="2" />
      <param name="quality" value="3" />
      <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
    </test>
    <!-- color space test -->
    <test>
      <param name="input_file" value="fastq_to_tabular_out_2.tabular" ftype="tabular" />
      <param name="identifier" value="1" />
      <param name="sequence" value="2" />
      <param name="quality" value="3" />
      <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
    </test>
  </tests>
  <help>
**What it does**

This tool attempts to convert a tabular file containing sequencing read data to a FASTQ formatted file. The FASTQ Groomer tool should always be used on the output of this tool. 

  </help>
  
  <citations>
    <citation type="doi">10.1093/bioinformatics/btq281</citation>
  </citations>
  
</tool>

3:643018aa1435

<tool id="tabular_to_fastq" name="Tabular to FASTQ" version="1.1.1">
    <description>converter</description>
    <command><![CDATA[
python '$__tool_directory__/tabular_to_fastq.py' '$input_file' '$output_file' '$identifier' '$sequence' '$quality'
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="tabular" label="Tabular file to convert" />
        <param name="identifier" type="data_column" data_ref="input_file" label="Identifier column" />
        <param name="sequence" type="data_column" data_ref="input_file" label="Sequence column" />
        <param name="quality" type="data_column" data_ref="input_file" label="Quality column" />
    </inputs>
    <outputs>
        <data name="output_file" format="fastq" />
    </outputs>
    <tests>
        <!-- basic test -->
        <test>
            <param name="input_file" value="fastq_to_tabular_out_1.tabular" ftype="tabular" />
            <param name="identifier" value="1" />
            <param name="sequence" value="2" />
            <param name="quality" value="3" />
            <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
        </test>
        <!-- color space test -->
        <test>
            <param name="input_file" value="fastq_to_tabular_out_2.tabular" ftype="tabular" />
            <param name="identifier" value="1" />
            <param name="sequence" value="2" />
            <param name="quality" value="3" />
            <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

This tool attempts to convert a tabular file containing sequencing read data to a FASTQ formatted file. The FASTQ Groomer tool should always be used on the output of this tool.
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btq281</citation>
    </citations>
</tool>