comparison trimmomatic.xml @ 17:b9aaed85cbd1 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic commit 6151dc895107d028c525362fb16b91388e10f2f2

16:9a38087e3bfd

      <param name="single_or_paired" type="select" label="Single-end or paired-end reads?">
         <option value="se" selected="true">Single-end</option>
         <option value="pair_of_files">Paired-end (two separate input files)</option>
         <option value="collection">Paired-end (as collection)</option>
      </param>
    <when value="se">
      <param name="fastq_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" label="Input FASTQ file" />
    </when>
    <when value="pair_of_files">
      <param name="fastq_r1_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz"
         label="Input FASTQ file (R1/first of pair)" />
      <param name="fastq_r2_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz"
         label="Input FASTQ file (R2/second of pair)" />
    </when>
      <when value="collection">
        <param name="fastq_pair" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" type="data_collection" collection_type="paired" label="Select FASTQ dataset collection with R1/R2 pair" />
      </when>
    </conditional>
    <conditional name="illuminaclip">

    </param>
    <param name="output_logs" argument="-trimlog" type="boolean" label="Output trimlog file?" truevalue="yes" falsevalue="no" checked="False" />
    <param name="output_err" type="boolean" label="Output trimmomatic log messages?" truevalue="yes" falsevalue="no" checked="False" help="these are the messages written to stderr (eg. for use in MultiQC)" />
  </inputs>
  <outputs>
    <data name="fastq_out_r1_paired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 paired)" format_source="fastq_r1_in">
      <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
    </data>
    <data name="fastq_out_r2_paired" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 paired)" format_source="fastq_r2_in">
      <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
    </data>
    <data name="fastq_out_r1_unpaired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 unpaired)" format_source="fastq_r1_in">
      <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
    </data>
    <data name="fastq_out_r2_unpaired" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 unpaired)" format_source="fastq_r2_in">
      <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
    </data>
    <data name="fastq_out" label="${tool.name} on ${readtype.fastq_in.name}" format_source="fastq_in">
      <filter>readtype['single_or_paired'] == 'se'</filter>
    </data>
    <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${on_string}: paired">
      <filter>readtype['single_or_paired'] == "collection"</filter>
      <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 paired)" format_source="fastq_pair['forward']"/>
      <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 paired)" format_source="fastq_pair['reverse']"/>
    </collection>
      <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${on_string}: unpaired">
        <filter>readtype['single_or_paired'] == "collection"</filter>
        <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 unpaired)" format_source="fastq_pair['forward']"/>
        <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 unpaired)" format_source="fastq_pair['reverse']"/>
    </collection>
    <data name="log_file" format="txt" label="${tool.name} on ${on_string} (trimlog file)" from_work_dir="trimlog">
      <filter>output_logs</filter>
    </data>
    <data name="err_file" format="txt" label="${tool.name} on ${on_string} (log file)" from_work_dir="trimmomatic.log">

17:b9aaed85cbd1

      <param name="single_or_paired" type="select" label="Single-end or paired-end reads?">
         <option value="se" selected="true">Single-end</option>
         <option value="pair_of_files">Paired-end (two separate input files)</option>
         <option value="collection">Paired-end (as collection)</option>
      </param>
      <when value="se">
        <param name="fastq_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" label="Input FASTQ file" />
      </when>
      <when value="pair_of_files">
        <param name="fastq_r1_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz"
          label="Input FASTQ file (R1/first of pair)" />
        <param name="fastq_r2_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz"
          label="Input FASTQ file (R2/second of pair)" />
      </when>
      <when value="collection">
        <param name="fastq_pair" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" type="data_collection" collection_type="paired" label="Select FASTQ dataset collection with R1/R2 pair" />
      </when>
    </conditional>
    <conditional name="illuminaclip">

    </param>
    <param name="output_logs" argument="-trimlog" type="boolean" label="Output trimlog file?" truevalue="yes" falsevalue="no" checked="False" />
    <param name="output_err" type="boolean" label="Output trimmomatic log messages?" truevalue="yes" falsevalue="no" checked="False" help="these are the messages written to stderr (eg. for use in MultiQC)" />
  </inputs>
  <outputs>
    <data name="fastq_out_r1_paired" default_identifier_source="readtype|fastq_r1_in" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 paired)" format_source="fastq_r1_in">
      <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
    </data>
    <data name="fastq_out_r2_paired" default_identifier_source="readtype|fastq_r2_in" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 paired)" format_source="fastq_r2_in">
      <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
    </data>
    <data name="fastq_out_r1_unpaired" default_identifier_source="readtype|fastq_r1_in" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 unpaired)" format_source="fastq_r1_in">
      <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
    </data>
    <data name="fastq_out_r2_unpaired" default_identifier_source="readtype|fastq_r2_in" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 unpaired)" format_source="fastq_r2_in">
      <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
    </data>
    <data name="fastq_out" default_identifier_source="readtype|fastq_in" label="${tool.name} on ${readtype.fastq_in.name}" format_source="fastq_in">
      <filter>readtype['single_or_paired'] == 'se'</filter>
    </data>
    <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${on_string}: paired">
      <filter>readtype['single_or_paired'] == "collection"</filter>
      <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 paired)" format_source="fastq_pair['forward']"/>
      <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 paired)" format_source="fastq_pair['reverse']"/>
    </collection>
    <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${on_string}: unpaired">
      <filter>readtype['single_or_paired'] == "collection"</filter>
      <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 unpaired)" format_source="fastq_pair['forward']"/>
      <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 unpaired)" format_source="fastq_pair['reverse']"/>
    </collection>
    <data name="log_file" format="txt" label="${tool.name} on ${on_string} (trimlog file)" from_work_dir="trimlog">
      <filter>output_logs</filter>
    </data>
    <data name="err_file" format="txt" label="${tool.name} on ${on_string} (log file)" from_work_dir="trimmomatic.log">