comparison picard_SamToFastq.xml @ 32:f9242e01365a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 285fab1660daa944d6833ae1e059b30cb1e88309

31:585027e65f3b

    INCLUDE_NON_PRIMARY_ALIGNMENTS="${include_non_primary_alignments}"

    VALIDATION_STRINGENCY="${validation_stringency}"
    QUIET=true
    VERBOSITY=ERROR
    @TMPDIR_OPTION@

  ]]></command>
  <inputs>

    <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>

        <filter>output_type['single_or_paired'] == 'pe_sep'</filter>
    </data>
  </outputs>

  <tests>
    <test>
      <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>
      <param name="single_or_paired" value="pe_interleaved" />
      <param name="re_reverse" value="true"/>
      <param name="include_non_pf_reads" value="false"/>
      <param name="clipping_attribute" value="" />

      <param name="read2_trim" value="0" />
      <param name="read2_max_bases_to_write" value="-1"/>
      <param name="include_non_primary_alignments" value="false"/>
      <output name="interleaved_fastq" file="picard_SamToFastq_test1.fq" ftype="fastqsanger"/>
    </test>
    <test>
      <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>
      <param name="single_or_paired" value="pe_sep" />
      <param name="re_reverse" value="true"/>
      <param name="include_non_pf_reads" value="false"/>
      <param name="clipping_attribute" value="" />

      <param name="include_non_primary_alignments" value="false"/>
      <output name="fq1" file="picard_SamToFastq_1.fq" ftype="fastqsanger"/>
      <output name="fq2" file="picard_SamToFastq_2.fq" ftype="fastqsanger"/>
      <output name="fq_u" file="picard_SamToFastq_u.fq" ftype="fastqsanger"/>
    </test>
    <test>
      <param name="inputFile" value="picard_SamToFastq_se.bam" ftype="bam"/>
      <param name="single_or_paired" value="se" />
      <param name="re_reverse" value="true"/>
      <param name="include_non_pf_reads" value="false"/>
      <param name="clipping_attribute" value="" />

**Purpose**

Extracts read sequences and qualities from the input SAM/BAM dataset and outputs them in Sanger fastq format. In the RE_REVERSE=True mode (default behavior), if the read is aligned and the alignment is to the reverse strand on the genome, the read's sequence from input SAM.BAM dataset will be reverse-complemented prior to writing it to fastq in order restore correctly the original read sequence as it was generated by the sequencer.

-----

.. class:: warningmark

@dataset_collections@

@description@

32:f9242e01365a

    INCLUDE_NON_PRIMARY_ALIGNMENTS="${include_non_primary_alignments}"

    VALIDATION_STRINGENCY="${validation_stringency}"
    QUIET=true
    VERBOSITY=ERROR

  ]]></command>
  <inputs>

    <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>

        <filter>output_type['single_or_paired'] == 'pe_sep'</filter>
    </data>
  </outputs>

  <tests>
    <test expect_num_outputs="5">
      <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>
      <param name="single_or_paired" value="pe_interleaved" />
      <param name="re_reverse" value="true"/>
      <param name="include_non_pf_reads" value="false"/>
      <param name="clipping_attribute" value="" />

      <param name="read2_trim" value="0" />
      <param name="read2_max_bases_to_write" value="-1"/>
      <param name="include_non_primary_alignments" value="false"/>
      <output name="interleaved_fastq" file="picard_SamToFastq_test1.fq" ftype="fastqsanger"/>
    </test>
    <test expect_num_outputs="5">
      <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>
      <param name="single_or_paired" value="pe_sep" />
      <param name="re_reverse" value="true"/>
      <param name="include_non_pf_reads" value="false"/>
      <param name="clipping_attribute" value="" />

      <param name="include_non_primary_alignments" value="false"/>
      <output name="fq1" file="picard_SamToFastq_1.fq" ftype="fastqsanger"/>
      <output name="fq2" file="picard_SamToFastq_2.fq" ftype="fastqsanger"/>
      <output name="fq_u" file="picard_SamToFastq_u.fq" ftype="fastqsanger"/>
    </test>
    <test expect_num_outputs="5">
      <param name="inputFile" value="picard_SamToFastq_se.bam" ftype="bam"/>
      <param name="single_or_paired" value="se" />
      <param name="re_reverse" value="true"/>
      <param name="include_non_pf_reads" value="false"/>
      <param name="clipping_attribute" value="" />

**Purpose**

Extracts read sequences and qualities from the input SAM/BAM dataset and outputs them in Sanger fastq format. In the RE_REVERSE=True mode (default behavior), if the read is aligned and the alignment is to the reverse strand on the genome, the read's sequence from input SAM.BAM dataset will be reverse-complemented prior to writing it to fastq in order restore correctly the original read sequence as it was generated by the sequencer.

.. class:: warningmark


@dataset_collections@

@description@