comparison picard_SamToFastq.xml @ 31:585027e65f3b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 70d2a66c405be58d4413753792bcadf212a4da84

30:b502c227b5e6

<tool name="SamToFastq" id="picard_SamToFastq" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
    <description>extract reads and qualities from SAM/BAM dataset and convert to fastq</description>
    <macros>
        <import>picard_macros.xml</import>
        <token name="@WRAPPER_VERSION@">2</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">picard_samtofastq</xref>
    </xrefs>
    <expand macro="requirements" />

  <tests>
    <test>
      <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>
      <param name="single_or_paired" value="pe_interleaved" />
      <param name="output_per_rg" value="false"/>
      <param name="re_reverse" value="true"/>
      <param name="include_non_pf_reads" value="false"/>
      <param name="clipping_attribute" value="" />
      <param name="clipping_action" value="" />
      <param name="read1_trim" value="0" />

      <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="output_per_rg" value="false"/>
      <param name="re_reverse" value="true"/>
      <param name="include_non_pf_reads" value="false"/>
      <param name="clipping_attribute" value="" />
      <param name="clipping_action" value="" />
      <param name="read1_trim" value="0" />

      <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="output_per_rg" value="false"/>
      <param name="re_reverse" value="true"/>
      <param name="include_non_pf_reads" value="false"/>
      <param name="clipping_attribute" value="" />
      <param name="clipping_action" value="" />
      <param name="read1_trim" value="0" />

-----

.. class:: warningmark

**DANGER: Multiple Outputs**

Generating per readgroup fastq (setting **OUTPUT_PER_RG** to True) may produce very large numbers of outputs. Know what you are doing!

@dataset_collections@

@description@

  FASTQ=File
  F=File                        Output fastq file (single-end fastq or, if paired, first end of the pair fastq).
                                Required.  Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)

  SECOND_END_FASTQ=File
  F2=File                       Output fastq file (if paired, second end of the pair fastq).  Default value: null.
                                Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)

  UNPAIRED_FASTQ=File
  FU=File                       Output fastq file for unpaired reads; may only be provided in paired-fastq mode  Default
                                value: null.  Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)

  OUTPUT_PER_RG=Boolean
  OPRG=Boolean                  Output a fastq file per read group (two fastq files per read group if the group is
                                paired).  Default value: false. Possible values: {true, false}  Cannot be used in
                                conjuction with option(s) SECOND_END_FASTQ (F2) UNPAIRED_FASTQ (FU) FASTQ (F)

  OUTPUT_DIR=File
  ODIR=File                     Directory in which to output the fastq file(s).  Used only when OUTPUT_PER_RG is true.
                                Default value: null.

  RE_REVERSE=Boolean
  RC=Boolean                    Re-reverse bases and qualities of reads with negative strand flag set before writing them
                                to fastq  Default value: true. Possible values: {true, false}

31:585027e65f3b

<tool name="SamToFastq" id="picard_SamToFastq" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
    <description>extract reads and qualities from SAM/BAM dataset and convert to fastq</description>
    <macros>
        <import>picard_macros.xml</import>
        <token name="@WRAPPER_VERSION@">3</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">picard_samtofastq</xref>
    </xrefs>
    <expand macro="requirements" />

  <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="clipping_action" value="" />
      <param name="read1_trim" value="0" />

      <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="clipping_action" value="" />
      <param name="read1_trim" value="0" />

      <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="" />
      <param name="clipping_action" value="" />
      <param name="read1_trim" value="0" />

-----

.. class:: warningmark

@dataset_collections@

@description@

  FASTQ=File
  F=File                        Output fastq file (single-end fastq or, if paired, first end of the pair fastq).
                                Required.

  SECOND_END_FASTQ=File
  F2=File                       Output fastq file (if paired, second end of the pair fastq).  Default value: null.
                                

  UNPAIRED_FASTQ=File
  FU=File                       Output fastq file for unpaired reads; may only be provided in paired-fastq mode  Default
                                value: null.

  RE_REVERSE=Boolean
  RC=Boolean                    Re-reverse bases and qualities of reads with negative strand flag set before writing them
                                to fastq  Default value: true. Possible values: {true, false}