annotate picard_FastqToSam.xml @ 33:3f254c5ced1d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8

<tool name="FastqToSam" id="picard_FastqToSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
    <description>convert Fastq data into unaligned BAM</description>
    <macros>
        <import>picard_macros.xml</import>
        <token name="@WRAPPER_VERSION@">0</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">picard_fastqtosam</xref>
    </xrefs>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
    @java_options@
    #if str( $input_type.input_type_selector ) == "se":
      #set fwd = $input_type.fastq
      #set rev = None
    #elif str( $input_type.input_type_selector ) == "pe":
      #set fwd = $input_type.fastq
      #set rev = $input_type.fastq2
    #else
      #set fwq = $input_type.fastq.forward
      #set rev = $input_type.fastq.reverse
    #end if

    #if $fwd.ext.endswith(".gz")
      gunzip -c '$fwd' > fwd.fastq &&
    #else
      ln -sf '$fwd' fwd.fastq &&
    #end if
    #if rev
      #if rev.ext.endswith(".gz")
        gunzip -c '$rev' > rev.fastq &&
      #else
        ln -sf '$rev' rev.fastq &&
      #end if
    #end if
   
    picard FastqToSam

    --FASTQ fwd.fastq
    #if rev
      --FASTQ2 rev.fastq
    #end if

    #if $fwd.ext.startswith("fastqillumina")
      --QUALITY_FORMAT "Illumina"
    #else if $fwd.ext.startswith("fastqsolexa")
      --QUALITY_FORMAT "Solexa"
    #else 
      --QUALITY_FORMAT "Standard"
    #end if
    --OUTPUT '${outFile}'
    --READ_GROUP_NAME '${read_group_name}'
    --SAMPLE_NAME '${sample_name}'

    #if str( $library_name ):
        --LIBRARY_NAME '${library_name}'
    #end if

    #if str( $platform_unit ):
        --PLATFORM_UNIT '${platform_unit}'
    #end if

    #if str( $platform ):
        --PLATFORM '${platform}'
    #end if

    #if str( $sequencing_center ):
        --SEQUENCING_CENTER '${sequencing_center}'
    #end if

    #if str( $predicted_insert_size ):
        --PREDICTED_INSERT_SIZE '${predicted_insert_size}'
    #end if

    #if str( $comment ):
        --COMMENT '${comment}'
    #end if

    #if str( $description ):
        --DESCRIPTION '${description}'
    #end if

    #if str( $run_date ):
        --RUN_DATE '${run_date}'
    #end if

    --MIN_Q '${min_q}'
    --MAX_Q '${max_q}'
    --STRIP_UNPAIRED_MATE_NUMBER '${strip_unpairied_mate_number}'
    --ALLOW_AND_IGNORE_EMPTY_LINES '${allow_and_ignore_empty_lines}'

    --SORT_ORDER coordinate
    --VALIDATION_STRINGENCY '${validation_stringency}'
    --QUIET true
    --VERBOSITY ERROR

  ]]></command>
    <inputs>
        <conditional name="input_type">
            <param name="input_type_selector" type="select" label="What is your input data" help="Select between single end, paired end, and collections. See help below for full explanation of dataset types">
                <option value="se">Single end (single dataset)</option>
                <option value="pe">Paired end (two datasets)</option>
                <option value="pc">Paired collection</option>
            </param>
            <when value="se">
                <param name="fastq" type="data" format="fastq,fastq.gz" label="Input fastq file for single end data" help="FASTQ"/>
            </when>
            <when value="pe">
                <param name="fastq" type="data" format="fastq,fastq.gz" label="Input fastq file for the first read in paired end data" help="FASTQ"/>
                <param name="fastq2" type="data" format="fastq,fastq.gz" label="Input fastq file for the second read of paired end data" help="FASTQ2"/>
            </when>
            <when value="pc">
                <param name="fastq" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="FASTQ paired dataset collection" help="FASTQ and FASTQ2; A collection of two datasets with forward and reverse reads. See help below on explanation of dataset collections"/>
            </when>
        </conditional>
        <param name="read_group_name" type="text" value="A" label="Read group name" help="READ_GROUP_NAME"/>
        <param name="sample_name" type="text" value="sample-a" label="Sample name" help="SAMPLE_NAME"/>
        <param name="library_name" type="text" optional="True" label="The library name" help="LIBRARY_NAME; Optional"/>
        <param name="platform_unit" type="text" optional="True" label="The platform unit (often run_barcode.lane)" help="PLATFORM_UNIT; Optional"/>
        <param name="platform" type="text" optional="True" label="The platform type (e.g. illumina, 454)" help="PLATFORM; Optional"/>
        <param name="sequencing_center" type="text" optional="True" label="The sequencing center from which the data originated" help="SEQUENCING_CENTER; Optional"/>
        <param name="predicted_insert_size" type="integer" min="0" max="100000" optional="True" label="Predicted median insert size, to insert into the read group header" help="PREDICTED_INSERT_SIZE; Optional"/>
        <param name="comment" type="text" optional="True" label="Comment to include in the output dataset's header" help="COMMENT; Optional"/>
        <param name="description" type="text" optional="True" label="Optional description information" help="DESCRIPTION; Optional"/>
        <param name="run_date" optional="True" type="text" label="Run date" help="RGDT; Optional; Format=YYYY-MM-DD (eg 1997-07-16)"/>
        <param name="min_q" type="integer" value="0" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MIN_Q; An exception will be thrown if a quality is less than this value; default=0"/>
        <param name="max_q" type="integer" value="93" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MAX_Q; An exception will be thrown if a quality is greater than this value; default=93"/>
        <param name="strip_unpairied_mate_number" type="boolean" truevalue="true" falsevalue="false" label="If true and this is an unpaired fastq any occurance of '/1' will be removed from the end of a read name" help="STRIP_UNPAIRED_MATE_NUMBER; default=false"/>
        <param name="allow_and_ignore_empty_lines" type="boolean" truevalue="true" falsevalue="false" label="Allow (and ignore) empty lines" help="ALLOW_AND_IGNORE_EMPTY_LINES; default=false"/>
        <expand macro="VS"/>
    </inputs>
    <outputs>
        <data format="unsorted.bam" name="outFile" label="${tool.name} on ${on_string}: reads as unaligned BAM"/>
    </outputs>
    <tests>
        <test>
            <param name="input_type_selector" value="pe"/>
            <param name="read_group_name" value="A"/>
            <param name="sample_name" value="sample-a"/>
            <param name="library_name" value="A"/>
            <param name="platform_unit" value="A"/>
            <param name="platform" value="Illumina"/>
            <param name="sequencing_center" value="A"/>
            <param name="predicted_insert_size" value="300"/>
            <param name="comment" value="A"/>
            <param name="description" value="A"/>
            <param name="run_date" value="2014-10-10"/>
            <param name="min_q" value="0"/>
            <param name="max_q" value="93"/>
            <param name="strip_unpairied_mate_number" value="False"/>
            <param name="allow_and_ignore_empty_lines" value="False"/>
            <param name="validation_stringency" value="LENIENT"/>
            <param name="fastq" value="picard_FastqToSam_read1.fq.gz" ftype="fastq.gz"/>
            <param name="fastq2" value="picard_FastqToSam_read2.fq.gz" ftype="fastq.gz"/>
            <output name="outFile" file="picard_FastqToSam_test1.bam" ftype="unsorted.bam" lines_diff="4"/>
        </test>
    </tests>
    <help>

.. class:: infomark

**Purpose**

Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.

@dataset_collections@

@RG@

@description@

  FASTQ=File
  F1=File                       Input fastq file for single end data, or first read in paired end
                                data.  Required.

  FASTQ2=File
  F2=File                       Input fastq file for the second read of paired end data (if used).

  QUALITY_FORMAT=FastqQualityFormat
  V=FastqQualityFormat          A value describing how the quality values are encoded in the fastq.  Either Solexa for
                                pre-pipeline 1.3 style scores (solexa scaling + 66), Illumina for pipeline 1.3 and above
                                (phred scaling + 64) or Standard for phred scaled scores with a character shift of 33.
                                If this value is not specified, the quality format will be detected automatically.
                                Default value: null. Possible values: {Solexa, Illumina, Standard}

  READ_GROUP_NAME=String
  RG=String                     Read group name  Default value: A.

  SAMPLE_NAME=String
  SM=String                     Sample name to insert into the read group header  Required.

  LIBRARY_NAME=String
  LB=String                     The library name to place into the LB attribute in the read group header.

  PLATFORM_UNIT=String
  PU=String                     The platform unit (often run_barcode.lane) to insert into the read group header.

  PLATFORM=String
  PL=String                     The platform type (e.g. illumina, solid) to insert into the read group header.

  SEQUENCING_CENTER=String
  CN=String                     The sequencing center from which the data originated.

  PREDICTED_INSERT_SIZE=Integer
  PI=Integer                    Predicted median insert size, to insert into the read group header.

  COMMENT=String
  CO=String                     Comment to include in the merged output file's header.

  DESCRIPTION=String
  DS=String                     Inserted into the read group header.

  RUN_DATE=Iso8601Date
  DT=Iso8601Date                Date the run was produced, to insert into the read group header.

  MIN_Q=Integer                 Minimum quality allowed in the input fastq.  An exception will be thrown if a quality is
                                less than this value.  Default value: 0.

  MAX_Q=Integer                 Maximum quality allowed in the input fastq.  An exception will be thrown if a quality is
                                greater than this value.  Default value: 93.

  STRIP_UNPAIRED_MATE_NUMBER=Boolean
                                If true and this is an unpaired fastq any occurance of '/1' will be removed from the end
                                of a read name.  Default value: false.  Possible values: {true, false}

  ALLOW_AND_IGNORE_EMPTY_LINES=Boolean
                                Allow (and ignore) empty lines  Default value: false. Possible values: {true, false}


@more_info@

  </help>
    <expand macro="citations"/>
</tool>