<tool id="picard_FastqToSam" name="FASTQ to BAM" version="1.56.0">
  <description>creates an unaligned BAM file</description>
  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
  <!-- Dan Blankenberg -->
  <command>java  -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC
    -jar "\$JAVA_JAR_PATH/FastqToSam.jar"
    FASTQ="${input_fastq1}"
    #if str( $input_fastq2) != "None":
        FASTQ2="${input_fastq2}"
    #end if
    QUALITY_FORMAT="${ dict( fastqsanger='Standard', fastqcssanger='Standard', fastqillumina='Illumina', fastqsolexa='Solexa' )[ $input_fastq1.ext ] }" ##Solexa, Illumina, Standard
    OUTPUT="${output_bam}"
    READ_GROUP_NAME="${read_group_name}"
    SAMPLE_NAME="${sample_name}" 
    #if $param_type.param_type_selector == "advanced":
        #if str( $param_type.library_name ) != "":
            LIBRARY_NAME="${param_type.library_name}" 
        #end if
        #if str( $param_type.platform_unit ) != "":
            PLATFORM_UNIT="${param_type.platform_unit}"
        #end if
        #if str( $param_type.platform ) != "":
            PLATFORM="${param_type.platform}"
        #end if 
        #if str( $param_type.sequencing_center ) != "":
            SEQUENCING_CENTER="${param_type.sequencing_center}"
        #end if 
        #if str( $param_type.predicted_insert_size ) != "":
            PREDICTED_INSERT_SIZE="${param_type.predicted_insert_size}"
        #end if 
        #if str( $param_type.description.value ) != "":
            DESCRIPTION="${param_type.description}"
        #end if 
        #if str( $param_type.run_date ) != "":
            RUN_DATE="${param_type.run_date}"
        #end if
        #if str( $param_type.min_q ) != "":
            MIN_Q="${param_type.min_q}"
        #end if
        #if str( $param_type.max_q ) != "":
            MAX_Q="${param_type.max_q}"
        #end if
        SORT_ORDER="${param_type.sort_order}"
    #else:
        SORT_ORDER=coordinate ##unsorted, queryname, coordinate; always use coordinate
    #end if
  2&gt;&amp;1 
  || echo "Error running Picard FastqToSAM" >&amp;2
  </command>
  <inputs>
    <param name="input_fastq1" type="data" format="fastqsanger,fastqillumina,fastqsolexa,fastqcssanger" label="FASTQ file" /> <!-- confirm that fastqcssanger also works -->
    <param name="input_fastq2" type="data" format="fastqsanger,fastqillumina,fastqsolexa,fastqcssanger" optional="True" label="Second FASTQ of paired end data" help="Only needed when using paired end data." >
      <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">
        <column name="name" index="0"/>
        <column name="value" index="0"/>
        <filter type="param_value" ref="input_fastq1" ref_attribute="ext" column="0"/> 
      </options>
    </param>
    <param name="read_group_name" type="text" value="A" label="Read Group Name" />
    <param name="sample_name" type="text" value="unknown sample" label="Sample Name" />
    <conditional name="param_type">
      <param name="param_type_selector" type="select" label="Basic or Advanced options">
        <option value="basic" selected="True">Basic</option>
        <option value="advanced">Advanced</option>
      </param>
      <when value="basic">
        <!-- Do nothing here -->
      </when>
      <when value="advanced">
        <param name="library_name" type="text" value="" label="Library Name" />
        <param name="platform_unit" type="text" value="" label="Platform Unit" />
        <param name="platform" type="text" value="" label="Platform" />
        <param name="sequencing_center" type="text" value="" label="Sequencing Center" />
        <param name="predicted_insert_size" type="integer" value="" optional="True" label="Predicted Insert Size" />
        <param name="description" type="text" value="" label="Description" />
        <param name="run_date" type="text" value="" label="Run Date" />
        <param name="min_q" type="integer" optional="True" value="0" label="Min Q" />
        <param name="max_q" type="integer" optional="True" value="93" label="Max Q" />
        <param name="sort_order" type="select" label="Sort order">
          <option value="coordinate" selected="True">coordinate</option>
          <option value="queryname">queryname</option>
          <option value="unsorted">unsorted</option>
        </param>
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="bam" name="output_bam" />
  </outputs>
  <tests>
      <test>
          <param name="input_fastq1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" />
          <param name="input_fastq2" />
          <param name="read_group_name" value="A" />
          <param name="sample_name" value="unknown sample" />
          <param name="param_type_selector" value="basic" />
          <output name="output_bam" file="picard_fastq_to_sam_out1.bam" ftype="bam"/> 
      </test>
      <test>
          <param name="input_fastq1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" />
          <param name="input_fastq2" value="bwa_wrapper_in3.fastqsanger" ftype="fastqsanger" />
          <param name="read_group_name" value="A" />
          <param name="sample_name" value="unknown sample" />
          <param name="param_type_selector" value="basic" />
          <output name="output_bam" file="picard_fastq_to_sam_out2.bam" ftype="bam"/> 
      </test>
  </tests>
  <help>
**What it does**

Picard: FastqToSam converts FASTQ files to unaligned BAM files.

------

Please cite the website "http://picard.sourceforge.net".

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**Input formats**

FastqToSam accepts FASTQ input files. If using paired-end data, you should select two FASTQ files.

------

**Outputs**

The output is in BAM format, see http://samtools.sourceforge.net for more details.

-------

**FastqToSam settings**

This is list of FastqToSam options::

 READ_GROUP_NAME=String	Read group name Default value: A. This option can be set to 'null' to clear the default value.
 SAMPLE_NAME=String	Sample name to insert into the read group header Required.
 LIBRARY_NAME=String	The library name to place into the LB attribute in the read group header Default value: null.
 PLATFORM_UNIT=String	The platform unit (often run_barcode.lane) to insert into the read group header Default value: null.
 PLATFORM=String	The platform type (e.g. illumina, solid) to insert into the read group header Default value: null.
 SEQUENCING_CENTER=String	The sequencing center from which the data originated Default value: null.
 PREDICTED_INSERT_SIZE=Integer	Predicted median insert size, to insert into the read group header Default value: null.
 DESCRIPTION=String	Inserted into the read group header Default value: null. 
  </help>
</tool>