comparison picard_FastqToSam.xml @ 4:2589e6207cb4 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

3:52fdfc45590a

  <description>convert Fastq data into unaligned BAM</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>
    @java_options@
    
    java -jar \$JAVA_JAR_PATH/picard.jar
    FastqToSam

      <when value="pe">
        <param name="fastq" type="data" format="fastq" label="Input fastq file for the first read in paired end data" help="FASTQ"/>
        <param name="fastq2" type="data" format="fastq" 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" 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="quality_format" type="select" label="Select quality encoding scheme" help="QUALITY_FORMAT">
      <option value="Standard" selected="True">Sanger (+33)</option>
      <option value="Illumina">Illumina (+64)</option>
      <option value="Solexa">Solexa (+66)</option>
    </param>

    <param name="read_group_name" type="text" size="20" value="A" label="Read group name" help="READ_GROUP_NAME"/>
    <param name="sample_name" type="text" size="20" value="sample-a" label="Sample name" help="SAMPLE_NAME"/>
    <param name="library_name" type="text" size="20" optional="True" label="The library name" help="LIBRARY_NAME; Optional"/>
    <param name="platform_unit" type="text" size="20" optional="True"  label="The platform unit (often run_barcode.lane)" help="PLATFORM_UNIT; Optional"/>
    <param name="platform" type="text" size="20" optional="True"  label="The platform type (e.g. illumina, 454)" help="PLATFORM; Optional"/>
    <param name="sequencing_center" type="text" size="20" 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" size="20" optional="True" label="Comment to include in the output dataset's header" help="COMMENT; Optional"/>
    <param name="description" type="text" size="20" 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"/>

      <param name="fastq2" value="picard_FastqToSam_read2.fq" ftype="fastq" />
      <output name="outFile" file="picard_FastqToSam_test1.bam" ftype="bam" lines_diff="4"/>
    </test> 
  </tests>
  
  <stdio>
    <exit_code range="1:"  level="fatal"/>
  </stdio>
  
  <help>

.. class:: infomark

**Purpose**

  

@more_info@

  </help>
</tool>

4:2589e6207cb4

  <description>convert Fastq data into unaligned BAM</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <stdio>
    <exit_code range="1:" level="fatal"/>
  </stdio>
  <command>
    @java_options@
    
    java -jar \$JAVA_JAR_PATH/picard.jar
    FastqToSam

      <when value="pe">
        <param name="fastq" type="data" format="fastq" label="Input fastq file for the first read in paired end data" help="FASTQ"/>
        <param name="fastq2" type="data" format="fastq" 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" 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="quality_format" type="select" label="Select quality encoding scheme" help="QUALITY_FORMAT">
      <option value="Standard" selected="True">Sanger (+33)</option>
      <option value="Illumina">Illumina (+64)</option>
      <option value="Solexa">Solexa (+66)</option>
    </param>

    <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"/>

      <param name="fastq2" value="picard_FastqToSam_read2.fq" ftype="fastq" />
      <output name="outFile" file="picard_FastqToSam_test1.bam" ftype="bam" lines_diff="4"/>
    </test> 
  </tests>
  
  <help>

.. class:: infomark

**Purpose**

  

@more_info@

  </help>
  <citations>
  </citations>
</tool>