comparison picard_CollectInsertSizeMetrics.xml @ 33:3f254c5ced1d draft default tip

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

32:f9242e01365a

<tool name="CollectInsertSizeMetrics" id="picard_CollectInsertSizeMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
  <description>plots distribution of insert sizes</description>
  <macros>
    <import>picard_macros.xml</import>
    <token name="@WRAPPER_VERSION@">2</token>
  </macros>
  <expand macro="requirements">
    <requirement type="package" version="3.4.1">r-base</requirement>
  </expand>
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    @symlink_element_identifier@
    ##set up input files

    #set $reference_fasta_filename = "localref.fa"

    @handle_reference_source@

    picard
    CollectInsertSizeMetrics
    INPUT='$escaped_element_identifier'
    OUTPUT="${outFile}"
    HISTOGRAM_FILE="${histFile}"
    DEVIATIONS="${deviations}"

    #if str( $hist_width ):
      HISTOGRAM_WIDTH="${hist_width}"
    #end if

    MINIMUM_PCT="${min_pct}"
    REFERENCE_SEQUENCE="${reference_fasta_filename}"
    ASSUME_SORTED="${assume_sorted}"
    METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}"

    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."/>
    <conditional name="reference_source">
      <param name="reference_source_selector" type="select" label="Load reference genome from">
        <option value="cached">Local cache</option>
        <option value="history">History</option>
      </param>
      <when value="cached">
        <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
          <options from_data_table="all_fasta">
          </options>
          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
        </param>
      </when>
      <when value="history">
        <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />
      </when>
    </conditional>
    <param name="deviations" type="float" value="10.0" label="Generate mean, sd and plots by trimming the data down to MEDIAN + DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION" help="DEVIATIONS; This option is offered because insert size data typically includes enough anomalous values from chimeras and other artifacts to make the mean and SD grossly misleading regarding the real distribution. default=10.0"/>
    <param name="hist_width" type="integer" optional="True" label="Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail" help="HISTOGRAM_WIDTH; optional"/>
    <param name="min_pct" type="float" value="0.05" label="When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads" help="MINIMUM_PCT; (Range: 0 to 1). default=0.05. "/>
    <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
    <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL">
      <option value="ALL_READS" selected="True">All reads</option>
      <option value="SAMPLE">Sample</option>
      <option value="LIBRARY">Library</option>
      <option value="READ_GROUP">Read group</option>
    </param>

    <expand macro="VS" />

  </inputs>

  <outputs>
    <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: tabular"/>
    <data format="pdf" name="histFile" label="${tool.name} on ${on_string}: PDF"/>
  </outputs>

  <tests>
    <test>
      <param name="metric_accumulation_level" value="ALL_READS"/>
      <param name="deviations" value="10.0" />
      <param name="hist_width" value="500" />
      <param name="min_pct" value="0.05" />
      <param name="assume_sorted" value="true" />
      <param name="reference_source_selector" value="history" />
      <param name="ref_file" value="picard_CollectInsertSizeMetrics_ref.fa" />
      <param name="inputFile" value="picard_CollectInsertSizeMetrics.bam" ftype="bam" />
      <output name="outFile" file="picard_CollectInsertSizeMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
    </test>
  </tests>


  <help>

.. class:: infomark

**Purpose**

                                values: {true, false}

@more_info@

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

33:3f254c5ced1d

<tool name="CollectInsertSizeMetrics" id="picard_CollectInsertSizeMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
    <description>plots distribution of insert sizes</description>
    <macros>
        <import>picard_macros.xml</import>
        <token name="@WRAPPER_VERSION@">0</token>
    </macros>
    <expand macro="requirements">
  </expand>
    <command detect_errors="exit_code"><![CDATA[
    @java_options@
    @symlink_element_identifier@
    ##set up input files

    #set $reference_fasta_filename = "localref.fa"

    @handle_reference_source@

    picard CollectInsertSizeMetrics
    --INPUT '$escaped_element_identifier'
    --OUTPUT '${outFile}'
    --Histogram_FILE '${histFile}'
    --DEVIATIONS '${deviations}'

    #if str( $hist_width ):
        --HISTOGRAM_WIDTH '${hist_width}'
    #end if

    --MINIMUM_PCT '${min_pct}'
    --REFERENCE_SEQUENCE '${reference_fasta_filename}'
    --ASSUME_SORTED '${assume_sorted}'
    --METRIC_ACCUMULATION_LEVEL '${metric_accumulation_level}'

    --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."/>
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Load reference genome from">
                <option value="cached">Local cache</option>
                <option value="history">History</option>
            </param>
            <when value="cached">
                <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
                    <options from_data_table="all_fasta">
          </options>
                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                </param>
            </when>
            <when value="history">
                <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference"/>
            </when>
        </conditional>
        <param name="deviations" type="float" value="10.0" label="Generate mean, sd and plots by trimming the data down to MEDIAN + DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION" help="DEVIATIONS; This option is offered because insert size data typically includes enough anomalous values from chimeras and other artifacts to make the mean and SD grossly misleading regarding the real distribution. default=10.0"/>
        <param name="hist_width" type="integer" optional="True" label="Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail" help="HISTOGRAM_WIDTH; optional"/>
        <param name="min_pct" type="float" value="0.05" label="When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads" help="MINIMUM_PCT; (Range: 0 to 1). default=0.05. "/>
        <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
        <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL">
            <option value="ALL_READS" selected="True">All reads</option>
            <option value="SAMPLE">Sample</option>
            <option value="LIBRARY">Library</option>
            <option value="READ_GROUP">Read group</option>
        </param>
        <expand macro="VS"/>
    </inputs>
    <outputs>
        <data format="tabular" name="outFile" label="${tool.name} on ${on_string}"/>
        <data format="pdf" name="histFile" label="${tool.name} on ${on_string}: Histogram"/>
    </outputs>
    <tests>
        <test>
            <param name="metric_accumulation_level" value="ALL_READS"/>
            <param name="deviations" value="10.0"/>
            <param name="hist_width" value="500"/>
            <param name="min_pct" value="0.05"/>
            <param name="assume_sorted" value="true"/>
            <param name="reference_source_selector" value="history"/>
            <param name="ref_file" value="picard_CollectInsertSizeMetrics_ref.fa"/>
            <param name="inputFile" value="picard_CollectInsertSizeMetrics.bam" ftype="bam"/>
            <output name="outFile" file="picard_CollectInsertSizeMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
        </test>
    </tests>
    <help>

.. class:: infomark

**Purpose**

                                values: {true, false}

@more_info@

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