comparison picard_CollectSequencingArtifactsMetrics.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 id='picard_artifact_metrics' name='Picard Collect Sequencing Artifact Metrics' version="@TOOL_VERSION@.@WRAPPER_VERSION@">
  <description>Collect metrics to quantify single-base sequencing artifacts</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 $reference_fasta_filename = "localref.fa"
    @handle_reference_source@
    
    picard 
    CollectSequencingArtifactMetrics 
    I='$escaped_element_identifier'
    O='OutPut'
    R='${reference_fasta_filename}'
    AS=${assume_sorted}
    CONTEXT_SIZE=${context_size}
    INCLUDE_DUPLICATES='${duplicates}'
    #if $contexts_to_print 
      #for $context in str($contexts_to_print).split(','):
          CONTEXTS_TO_PRINT='${context}'
      #end for;
    #end if;
    MINIMUM_QUALITY_SCORE='${min_quality_score}'
    INCLUDE_UNPAIRED='${unpaired}'
    MAXIMUM_INSERT_SIZE='${max_size}'
    MINIMUM_INSERT_SIZE='${min_size}'
    MINIMUM_MAPPING_QUALITY='${minim_map_quality}'
    VALIDATION_STRINGENCY='${validation_stringency}';
  ]]></command>  
  <inputs>
    <param name='inputFile' format="sam,bam" type='data' label='SAM/BAM Input file'/>
    <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="Use dictionary from the list" help="Select genome from the list">
          <options from_data_table="picard_indexes">
            <filter type="sort_by" column="2" />
            <validator type="no_options" message="No indexes are available" />
          </options>
          <validator type="no_options" message="A built-in dictionary 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 following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" />
      </when>
    </conditional>
  
    <param name='context_size' value="1" type='integer' label='How many nucleotides (context) on each side to consider' help='e.g NXN corresponds to 1 "N" on each side of "X"'/>
    <param name="contexts_to_print" type="text" label="Contexts to print in the detailed tables, separated by comma (avoid spaces)" help="e.g. (for context size=1) AAA,AGG. Default prints all contexts">
        <sanitizer>
            <valid initial="string.letters"><add value="," /></valid>
        </sanitizer>
    </param>  
    <param name='min_quality_score' type='integer' value='30' label='Minimum base quality score'/>
    <param name="max_size" type="integer" value="600" label="Maximum insert size"/>
    <param name="min_size" type="integer" value="30" label="Minimum insert size"/>
    <param name="minim_map_quality" type="integer" value="20" label="Minimum mapping quality"/>
    <param name='assume_sorted' type='boolean' label='Assume SAM/BAM is sorted'/>
    <param name='duplicates' type='boolean' label='Include duplicates' checked="false" truevalue="true" falsevalue="false"/>
    <param name='unpaired' type='boolean' label='Include unpaired reads' checked="false" truevalue="true" falsevalue="false"/>

    <expand macro="VS" />

  </inputs>

  <outputs>
    <data name='pre_details' format="tabular"  from_work_dir="OutPut.pre_adapter_detail_metrics" label='Detailed table for artifacts introduced prior to the addition of adapters'/>
    <data name='pre_summary' format="tabular"  from_work_dir="OutPut.pre_adapter_summary_metrics" label='Summary table for artifacts introduced prior to the addition of adapters'/>
    <data name='pos_details' format="tabular"  from_work_dir="OutPut.bait_bias_detail_metrics" label='Detailed table for artifacts introduced posterior to the addition of adapters'/>
    <data name='pos_summary' format="tabular"  from_work_dir="OutPut.bait_bias_summary_metrics" label='Summary table for artifacts introduced posterior to the addition of adapters'/>
    <data name='err_summary' format="tabular"  from_work_dir="OutPut.error_summary_metrics" label='General Summary of artifactual errors'/>
  </outputs>
  
  <tests>
    <test>
      <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam" />
      <param name="reference_source_selector" value="history"/>
      <param name="ref_file" value="picard_BedToIntervalList_ref.fa" />
      <param name="context_size" value="1" />
      <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG" />
      <output name='pre_details' file='pre_details' ftype="tabular"  value="pre_detail" lines_diff="4"/>
      <output name='pre_summary' file='pre_summary' ftype="tabular"  value="pre_summary" lines_diff="4"/>
      <output name='pos_details' file='pos_details' ftype="tabular"  value="pos_detail" lines_diff="4"/>
      <output name='pos_summary' file='pos_summary' ftype="tabular"  value="pos_summary" lines_diff="4"/>
      <output name='err_summary' file='err_summary' ftype="tabular"  value="err_summary" lines_diff="4"/>
    </test>
    <test>
      <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam" dbkey="hg38"/>
      <param name="reference_source_selector" value="cached"/>
      <param name="context_size" value="1" />
      <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG" />
      <output name='pre_details' file='pre_details' ftype="tabular"  value="pre_detail" lines_diff="4"/>
      <output name='pre_summary' file='pre_summary' ftype="tabular"  value="pre_summary" lines_diff="4"/>
      <output name='pos_details' file='pos_details' ftype="tabular"  value="pos_detail" lines_diff="4"/>
      <output name='pos_summary' file='pos_summary' ftype="tabular"  value="pos_summary" lines_diff="4"/>
      <output name='err_summary' file='err_summary' ftype="tabular"  value="err_summary" lines_diff="4"/>
    </test>
  </tests>
  <help>

.. class:: infomark

**Purpose**

  MINIMUM_QUALITY_SCORE           The minimum base quality score for a base to be included in analysis. Default = 20

@more_info@

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

33:3f254c5ced1d

<tool id="picard_artifact_metrics" name="Picard Collect Sequencing Artifact Metrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
    <description>Collect metrics to quantify single-base sequencing artifacts</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 $reference_fasta_filename = "localref.fa"
    @handle_reference_source@
    
    picard CollectSequencingArtifactMetrics 
    --I '$escaped_element_identifier'
    --O 'OutPut'
    --R '${reference_fasta_filename}'
    --AS ${assume_sorted}
    --CONTEXT_SIZE ${context_size}
    --INCLUDE_DUPLICATES '${duplicates}'
    #if $contexts_to_print 
        #for $context in str($contexts_to_print).split(','):
          --CONTEXTS_TO_PRINT '${context}'
        #end for;
    #end if;
    --MINIMUM_QUALITY_SCORE '${min_quality_score}'
    --INCLUDE_UNPAIRED '${unpaired}'
    --MAXIMUM_INSERT_SIZE '${max_size}'
    --MINIMUM_INSERT_SIZE '${min_size}'
    --MINIMUM_MAPPING_QUALITY '${minim_map_quality}'
    --VALIDATION_STRINGENCY '${validation_stringency}';
  ]]></command>
    <inputs>
        <param name="inputFile" format="sam,bam" type="data" label="SAM/BAM Input file"/>
        <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="Use dictionary from the list" help="Select genome from the list">
                    <options from_data_table="picard_indexes">
                        <filter type="sort_by" column="2"/>
                        <validator type="no_options" message="No indexes are available"/>
                    </options>
                    <validator type="no_options" message="A built-in dictionary 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 following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command"/>
            </when>
        </conditional>
        <param name="context_size" value="1" type="integer" label="How many nucleotides (context) on each side to consider" help="e.g NXN corresponds to 1 &quot;N&quot; on each side of &quot;X&quot;"/>
        <param name="contexts_to_print" type="text" label="Contexts to print in the detailed tables, separated by comma (avoid spaces)" help="e.g. (for context size=1) AAA,AGG. Default prints all contexts">
            <sanitizer>
                <valid initial="string.letters">
                    <add value=","/>
                </valid>
            </sanitizer>
        </param>
        <param name="min_quality_score" type="integer" value="30" label="Minimum base quality score"/>
        <param name="max_size" type="integer" value="600" label="Maximum insert size"/>
        <param name="min_size" type="integer" value="30" label="Minimum insert size"/>
        <param name="minim_map_quality" type="integer" value="20" label="Minimum mapping quality"/>
        <param name="assume_sorted" type="boolean" label="Assume SAM/BAM is sorted"/>
        <param name="duplicates" type="boolean" label="Include duplicates" checked="false" truevalue="true" falsevalue="false"/>
        <param name="unpaired" type="boolean" label="Include unpaired reads" checked="false" truevalue="true" falsevalue="false"/>
        <expand macro="VS"/>
    </inputs>
    <outputs>
        <data name="pre_details" format="tabular" from_work_dir="OutPut.pre_adapter_detail_metrics" label="Detailed table for artifacts introduced prior to the addition of adapters"/>
        <data name="pre_summary" format="tabular" from_work_dir="OutPut.pre_adapter_summary_metrics" label="Summary table for artifacts introduced prior to the addition of adapters"/>
        <data name="pos_details" format="tabular" from_work_dir="OutPut.bait_bias_detail_metrics" label="Detailed table for artifacts introduced posterior to the addition of adapters"/>
        <data name="pos_summary" format="tabular" from_work_dir="OutPut.bait_bias_summary_metrics" label="Summary table for artifacts introduced posterior to the addition of adapters"/>
        <data name="err_summary" format="tabular" from_work_dir="OutPut.error_summary_metrics" label="General Summary of artifactual errors"/>
    </outputs>
    <tests>
        <test>
            <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam"/>
            <param name="reference_source_selector" value="history"/>
            <param name="ref_file" value="picard_BedToIntervalList_ref.fa"/>
            <param name="context_size" value="1"/>
            <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG"/>
            <output name="pre_details" file="pre_details" ftype="tabular" value="pre_detail" lines_diff="4"/>
            <output name="pre_summary" file="pre_summary" ftype="tabular" value="pre_summary" lines_diff="4"/>
            <output name="pos_details" file="pos_details" ftype="tabular" value="pos_detail" lines_diff="4"/>
            <output name="pos_summary" file="pos_summary" ftype="tabular" value="pos_summary" lines_diff="4"/>
            <output name="err_summary" file="err_summary" ftype="tabular" value="err_summary" lines_diff="4"/>
        </test>
        <test>
            <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam" dbkey="hg38"/>
            <param name="reference_source_selector" value="cached"/>
            <param name="context_size" value="1"/>
            <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG"/>
            <output name="pre_details" file="pre_details" ftype="tabular" value="pre_detail" lines_diff="4"/>
            <output name="pre_summary" file="pre_summary" ftype="tabular" value="pre_summary" lines_diff="4"/>
            <output name="pos_details" file="pos_details" ftype="tabular" value="pos_detail" lines_diff="4"/>
            <output name="pos_summary" file="pos_summary" ftype="tabular" value="pos_summary" lines_diff="4"/>
            <output name="err_summary" file="err_summary" ftype="tabular" value="err_summary" lines_diff="4"/>
        </test>
    </tests>
    <help>

.. class:: infomark

**Purpose**

  MINIMUM_QUALITY_SCORE           The minimum base quality score for a base to be included in analysis. Default = 20

@more_info@

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