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annotate picard_CollectWgsMetrics.xml @ 3:52fdfc45590a draft

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author devteam
date Thu, 16 Jul 2015 15:32:31 -0400
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1 <tool name="CollectWgsMetrics" id="picard_CollectWgsMetrics" version="@TOOL_VERSION@.0">
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2 <description>compute metrics for evaluating of whole genome sequencing experiments</description>
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3 <macros>
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4 <import>picard_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command>
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8 @java_options@
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9 ##set up input files
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11 #set $reference_fasta_filename = "localref.fa"
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13 #if str( $reference_source.reference_source_selector ) == "history":
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14 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
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15 #else:
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16 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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17 #end if
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19 java -jar \$JAVA_JAR_PATH/picard.jar
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20 CollectWgsMetrics
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21 INPUT="${inputFile}"
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22 OUTPUT="${outFile}"
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23 REFERENCE_SEQUENCE="${reference_fasta_filename}"
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24 MINIMUM_MAPPING_QUALITY="${minimum_mapping_quality}"
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25 MINIMUM_BASE_QUALITY="${minimum_base_quality}"
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26 COVERAGE_CAP="${coverage_cap}"
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27
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28 VALIDATION_STRINGENCY="${validation_stringency}"
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29 QUIET=true
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30 VERBOSITY=ERROR
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32 </command>
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33 <inputs>
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34 <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"/>
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35 <conditional name="reference_source">
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36 <param name="reference_source_selector" type="select" label="Load reference genome from">
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37 <option value="cached">Local cache</option>
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38 <option value="history">History</option>
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39 </param>
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40 <when value="cached">
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41 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
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42 <options from_data_table="all_fasta">
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43 </options>
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44 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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45 </param>
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46 </when>
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47 <when value="history">
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48 <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" />
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49 </when>
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50 </conditional>
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51 <param name="minimum_mapping_quality" type="integer" value="20" label="Minimum mapping quality for a read to contribute coverage" help="MINIMUM_MAPPING_QUALITY; default=20"/>
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52 <param name="minimum_base_quality" type="integer" value="20" label="Minimum base quality for a base to contribute coverage" help="MINIMUM_BASE_QUALITY; default=20"/>
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53 <param name="coverage_cap" type="integer" value="250" label="Treat bases with coverage exceeding this value as if they had coverage at this value" help="COVERAGE_CAP; default=250"/>
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54
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55
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56 <expand macro="VS" />
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57
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58 </inputs>
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59
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60 <outputs>
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61 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
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62 </outputs>
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63
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64 <tests>
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65 <test>
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66 <param name="reference_source_selector" value="history" />
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67 <param name="minimum_mapping_quality" value="20" />
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68 <param name="minimum_base_quality" value="20" />
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69 <param name="coverage_cap" value="250" />
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70 <param name="ref_file" value="picard_CollectWgsMetrics_ref.fa" />
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71 <param name="inputFile" value="picard_CollectWgsMetrics.bam" ftype="bam" />
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72 <output name="outFile" file="picard_CollectWgsMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
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73 </test>
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74 </tests>
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75
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76 <stdio>
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77 <exit_code range="1:" level="fatal"/>
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78 </stdio>
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79
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80 <help>
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81
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82 .. class:: infomark
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83
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84 **Purpose**
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85
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86 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
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87
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88 @dataset_collections@
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90 @description@
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92 MINIMUM_MAPPING_QUALITY=Integer
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93 MQ=Integer Minimum mapping quality for a read to contribute coverage. Default value: 20.
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95 MINIMUM_BASE_QUALITY=Integer
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96 Q=Integer Minimum base quality for a base to contribute coverage. Default value: 20.
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98 COVERAGE_CAP=Integer
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99 CAP=Integer Treat bases with coverage exceeding this value as if they had coverage at this value.
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100 Default value: 250.
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102 @more_info@
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104 </help>
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105 </tool>
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107