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annotate picard_CollectWgsMetrics.xml @ 9:41b8d087a2d2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
author devteam
date Wed, 07 Dec 2016 14:56:16 -0500
parents e417b1d6288d
children 486d7500da69
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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 detect_errors="exit_code"><![CDATA[
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8 @java_options@
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9 @symlink_element_identifier@
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10 ##set up input files
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12 #set $reference_fasta_filename = "localref.fa"
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14 #if str( $reference_source.reference_source_selector ) == "history":
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15 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
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16 #else:
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17 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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18 #end if
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20 picard
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21 CollectWgsMetrics
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22 INPUT='$escaped_element_identifier'
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23 OUTPUT="${outFile}"
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24 REFERENCE_SEQUENCE="${reference_fasta_filename}"
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25 MINIMUM_MAPPING_QUALITY="${minimum_mapping_quality}"
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26 MINIMUM_BASE_QUALITY="${minimum_base_quality}"
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27 COVERAGE_CAP="${coverage_cap}"
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29 VALIDATION_STRINGENCY="${validation_stringency}"
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30 QUIET=true
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31 VERBOSITY=ERROR
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33 ]]></command>
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34 <inputs>
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35 <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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36 <conditional name="reference_source">
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37 <param name="reference_source_selector" type="select" label="Load reference genome from">
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38 <option value="cached">Local cache</option>
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39 <option value="history">History</option>
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40 </param>
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41 <when value="cached">
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42 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
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43 <options from_data_table="all_fasta">
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44 </options>
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45 <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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46 </param>
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47 </when>
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48 <when value="history">
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49 <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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50 </when>
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51 </conditional>
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52 <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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53 <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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54 <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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57 <expand macro="VS" />
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59 </inputs>
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61 <outputs>
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62 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
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63 </outputs>
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64
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65 <tests>
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66 <test>
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67 <param name="reference_source_selector" value="history" />
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68 <param name="minimum_mapping_quality" value="20" />
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69 <param name="minimum_base_quality" value="20" />
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70 <param name="coverage_cap" value="250" />
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71 <param name="ref_file" value="picard_CollectWgsMetrics_ref.fa" />
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72 <param name="inputFile" value="picard_CollectWgsMetrics.bam" ftype="bam" />
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73 <output name="outFile" file="picard_CollectWgsMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
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74 </test>
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75 </tests>
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77
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78 <help>
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79
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80 .. class:: infomark
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82 **Purpose**
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84 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
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85
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86 @dataset_collections@
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87
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88 @description@
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89
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90 MINIMUM_MAPPING_QUALITY=Integer
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91 MQ=Integer Minimum mapping quality for a read to contribute coverage. Default value: 20.
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92
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93 MINIMUM_BASE_QUALITY=Integer
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94 Q=Integer Minimum base quality for a base to contribute coverage. Default value: 20.
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95
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96 COVERAGE_CAP=Integer
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97 CAP=Integer Treat bases with coverage exceeding this value as if they had coverage at this value.
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98 Default value: 250.
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99
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100 @more_info@
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101
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102 </help>
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103 </tool>
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104
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105