Mercurial > repos > devteam > picard
annotate picard_CollectWgsMetrics.xml @ 7:08f69add4d06 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
author | devteam |
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date | Sun, 27 Nov 2016 15:11:36 -0500 |
parents | 52fdfc45590a |
children | e417b1d6288d |
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52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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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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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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7 <command detect_errors="exit_code"><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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8 @java_options@ |
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9 ##set up input files |
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10 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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11 #set $reference_fasta_filename = "localref.fa" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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12 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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13 #if str( $reference_source.reference_source_selector ) == "history": |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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14 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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15 #else: |
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16 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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17 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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18 |
7
08f69add4d06
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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19 picard |
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52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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20 CollectWgsMetrics |
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21 INPUT="${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="${minimum_mapping_quality}" |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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25 MINIMUM_BASE_QUALITY="${minimum_base_quality}" |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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26 COVERAGE_CAP="${coverage_cap}" |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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27 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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28 VALIDATION_STRINGENCY="${validation_stringency}" |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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29 QUIET=true |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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30 VERBOSITY=ERROR |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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31 |
7
08f69add4d06
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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32 ]]></command> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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33 <inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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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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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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35 <conditional name="reference_source"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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36 <param name="reference_source_selector" type="select" label="Load reference genome from"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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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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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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39 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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40 <when value="cached"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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41 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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42 <options from_data_table="all_fasta"> |
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43 </options> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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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 |
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77 <help> |
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78 |
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79 .. class:: infomark |
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80 |
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81 **Purpose** |
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82 |
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83 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments. |
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84 |
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85 @dataset_collections@ |
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86 |
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87 @description@ |
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88 |
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89 MINIMUM_MAPPING_QUALITY=Integer |
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90 MQ=Integer Minimum mapping quality for a read to contribute coverage. Default value: 20. |
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91 |
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92 MINIMUM_BASE_QUALITY=Integer |
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93 Q=Integer Minimum base quality for a base to contribute coverage. Default value: 20. |
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94 |
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95 COVERAGE_CAP=Integer |
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96 CAP=Integer Treat bases with coverage exceeding this value as if they had coverage at this value. |
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97 Default value: 250. |
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98 |
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99 @more_info@ |
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100 |
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101 </help> |
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102 </tool> |
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103 |
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104 |