Mercurial > repos > devteam > picard
annotate picard_CollectGcBiasMetrics.xml @ 13:c7dd8d7946b8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 3ce5dea3af8f4816b4a83914b53402aa84e08fca
author | iuc |
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date | Sat, 20 Jan 2018 08:28:02 -0500 |
parents | 41b8d087a2d2 |
children | 486d7500da69 |
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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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1 <tool name="CollectGcBiasMetrics" id="picard_CollectGcBiasMetrics" version="@TOOL_VERSION@.0"> |
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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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2 <description>charts the GC bias metrics</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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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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6 <expand macro="requirements"> |
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7 <requirement type="package" version="3.3.1">r</requirement> |
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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 </expand> |
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9 <command detect_errors="exit_code"><![CDATA[ |
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10 @java_options@ |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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11 @symlink_element_identifier@ |
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12 ##set up input files |
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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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13 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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14 #set $reference_fasta_filename = "localref.fa" |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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15 |
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16 #if str( $reference_source.reference_source_selector ) == "history": |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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17 ln -s "${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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18 #else: |
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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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19 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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20 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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21 |
08f69add4d06
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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22 picard |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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23 CollectGcBiasMetrics |
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41b8d087a2d2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
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24 INPUT='$escaped_element_identifier' |
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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 OUTPUT="${outFile}" |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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26 CHART_OUTPUT="${pdfFile}" |
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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 SUMMARY_OUTPUT="${summaryFile}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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28 WINDOW_SIZE="${window_size}" |
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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 MINIMUM_GENOME_FRACTION="${minimum_genome_fraction}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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30 IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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31 REFERENCE_SEQUENCE="${reference_fasta_filename}" |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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32 ASSUME_SORTED="${assume_sorted}" |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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33 |
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34 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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35 QUIET=true |
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36 VERBOSITY=ERROR |
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37 |
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38 ]]></command> |
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39 <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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40 <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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41 <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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42 <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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43 <option value="cached">Local cache</option> |
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44 <option value="history">History</option> |
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45 </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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46 <when value="cached"> |
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47 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> |
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48 <options from_data_table="all_fasta"> |
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49 </options> |
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50 <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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51 </param> |
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52 </when> |
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53 <when value="history"> |
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54 <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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55 </when> |
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56 </conditional> |
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57 <param name="window_size" type="integer" value="100" label="The size of windows on the genome that are used to bin reads" help="WINDOW_SIZE; default=100"/> |
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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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58 <param name="minimum_genome_fraction" type="float" value="0.00005" label="For summary metrics, exclude GC windows that include less than this fraction of the genome" help="MINIMUM_GENOME_FRACTION; default=0.0005"/> |
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59 <param name="is_bisulfite_sequenced" type="boolean" label="Calculate the base distribution over PF (passing filtering) reads only" checked="true" truevalue="true" falsevalue="false" help="PF_READS_ONLY"/> |
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60 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> |
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61 |
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62 <expand macro="VS" /> |
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63 |
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64 </inputs> |
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65 |
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66 <outputs> |
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67 <data format="tabular" name="summaryFile" label="${tool.name} on ${on_string}: Summary stats"/> |
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68 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/> |
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69 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/> |
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70 </outputs> |
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71 |
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72 <tests> |
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73 <test> |
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74 <param name="window_size" value="100" /> |
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75 <param name="minimum_genome_fraction" value="0.00005" /> |
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76 <param name="assume_sorted" value="true" /> |
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77 <param name="is_bisulfite_sequenced" value="true" /> |
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78 <param name="reference_source_selector" value="history" /> |
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79 <param name="ref_file" value="picard_CollectGcBiasMetrics_ref.fa" /> |
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80 <param name="inputFile" value="picard_CollectGcBiasMetrics.bam" ftype="bam" /> |
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81 <output name="outFile" file="picard_CollectGcBiasMetrics_test1.tab" ftype="tabular" lines_diff="4"/> |
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82 </test> |
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83 </tests> |
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84 |
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85 |
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86 <help> |
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87 |
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88 .. class:: infomark |
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89 |
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90 **Purpose** |
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91 |
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92 Program to chart the nucleotide distribution per cycle in a SAM or BAM file. |
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93 |
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94 @dataset_collections@ |
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95 |
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96 @description@ |
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97 |
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98 ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value: |
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99 false. Possible values: {true, false} |
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100 |
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101 PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false. |
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102 This option can be set to 'null' to clear the default value. Possible values: {true, |
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103 false} |
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104 |
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105 ASSUME_SORTED=Boolean |
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106 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True |
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107 |
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108 @more_info@ |
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109 |
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110 </help> |
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111 </tool> |
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112 |
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113 |