Mercurial > repos > devteam > picard
annotate picard_CollectGcBiasMetrics.xml @ 3:52fdfc45590a draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author | devteam |
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date | Thu, 16 Jul 2015 15:32:31 -0400 |
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children | 08f69add4d06 |
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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="CollectGcBiasMetrics" id="picard_CollectGcBiasMetrics" version="@TOOL_VERSION@.0"> |
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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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6 <expand macro="requirements"> |
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7 <requirement type="package" version="3.1.2">R</requirement> |
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8 </expand> |
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9 <command> |
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10 @java_options@ |
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11 ##set up input files |
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12 |
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13 #set $reference_fasta_filename = "localref.fa" |
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14 |
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15 #if str( $reference_source.reference_source_selector ) == "history": |
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16 ln -s "${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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17 #else: |
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18 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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19 #end if |
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20 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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21 java -jar \$JAVA_JAR_PATH/picard.jar |
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22 CollectGcBiasMetrics |
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23 INPUT="${inputFile}" |
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24 OUTPUT="${outFile}" |
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25 CHART_OUTPUT="${pdfFile}" |
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26 SUMMARY_OUTPUT="${summaryFile}" |
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27 WINDOW_SIZE="${window_size}" |
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28 MINIMUM_GENOME_FRACTION="${minimum_genome_fraction}" |
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29 IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}" |
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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 REFERENCE_SEQUENCE="${reference_fasta_filename}" |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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31 ASSUME_SORTED="${assume_sorted}" |
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32 |
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33 VALIDATION_STRINGENCY="${validation_stringency}" |
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34 QUIET=true |
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35 VERBOSITY=ERROR |
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36 |
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37 </command> |
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38 <inputs> |
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39 <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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40 <conditional name="reference_source"> |
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41 <param name="reference_source_selector" type="select" label="Load reference genome from"> |
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42 <option value="cached">Local cache</option> |
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43 <option value="history">History</option> |
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44 </param> |
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45 <when value="cached"> |
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46 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> |
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47 <options from_data_table="all_fasta"> |
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48 </options> |
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49 <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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50 </param> |
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51 </when> |
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52 <when value="history"> |
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53 <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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54 </when> |
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55 </conditional> |
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56 <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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57 <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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58 <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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59 <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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60 |
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61 <expand macro="VS" /> |
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62 |
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63 </inputs> |
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64 |
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65 <outputs> |
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66 <data format="tabular" name="summaryFile" label="${tool.name} on ${on_string}: Summary stats"/> |
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67 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/> |
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68 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/> |
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69 </outputs> |
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70 |
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71 <tests> |
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72 <test> |
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73 <param name="window_size" value="100" /> |
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74 <param name="minimum_genome_fraction" value="0.00005" /> |
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75 <param name="assume_sorted" value="true" /> |
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76 <param name="is_bisulfite_sequenced" value="true" /> |
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77 <param name="reference_source_selector" value="history" /> |
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78 <param name="ref_file" value="picard_CollectGcBiasMetrics_ref.fa" /> |
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79 <param name="inputFile" value="picard_CollectGcBiasMetrics.bam" ftype="bam" /> |
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80 <output name="outFile" file="picard_CollectGcBiasMetrics_test1.tab" ftype="tabular" lines_diff="4"/> |
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81 </test> |
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82 </tests> |
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83 |
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84 <stdio> |
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85 <exit_code range="1:" level="fatal"/> |
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86 </stdio> |
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87 |
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88 <help> |
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89 |
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90 .. class:: infomark |
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91 |
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92 **Purpose** |
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93 |
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94 Program to chart the nucleotide distribution per cycle in a SAM or BAM file. |
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95 |
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96 @dataset_collections@ |
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97 |
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98 @description@ |
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99 |
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100 ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value: |
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101 false. Possible values: {true, false} |
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102 |
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103 PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false. |
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104 This option can be set to 'null' to clear the default value. Possible values: {true, |
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105 false} |
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106 |
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107 ASSUME_SORTED=Boolean |
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108 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True |
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109 |
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110 @more_info@ |
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111 |
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112 </help> |
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113 </tool> |
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114 |
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115 |