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annotate picard_RevertSam.xml @ 10:126c30841c38 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
author devteam
date Thu, 08 Dec 2016 06:43:24 -0500
parents e417b1d6288d
children 486d7500da69
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1 <tool name="RevertSam" id="picard_RevertSam" version="@TOOL_VERSION@.0">
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2 <description>revert SAM/BAM datasets to a previous state</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 picard
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10 RevertSam
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12 INPUT='$inputFile'
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13 OUTPUT="${outFile}"
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15 RESTORE_ORIGINAL_QUALITIES="${restore_original_qualities}"
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16 REMOVE_DUPLICATE_INFORMATION="${remove_duplicate_information}"
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17 REMOVE_ALIGNMENT_INFORMATION="${remove_alignment_information}"
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19 #for $attribute_to_clear in $attributes_to_clear:
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20 ATTRIBUTE_TO_CLEAR="${attribute_to_clear.attribute}"
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21 #end for
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23 SANITIZE="${sanitize}"
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24 MAX_DISCARD_FRACTION="${max_discard_fraction}"
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25 SAMPLE_ALIAS="${sample_alias}"
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26 LIBRARY_NAME="${library_name}"
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27
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28 SORT_ORDER="${sort_order}"
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29 VALIDATION_STRINGENCY="${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" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
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36 <param name="restore_original_qualities" type="boolean" checked="True" label="Restore original qualities from the OQ field to the QUAL field if available" help="RESTORE_ORIGINAL_QUALITIES; default=True"/>
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37 <param name="remove_duplicate_information" type="boolean" checked="True" label="Remove duplicate read flags from all reads" help="REMOVE_DUPLICATE_INFORMATION; Note that if this is true and REMOVE_ALIGNMENT_INFORMATION is set to False, the output may have the unusual but sometimes desirable trait of having unmapped reads that are marked as duplicates; default=True"/>
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38 <param name="remove_alignment_information" type="boolean" checked="True" label="Remove all alignment information from the file" help="REMOVE_ALIGNMENT_INFORMATION; default=True"/>
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39 <repeat name="attributes_to_clear" title="Clear attribute" min="0" help="You can provide multiple attributes">
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40 <param name="attribute" type="text" label="When removing alignment information, specify optional tags to remove (e.g., XM)" help="ATTRIBUTE_TO_CLEAR"/>
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41 </repeat>
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42 <param name="sanitize" type="boolean" label="Discard reads in order to produce a consistent output BAM" help="SANITIZE; WARNING: This option is potentially destructive. Reads discarded include (but are not limited to) paired reads with missing mates, duplicated records, records with mismatches in length of bases and qualities. This option can only be enabled if the output sort order is queryname and will always cause sorting to occur; default=False"/>
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43 <param name="max_discard_fraction" value="0.01" type="float" min="0.0" max="1.0" label="If SANITIZE=true and higher than MAX_DISCARD_FRACTION reads are discarded due to sanitization then the program will exit with an Exception instead of exiting cleanly" help="MAX_DISCARD_FRACTION; default=0.01"/>
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44 <param name="sample_alias" type="text" value="null" label="The sample alias to use in the reverted output file. This will override the existing sample alias in the file and is used only if all the read groups in the input file have the same sample alias" help="SAMPLE_ALIAS; default=Null"/>
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45 <param name="library_name" type="text" value="null" label="The library name to use in the reverted output file. This will override the existing sample alias in the file and is used only if all the read groups in the input file have the same sample alias" help="LIBRARY_NAME; default=Null"/>
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46 <param name="sort_order" type="select" label="The sort order to create the reverted output file with" help="SORT_ORDER; Picard default=queryname; Galaxy default=coordinate">
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47 <option value="coordinate" selected="True">Coordinate</option>
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48 <option value="queryname">Queryname</option>
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49 <option value="unsorted">Unsorted</option>
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50 </param>
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51 <expand macro="VS" />
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53 </inputs>
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54
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55 <outputs>
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56 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Reverted BAM dataset"/>
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57 </outputs>
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58
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59 <tests>
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60 <test>
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61 <param name="inputFile" value="picard_RevertSam.bam" ftype="bam"/>
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62 <param name="restore_original_qualities" value="True"/>
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63 <param name="remove_duplicate_information" value="True"/>
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64 <param name="remove_alignment_information" value="True"/>
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65 <param name="attribute" value="XM"/>
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66 <param name="sanitize" value="False"/>
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67 <param name="max_discard_fraction" value="0.01"/>
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68 <param name="sample_alias" value="null"/>
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69 <param name="library_name" value="null"/>
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70 <param name="sort_order" value="coordinate"/>
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71 <param name="validation_stringency" value="LENIENT"/>
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72 <output name="outFile" file="picard_RevertSam_test1.bam" ftype="bam" lines_diff="4"/>
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73 </test>
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74 </tests>
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76
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77 <help>
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79 **Purpose**
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81 Reverts SAM or BAM files to a previous state by removing certain types of information and/or substituting in the original quality scores when available.
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82
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83 @dataset_collections@
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84
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85 @description@
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86
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87 SORT_ORDER=SortOrder
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88 SO=SortOrder The sort order to create the reverted output file with. Default value: queryname.
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89 Possible values: {unsorted, queryname, coordinate}
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90
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91 RESTORE_ORIGINAL_QUALITIES=Boolean
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92 OQ=Boolean True to restore original qualities from the OQ field to the QUAL field if available.
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93 Default value: true. Possible values: {true, false}
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94
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95 REMOVE_DUPLICATE_INFORMATION=Boolean
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96 Remove duplicate read flags from all reads. Note that if this is true and
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97 REMOVE_ALIGNMENT_INFORMATION==false, the output may have the unusual but sometimes
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98 desirable trait of having unmapped reads that are marked as duplicates. Default value:
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99 true. Possible values: {true, false}
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100
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101 REMOVE_ALIGNMENT_INFORMATION=Boolean
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102 Remove all alignment information from the file. Default value: true. TPossible values: {true, false}
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103
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104 ATTRIBUTE_TO_CLEAR=String When removing alignment information, the set of optional tags to remove. This option may
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105 be specified 0 or more times.
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106
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107 SANITIZE=Boolean WARNING: This option is potentially destructive. If enabled will discard reads in order
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108 to produce a consistent output BAM. Reads discarded include (but are not limited to)
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109 paired reads with missing mates, duplicated records, records with mismatches in length of
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110 bases and qualities. This option can only be enabled if the output sort order is
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111 queryname and will always cause sorting to occur. Possible values: {true, false}
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112
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113 MAX_DISCARD_FRACTION=Double If SANITIZE=true and higher than MAX_DISCARD_FRACTION reads are discarded due to
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114 sanitization thenthe program will exit with an Exception instead of exiting cleanly.
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115 Output BAM will still be valid. Default value: 0.01.
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116
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117 SAMPLE_ALIAS=String
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118 ALIAS=String The sample alias to use in the reverted output file. This will override the existing
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119 sample alias in the file and is used only if all the read groups in the input file have
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120 the same sample alias Default value: null.
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121
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122 LIBRARY_NAME=String
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123 LIB=String The library name to use in the reverted output file. This will override the existing
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124 sample alias in the file and is used only if all the read groups in the input file have
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125 the same sample alias Default value: null.
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126
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127 @more_info@
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128
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129 </help>
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130 </tool>
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131
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132