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comparison picard_RevertSam.xml @ 13:7e6fd3d0f16e draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
author devteam
date Tue, 06 Dec 2016 10:04:41 -0500
parents 05087b27692a
children 5053a18d9bc8
comparison
equal deleted inserted replaced
12:05087b27692a 13:7e6fd3d0f16e
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 @java_options@ 8 @java_options@
9
10 picard 9 picard
11 RevertSam 10 RevertSam
12 11
13 INPUT="${inputFile}" 12 INPUT='$inputFile'
14 OUTPUT="${outFile}" 13 OUTPUT="${outFile}"
15 14
16 RESTORE_ORIGINAL_QUALITIES="${restore_original_qualities}" 15 RESTORE_ORIGINAL_QUALITIES="${restore_original_qualities}"
17 REMOVE_DUPLICATE_INFORMATION="${remove_duplicate_information}" 16 REMOVE_DUPLICATE_INFORMATION="${remove_duplicate_information}"
18 REMOVE_ALIGNMENT_INFORMATION="${remove_alignment_information}" 17 REMOVE_ALIGNMENT_INFORMATION="${remove_alignment_information}"
19 18
20 #for $attribute_to_clear in $attributes_to_clear: 19 #for $attribute_to_clear in $attributes_to_clear:
21 ATTRIBUTE_TO_CLEAR="${attribute_to_clear.attribute}" 20 ATTRIBUTE_TO_CLEAR="${attribute_to_clear.attribute}"
22 #end for 21 #end for
23 22
24 SANITIZE="${sanitize}" 23 SANITIZE="${sanitize}"
25 MAX_DISCARD_FRACTION="${max_discard_fraction}" 24 MAX_DISCARD_FRACTION="${max_discard_fraction}"
26 SAMPLE_ALIAS="${sample_alias}" 25 SAMPLE_ALIAS="${sample_alias}"
27 LIBRARY_NAME="${library_name}" 26 LIBRARY_NAME="${library_name}"
28 27
29 SORT_ORDER="${sort_order}" 28 SORT_ORDER="${sort_order}"
30 VALIDATION_STRINGENCY="${validation_stringency}" 29 VALIDATION_STRINGENCY="${validation_stringency}"
31 QUIET=true 30 QUIET=true
32 VERBOSITY=ERROR 31 VERBOSITY=ERROR
33 32
34 ]]></command> 33 ]]></command>
35 <inputs> 34 <inputs>
36 <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"/> 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"/>
37 <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"/> 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"/>
38 <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"/> 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"/>
48 <option value="coordinate" selected="True">Coordinate</option> 47 <option value="coordinate" selected="True">Coordinate</option>
49 <option value="queryname">Queryname</option> 48 <option value="queryname">Queryname</option>
50 <option value="unsorted">Unsorted</option> 49 <option value="unsorted">Unsorted</option>
51 </param> 50 </param>
52 <expand macro="VS" /> 51 <expand macro="VS" />
53 52
54 </inputs> 53 </inputs>
55 54
56 <outputs> 55 <outputs>
57 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Reverted BAM dataset"/> 56 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Reverted BAM dataset"/>
58 </outputs> 57 </outputs>
59 58
60 <tests> 59 <tests>
61 <test> 60 <test>
62 <param name="inputFile" value="picard_RevertSam.bam" ftype="bam"/> 61 <param name="inputFile" value="picard_RevertSam.bam" ftype="bam"/>
63 <param name="restore_original_qualities" value="True"/> 62 <param name="restore_original_qualities" value="True"/>
64 <param name="remove_duplicate_information" value="True"/> 63 <param name="remove_duplicate_information" value="True"/>
71 <param name="sort_order" value="coordinate"/> 70 <param name="sort_order" value="coordinate"/>
72 <param name="validation_stringency" value="LENIENT"/> 71 <param name="validation_stringency" value="LENIENT"/>
73 <output name="outFile" file="picard_RevertSam_test1.bam" ftype="bam" lines_diff="4"/> 72 <output name="outFile" file="picard_RevertSam_test1.bam" ftype="bam" lines_diff="4"/>
74 </test> 73 </test>
75 </tests> 74 </tests>
76 75
77 76
78 <help> 77 <help>
79 78
80 **Purpose** 79 **Purpose**
81 80
82 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. 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.
83 82
84 @dataset_collections@ 83 @dataset_collections@
85 84
86 @description@ 85 @description@
87 86
88 SORT_ORDER=SortOrder 87 SORT_ORDER=SortOrder
89 SO=SortOrder The sort order to create the reverted output file with. Default value: queryname. 88 SO=SortOrder The sort order to create the reverted output file with. Default value: queryname.
90 Possible values: {unsorted, queryname, coordinate} 89 Possible values: {unsorted, queryname, coordinate}
91 90
92 RESTORE_ORIGINAL_QUALITIES=Boolean 91 RESTORE_ORIGINAL_QUALITIES=Boolean
93 OQ=Boolean True to restore original qualities from the OQ field to the QUAL field if available. 92 OQ=Boolean True to restore original qualities from the OQ field to the QUAL field if available.
94 Default value: true. Possible values: {true, false} 93 Default value: true. Possible values: {true, false}
95 94
96 REMOVE_DUPLICATE_INFORMATION=Boolean 95 REMOVE_DUPLICATE_INFORMATION=Boolean
97 Remove duplicate read flags from all reads. Note that if this is true and 96 Remove duplicate read flags from all reads. Note that if this is true and
98 REMOVE_ALIGNMENT_INFORMATION==false, the output may have the unusual but sometimes 97 REMOVE_ALIGNMENT_INFORMATION==false, the output may have the unusual but sometimes
99 desirable trait of having unmapped reads that are marked as duplicates. Default value: 98 desirable trait of having unmapped reads that are marked as duplicates. Default value:
100 true. Possible values: {true, false} 99 true. Possible values: {true, false}
101 100
102 REMOVE_ALIGNMENT_INFORMATION=Boolean 101 REMOVE_ALIGNMENT_INFORMATION=Boolean
103 Remove all alignment information from the file. Default value: true. TPossible values: {true, false} 102 Remove all alignment information from the file. Default value: true. TPossible values: {true, false}
104 103
105 ATTRIBUTE_TO_CLEAR=String When removing alignment information, the set of optional tags to remove. This option may 104 ATTRIBUTE_TO_CLEAR=String When removing alignment information, the set of optional tags to remove. This option may
106 be specified 0 or more times. 105 be specified 0 or more times.
107 106
108 SANITIZE=Boolean WARNING: This option is potentially destructive. If enabled will discard reads in order 107 SANITIZE=Boolean WARNING: This option is potentially destructive. If enabled will discard reads in order
109 to produce a consistent output BAM. Reads discarded include (but are not limited to) 108 to produce a consistent output BAM. Reads discarded include (but are not limited to)
110 paired reads with missing mates, duplicated records, records with mismatches in length of 109 paired reads with missing mates, duplicated records, records with mismatches in length of
111 bases and qualities. This option can only be enabled if the output sort order is 110 bases and qualities. This option can only be enabled if the output sort order is
112 queryname and will always cause sorting to occur. Possible values: {true, false} 111 queryname and will always cause sorting to occur. Possible values: {true, false}
113 112
114 MAX_DISCARD_FRACTION=Double If SANITIZE=true and higher than MAX_DISCARD_FRACTION reads are discarded due to 113 MAX_DISCARD_FRACTION=Double If SANITIZE=true and higher than MAX_DISCARD_FRACTION reads are discarded due to
115 sanitization thenthe program will exit with an Exception instead of exiting cleanly. 114 sanitization thenthe program will exit with an Exception instead of exiting cleanly.
116 Output BAM will still be valid. Default value: 0.01. 115 Output BAM will still be valid. Default value: 0.01.
117 116
118 SAMPLE_ALIAS=String 117 SAMPLE_ALIAS=String
119 ALIAS=String The sample alias to use in the reverted output file. This will override the existing 118 ALIAS=String The sample alias to use in the reverted output file. This will override the existing
120 sample alias in the file and is used only if all the read groups in the input file have 119 sample alias in the file and is used only if all the read groups in the input file have
121 the same sample alias Default value: null. 120 the same sample alias Default value: null.
122 121
123 LIBRARY_NAME=String 122 LIBRARY_NAME=String
124 LIB=String The library name to use in the reverted output file. This will override the existing 123 LIB=String The library name to use in the reverted output file. This will override the existing
125 sample alias in the file and is used only if all the read groups in the input file have 124 sample alias in the file and is used only if all the read groups in the input file have
126 the same sample alias Default value: null. 125 the same sample alias Default value: null.
127 126
128 @more_info@ 127 @more_info@
129 128
130 </help> 129 </help>
131 </tool> 130 </tool>
132 131