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comparison picard_RevertSam.xml @ 5:3d4f1fa26f0e draft

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author devteam
date Tue, 16 Dec 2014 19:03:21 -0500
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4:ab1f60c26526 5:3d4f1fa26f0e
1 <tool name="RevertSam" id="picard_RevertSam" version="1.126.0">
2 <description>revert SAM/BAM datasets to a previous state</description>
3 <requirements>
4 <requirement type="package" version="1.126.0">picard</requirement>
5 </requirements>
6
7 <macros>
8 <import>picard_macros.xml</import>
9 </macros>
10
11 <command>
12 @java_options@
13
14 java -jar \$JAVA_JAR_PATH/picard.jar
15 RevertSam
16
17 INPUT="${inputFile}"
18 OUTPUT="${outFile}"
19
20 RESTORE_ORIGINAL_QUALITIES="${restore_original_qualities}"
21 REMOVE_DUPLICATE_INFORMATION="${remove_duplicate_information}"
22 REMOVE_ALIGNMENT_INFORMATION="${remove_alignment_information}"
23
24 #for $attribute_to_clear in $attributes_to_clear:
25 ATTRIBUTE_TO_CLEAR="${attribute_to_clear.attribute}"
26 #end for
27
28 SANITIZE="${sanitize}"
29 MAX_DISCARD_FRACTION="${max_discard_fraction}"
30 SAMPLE_ALIAS="${sample_alias}"
31 LIBRARY_NAME="${library_name}"
32
33 SORT_ORDER="${sort_order}"
34 VALIDATION_STRINGENCY="${validation_stringency}"
35 QUIET=true
36 VERBOSITY=ERROR
37
38 </command>
39 <inputs>
40 <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"/>
41 <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"/>
42 <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"/>
43 <param name="remove_alignment_information" type="boolean" checked="True" label="Remove all alignment information from the file" help="REMOVE_ALIGNMENT_INFORMATION; default=True"/>
44 <repeat name="attributes_to_clear" title="Clear attribute" min="0" help="You can provide multiple attributes">
45 <param name="attribute" type="text" size="10" label="When removing alignment information, specify optional tags to remove (e.g., XM)" help="ATTRIBUTE_TO_CLEAR"/>
46 </repeat>
47 <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"/>
48 <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"/>
49 <param name="sample_alias" type="text" size="40" 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"/>
50 <param name="library_name" type="text" size="40" 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"/>
51 <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">
52 <option value="coordinate" selected="True">Coordinate</option>
53 <option value="queryname">Queryname</option>
54 <option value="unsorted">Unsorted</option>
55 </param>
56 <expand macro="VS" />
57
58 </inputs>
59
60 <outputs>
61 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Reverted BAM dataset"/>
62 </outputs>
63
64 <tests>
65 <test>
66 <param name="inputFile" value="picard_RevertSam.bam" ftype="bam"/>
67 <param name="restore_original_qualities" value="True"/>
68 <param name="remove_duplicate_information" value="True"/>
69 <param name="remove_alignment_information" value="True"/>
70 <param name="attribute" value="XM"/>
71 <param name="sanitize" value="False"/>
72 <param name="max_discard_fraction" value="0.01"/>
73 <param name="sample_alias" value="null"/>
74 <param name="library_name" value="null"/>
75 <param name="sort_order" value="coordinate"/>
76 <param name="validation_stringency" value="LENIENT"/>
77 <output name="outFile" file="picard_RevertSam_test1.bam" ftype="bam" lines_diff="2"/>
78 </test>
79 </tests>
80
81 <stdio>
82 <exit_code range="1:" level="fatal"/>
83 </stdio>
84
85 <help>
86
87 **Purpose**
88
89 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.
90
91 @dataset_collections@
92
93 @description@
94
95 SORT_ORDER=SortOrder
96 SO=SortOrder The sort order to create the reverted output file with. Default value: queryname.
97 Possible values: {unsorted, queryname, coordinate}
98
99 RESTORE_ORIGINAL_QUALITIES=Boolean
100 OQ=Boolean True to restore original qualities from the OQ field to the QUAL field if available.
101 Default value: true. Possible values: {true, false}
102
103 REMOVE_DUPLICATE_INFORMATION=Boolean
104 Remove duplicate read flags from all reads. Note that if this is true and
105 REMOVE_ALIGNMENT_INFORMATION==false, the output may have the unusual but sometimes
106 desirable trait of having unmapped reads that are marked as duplicates. Default value:
107 true. Possible values: {true, false}
108
109 REMOVE_ALIGNMENT_INFORMATION=Boolean
110 Remove all alignment information from the file. Default value: true. TPossible values: {true, false}
111
112 ATTRIBUTE_TO_CLEAR=String When removing alignment information, the set of optional tags to remove. This option may
113 be specified 0 or more times.
114
115 SANITIZE=Boolean WARNING: This option is potentially destructive. If enabled will discard reads in order
116 to produce a consistent output BAM. Reads discarded include (but are not limited to)
117 paired reads with missing mates, duplicated records, records with mismatches in length of
118 bases and qualities. This option can only be enabled if the output sort order is
119 queryname and will always cause sorting to occur. Possible values: {true, false}
120
121 MAX_DISCARD_FRACTION=Double If SANITIZE=true and higher than MAX_DISCARD_FRACTION reads are discarded due to
122 sanitization thenthe program will exit with an Exception instead of exiting cleanly.
123 Output BAM will still be valid. Default value: 0.01.
124
125 SAMPLE_ALIAS=String
126 ALIAS=String The sample alias to use in the reverted output file. This will override the existing
127 sample alias in the file and is used only if all the read groups in the input file have
128 the same sample alias Default value: null.
129
130 LIBRARY_NAME=String
131 LIB=String The library name to use in the reverted output file. This will override the existing
132 sample alias in the file and is used only if all the read groups in the input file have
133 the same sample alias Default value: null.
134
135 @more_info@
136
137 </help>
138 </tool>
139
140