Mercurial > repos > devteam > picard
annotate picard_RevertSam.xml @ 5:2f3cdd537834 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 6e148b31fed1b322ce720804d8525088ec6d43f9
author | devteam |
---|---|
date | Thu, 29 Oct 2015 22:23:28 -0400 |
parents | 2589e6207cb4 |
children | 08f69add4d06 |
rev | line source |
---|---|
3
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
1 <tool name="RevertSam" id="picard_RevertSam" version="@TOOL_VERSION@.0"> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
2 <description>revert SAM/BAM datasets to a previous state</description> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
3 <macros> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
4 <import>picard_macros.xml</import> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
5 </macros> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
6 <expand macro="requirements" /> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
7 <command> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
8 @java_options@ |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
9 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
10 java -jar \$JAVA_JAR_PATH/picard.jar |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
11 RevertSam |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
12 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
13 INPUT="${inputFile}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
14 OUTPUT="${outFile}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
15 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
16 RESTORE_ORIGINAL_QUALITIES="${restore_original_qualities}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
17 REMOVE_DUPLICATE_INFORMATION="${remove_duplicate_information}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
18 REMOVE_ALIGNMENT_INFORMATION="${remove_alignment_information}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
19 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
20 #for $attribute_to_clear in $attributes_to_clear: |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
21 ATTRIBUTE_TO_CLEAR="${attribute_to_clear.attribute}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
22 #end for |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
23 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
24 SANITIZE="${sanitize}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
25 MAX_DISCARD_FRACTION="${max_discard_fraction}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
26 SAMPLE_ALIAS="${sample_alias}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
27 LIBRARY_NAME="${library_name}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
28 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
29 SORT_ORDER="${sort_order}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
30 VALIDATION_STRINGENCY="${validation_stringency}" |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
31 QUIET=true |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
32 VERBOSITY=ERROR |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
33 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
34 </command> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
35 <inputs> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
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"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
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"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
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"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
39 <param name="remove_alignment_information" type="boolean" checked="True" label="Remove all alignment information from the file" help="REMOVE_ALIGNMENT_INFORMATION; default=True"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
40 <repeat name="attributes_to_clear" title="Clear attribute" min="0" help="You can provide multiple attributes"> |
4
2589e6207cb4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
3
diff
changeset
|
41 <param name="attribute" type="text" label="When removing alignment information, specify optional tags to remove (e.g., XM)" help="ATTRIBUTE_TO_CLEAR"/> |
3
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
42 </repeat> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
43 <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"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
44 <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"/> |
4
2589e6207cb4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
3
diff
changeset
|
45 <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"/> |
2589e6207cb4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
3
diff
changeset
|
46 <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"/> |
3
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
47 <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"> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
48 <option value="coordinate" selected="True">Coordinate</option> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
49 <option value="queryname">Queryname</option> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
50 <option value="unsorted">Unsorted</option> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
51 </param> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
52 <expand macro="VS" /> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
53 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
54 </inputs> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
55 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
56 <outputs> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
57 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Reverted BAM dataset"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
58 </outputs> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
59 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
60 <tests> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
61 <test> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
62 <param name="inputFile" value="picard_RevertSam.bam" ftype="bam"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
63 <param name="restore_original_qualities" value="True"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
64 <param name="remove_duplicate_information" value="True"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
65 <param name="remove_alignment_information" value="True"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
66 <param name="attribute" value="XM"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
67 <param name="sanitize" value="False"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
68 <param name="max_discard_fraction" value="0.01"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
69 <param name="sample_alias" value="null"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
70 <param name="library_name" value="null"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
71 <param name="sort_order" value="coordinate"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
72 <param name="validation_stringency" value="LENIENT"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
73 <output name="outFile" file="picard_RevertSam_test1.bam" ftype="bam" lines_diff="2"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
74 </test> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
75 </tests> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
76 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
77 <stdio> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
78 <exit_code range="1:" level="fatal"/> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
79 </stdio> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
80 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
81 <help> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
82 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
83 **Purpose** |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
84 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
85 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. |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
86 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
87 @dataset_collections@ |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
88 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
89 @description@ |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
90 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
91 SORT_ORDER=SortOrder |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
92 SO=SortOrder The sort order to create the reverted output file with. Default value: queryname. |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
93 Possible values: {unsorted, queryname, coordinate} |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
94 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
95 RESTORE_ORIGINAL_QUALITIES=Boolean |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
96 OQ=Boolean True to restore original qualities from the OQ field to the QUAL field if available. |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
97 Default value: true. Possible values: {true, false} |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
98 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
99 REMOVE_DUPLICATE_INFORMATION=Boolean |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
100 Remove duplicate read flags from all reads. Note that if this is true and |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
101 REMOVE_ALIGNMENT_INFORMATION==false, the output may have the unusual but sometimes |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
102 desirable trait of having unmapped reads that are marked as duplicates. Default value: |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
103 true. Possible values: {true, false} |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
104 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
105 REMOVE_ALIGNMENT_INFORMATION=Boolean |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
106 Remove all alignment information from the file. Default value: true. TPossible values: {true, false} |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
107 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
108 ATTRIBUTE_TO_CLEAR=String When removing alignment information, the set of optional tags to remove. This option may |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
109 be specified 0 or more times. |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
110 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
111 SANITIZE=Boolean WARNING: This option is potentially destructive. If enabled will discard reads in order |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
112 to produce a consistent output BAM. Reads discarded include (but are not limited to) |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
113 paired reads with missing mates, duplicated records, records with mismatches in length of |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
114 bases and qualities. This option can only be enabled if the output sort order is |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
115 queryname and will always cause sorting to occur. Possible values: {true, false} |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
116 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
117 MAX_DISCARD_FRACTION=Double If SANITIZE=true and higher than MAX_DISCARD_FRACTION reads are discarded due to |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
118 sanitization thenthe program will exit with an Exception instead of exiting cleanly. |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
119 Output BAM will still be valid. Default value: 0.01. |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
120 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
121 SAMPLE_ALIAS=String |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
122 ALIAS=String The sample alias to use in the reverted output file. This will override the existing |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
123 sample alias in the file and is used only if all the read groups in the input file have |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
124 the same sample alias Default value: null. |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
125 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
126 LIBRARY_NAME=String |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
127 LIB=String The library name to use in the reverted output file. This will override the existing |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
128 sample alias in the file and is used only if all the read groups in the input file have |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
129 the same sample alias Default value: null. |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
130 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
131 @more_info@ |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
132 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
133 </help> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
134 </tool> |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
135 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
136 |