Mercurial > repos > devteam > picard_122_up
comparison picard_ReorderSam.xml @ 0:b76a4f17bbbb draft
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author | devteam |
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date | Thu, 23 Oct 2014 11:31:30 -0400 |
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-1:000000000000 | 0:b76a4f17bbbb |
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1 <tool name="ReorderSam" id="picard_ReorderSam" version="1.122.0"> | |
2 <description>reorder reads to match ordering in reference sequences</description> | |
3 <requirements><requirement type="package" version="1.122.0">picard</requirement></requirements> | |
4 | |
5 <macros> | |
6 <import>picard_macros.xml</import> | |
7 </macros> | |
8 | |
9 <command> | |
10 @java_options@ | |
11 #set $picard_dict = "localref.dict" | |
12 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension | |
13 | |
14 ln -s "${reference_source.ref_file}" "${ref_fasta}" && | |
15 | |
16 #if str( $reference_source.reference_source_selector ) == "history": | |
17 | |
18 java -jar \$JAVA_JAR_PATH/CreateSequenceDictionary.jar REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" | |
19 QUIET=true | |
20 VERBOSITY=ERROR | |
21 | |
22 && | |
23 | |
24 #else: | |
25 | |
26 #set $ref_fasta = str( $reference_source.ref_file.fields.path ) | |
27 | |
28 #end if | |
29 | |
30 java -jar \$JAVA_JAR_PATH/ReorderSam.jar | |
31 INPUT="${inputFile}" | |
32 OUTPUT="${outFile}" | |
33 REFERENCE="${ref_fasta}" | |
34 ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}" | |
35 ALLOW_CONTIG_LENGTH_DISCORDANCE="${allow_contig_length_discordance}" | |
36 | |
37 VALIDATION_STRINGENCY="${validation_stringency}" | |
38 QUIET=true | |
39 VERBOSITY=ERROR | |
40 | |
41 </command> | |
42 | |
43 <inputs> | |
44 | |
45 <conditional name="reference_source"> | |
46 <param name="reference_source_selector" type="select" label="Load reference genome from"> | |
47 <option value="cached">Local cache</option> | |
48 <option value="history">History</option> | |
49 </param> | |
50 <when value="cached"> | |
51 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list"> | |
52 <options from_data_table="picard_indexes"> | |
53 <filter type="sort_by" column="2" /> | |
54 <validator type="no_options" message="No indexes are available" /> | |
55 </options> | |
56 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> | |
57 </param> | |
58 </when> | |
59 <when value="history"> | |
60 <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" /> | |
61 </when> | |
62 </conditional> | |
63 | |
64 <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"/> | |
65 <param name="allow_incomplete_dict_concordance" type="boolean" label="If true, then allows only a partial overlap of the BAM contigs with the new reference sequence contigs" help="ALLOW_INCOMPLETE_DICT_CONCORDANCE; By default, this tool requires a corresponding contig in the new reference for each read contig; default=False"/> | |
66 <param name="allow_contig_length_discordance" type="boolean" label="If true, then permits mapping from a read contig to a new reference contig with the same name but a different length" help="ALLOW_CONTIG_LENGTH_DISCORDANCE; HIGHLY DANGEROUS! Only use if you know what you are doing; default=False"/> | |
67 <expand macro="VS" /> | |
68 | |
69 </inputs> | |
70 <outputs> | |
71 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Reordered BAM"/> | |
72 </outputs> | |
73 <tests> | |
74 <test> | |
75 <param name="reference_source_selector" value="history" /> | |
76 <param name="ref_file" value="picard_ReorderSam_ref.fa" ftype="fasta" /> | |
77 <param name="inputFile" value="picard_ReorderSam.bam" ftype="bam"/> | |
78 <param name="allow_incomplete_dict_concordance" value="false"/> | |
79 <param name="allow_contig_length_discordance" value="false"/> | |
80 <output name="outFile" file="picard_ReorderSam_test1.bam" ftype="bam" lines_diff="2"/> | |
81 </test> | |
82 </tests> | |
83 | |
84 <stdio> | |
85 <exit_code range="1:" level="fatal"/> | |
86 </stdio> | |
87 | |
88 <help> | |
89 | |
90 .. class:: infomark | |
91 | |
92 **Purpose** | |
93 | |
94 ReorderSam reorders reads in a SAM/BAM file to match the contig ordering in a provided reference file, as determined by exact name matching of contigs. Reads mapped to contigs absent in the new reference are dropped. | |
95 | |
96 @dataset_collections@ | |
97 | |
98 ---- | |
99 | |
100 .. class:: warningmark | |
101 | |
102 Not to be confused with **SortSam**. | |
103 | |
104 @description@ | |
105 | |
106 ALLOW_INCOMPLETE_DICT_CONCORDANCE=Boolean | |
107 S=Boolean If true, then allows only a partial overlap of the BAM contigs with the new reference | |
108 sequence contigs. By default, this tool requires a corresponding contig in the new | |
109 reference for each read contig Default value: false. Possible values: {true, false} | |
110 | |
111 ALLOW_CONTIG_LENGTH_DISCORDANCE=Boolean | |
112 U=Boolean If true, then permits mapping from a read contig to a new reference contig with the same | |
113 name but a different length. Highly dangerous, only use if you know what you are doing. | |
114 Default value: false. Possible values: {true, false} | |
115 | |
116 @more_info@ | |
117 </help> | |
118 </tool> | |
119 | |
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