Mercurial > repos > devteam > picard_122_up

comparison picard_ReorderSam.xml @ 0:b76a4f17bbbb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author devteam
date Thu, 23 Oct 2014 11:31:30 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:b76a4f17bbbb
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}" &amp;&amp;
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 &amp;&amp;
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
120
121
122
123
124
125
126
127
128
129
130
131