annotate picard_ReorderSam.xml @ 2:801f5e934011 draft default tip

Uploaded
author devteam
date Thu, 23 Oct 2014 11:40:52 -0400
parents b76a4f17bbbb
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
1 <tool name="ReorderSam" id="picard_ReorderSam" version="1.122.0">
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
2 <description>reorder reads to match ordering in reference sequences</description>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
3 <requirements><requirement type="package" version="1.122.0">picard</requirement></requirements>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
4
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
5 <macros>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
6 <import>picard_macros.xml</import>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
7 </macros>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
8
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
9 <command>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
10 @java_options@
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
11 #set $picard_dict = "localref.dict"
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
12 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
13
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
14 ln -s "${reference_source.ref_file}" "${ref_fasta}" &amp;&amp;
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
15
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
16 #if str( $reference_source.reference_source_selector ) == "history":
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
17
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
18 java -jar \$JAVA_JAR_PATH/CreateSequenceDictionary.jar REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
19 QUIET=true
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
20 VERBOSITY=ERROR
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
21
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
22 &amp;&amp;
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
23
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
24 #else:
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
25
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
26 #set $ref_fasta = str( $reference_source.ref_file.fields.path )
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
27
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
28 #end if
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
29
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
30 java -jar \$JAVA_JAR_PATH/ReorderSam.jar
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
31 INPUT="${inputFile}"
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
32 OUTPUT="${outFile}"
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
33 REFERENCE="${ref_fasta}"
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
34 ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}"
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
35 ALLOW_CONTIG_LENGTH_DISCORDANCE="${allow_contig_length_discordance}"
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
36
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
37 VALIDATION_STRINGENCY="${validation_stringency}"
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
38 QUIET=true
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
39 VERBOSITY=ERROR
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
40
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
41 </command>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
42
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
43 <inputs>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
44
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
45 <conditional name="reference_source">
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
46 <param name="reference_source_selector" type="select" label="Load reference genome from">
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
47 <option value="cached">Local cache</option>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
48 <option value="history">History</option>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
49 </param>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
50 <when value="cached">
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
51 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
52 <options from_data_table="picard_indexes">
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
53 <filter type="sort_by" column="2" />
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
54 <validator type="no_options" message="No indexes are available" />
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
55 </options>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
56 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
57 </param>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
58 </when>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
59 <when value="history">
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
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" />
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
61 </when>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
62 </conditional>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
63
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
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"/>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
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"/>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
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"/>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
67 <expand macro="VS" />
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
68
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
69 </inputs>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
70 <outputs>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
71 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Reordered BAM"/>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
72 </outputs>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
73 <tests>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
74 <test>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
75 <param name="reference_source_selector" value="history" />
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
76 <param name="ref_file" value="picard_ReorderSam_ref.fa" ftype="fasta" />
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
77 <param name="inputFile" value="picard_ReorderSam.bam" ftype="bam"/>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
78 <param name="allow_incomplete_dict_concordance" value="false"/>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
79 <param name="allow_contig_length_discordance" value="false"/>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
80 <output name="outFile" file="picard_ReorderSam_test1.bam" ftype="bam" lines_diff="2"/>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
81 </test>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
82 </tests>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
83
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
84 <stdio>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
85 <exit_code range="1:" level="fatal"/>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
86 </stdio>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
87
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
88 <help>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
89
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
90 .. class:: infomark
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
91
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
92 **Purpose**
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
93
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
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.
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
95
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
96 @dataset_collections@
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
97
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
98 ----
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
99
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
100 .. class:: warningmark
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
101
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
102 Not to be confused with **SortSam**.
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
103
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
104 @description@
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
105
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
106 ALLOW_INCOMPLETE_DICT_CONCORDANCE=Boolean
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
107 S=Boolean If true, then allows only a partial overlap of the BAM contigs with the new reference
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
108 sequence contigs. By default, this tool requires a corresponding contig in the new
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
109 reference for each read contig Default value: false. Possible values: {true, false}
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
110
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
111 ALLOW_CONTIG_LENGTH_DISCORDANCE=Boolean
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
112 U=Boolean If true, then permits mapping from a read contig to a new reference contig with the same
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
113 name but a different length. Highly dangerous, only use if you know what you are doing.
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
114 Default value: false. Possible values: {true, false}
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
115
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
116 @more_info@
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
117 </help>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
118 </tool>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
119
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
120
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
121
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
122
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
123
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
124
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
125
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
126
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
127
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
128
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
129
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
130
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
131