Mercurial > repos > devteam > picard_plus
comparison picard_FilterSamReads.xml @ 0:4419e9980172 draft
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author | devteam |
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date | Thu, 23 Oct 2014 12:03:34 -0400 |
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-1:000000000000 | 0:4419e9980172 |
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1 <tool name="FilterSamReads" id="picard_FilterSamReads" version="1.122.0"> | |
2 <description>include or exclude aligned and unaligned reads and read lists</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.122.0">picard</requirement> | |
5 </requirements> | |
6 | |
7 <macros> | |
8 <import>picard_macros.xml</import> | |
9 </macros> | |
10 | |
11 <command> | |
12 @java_options@ | |
13 | |
14 ##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order | |
15 | |
16 java -jar \$JAVA_JAR_PATH/SortSam.jar | |
17 INPUT="${inputFile}" | |
18 OUTPUT=query_sorted_bam.bam | |
19 SORT_ORDER=queryname | |
20 VALIDATION_STRINGENCY=LENIENT | |
21 QUIET=true | |
22 VERBOSITY=ERROR | |
23 | |
24 && | |
25 | |
26 java -jar \$JAVA_JAR_PATH/FilterSamReads.jar | |
27 INPUT=query_sorted_bam.bam | |
28 FILTER="${filter_type.filter}" | |
29 | |
30 #if ( str( $filter_type.filter ) == "includeReadList" or str( $filter_type.filter ) == "excludeReadList" ): | |
31 READ_LIST_FILE="${filter_type.read_list_file}" | |
32 #end if | |
33 | |
34 OUTPUT="${outFile}" | |
35 SORT_ORDER=coordinate | |
36 VALIDATION_STRINGENCY="${validation_stringency}" | |
37 QUIET=true | |
38 VERBOSITY=ERROR | |
39 | |
40 </command> | |
41 <inputs> | |
42 <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> | |
43 <conditional name="filter_type"> | |
44 <param name="filter" type="select" label="Select filtering type" help="FILTER; see Help for deatiled info"> | |
45 <option value="includeAligned">Include aligned</option> | |
46 <option value="excludeAligned">Exclude aligned</option> | |
47 <option value="includeReadList">Include read list</option> | |
48 <option value="excludeReadList">Exclude read list</option> | |
49 </param> | |
50 <when value="includeAligned"/> <!-- do nothing --> | |
51 <when value="excludeAligned"/> <!-- do nothing --> | |
52 <when value="includeReadList"> | |
53 <param name="read_list_file" type="data" format="tabular" label="Dataset containing read names that will be INCLUDED in the output" help="READ_LIST_FILE"/> | |
54 </when> | |
55 <when value="excludeReadList"> | |
56 <param name="read_list_file" type="data" format="tabular" label="Dataset containing read names that will be EXCLUDED in the output" help="READ_LIST_FILE"/> | |
57 </when> | |
58 </conditional> | |
59 | |
60 <expand macro="VS" /> | |
61 | |
62 </inputs> | |
63 | |
64 <outputs> | |
65 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: filtered BAM"/> | |
66 </outputs> | |
67 | |
68 <tests> | |
69 <test> | |
70 <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/> | |
71 <param name="filter" value="includeReadList"/> | |
72 <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/> | |
73 <param name="validation_stringency" value="LENIENT"/> | |
74 <output name="outFile" file="picard_FilterSamReads_include_reads_test1.bam" ftype="bam" lines_diff="2"/> | |
75 </test> | |
76 <test> | |
77 <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/> | |
78 <param name="filter" value="excludeReadList"/> | |
79 <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/> | |
80 <param name="validation_stringency" value="LENIENT"/> | |
81 <output name="outFile" file="picard_FilterSamReads_exclude_reads_test2.bam" ftype="bam" lines_diff="2"/> | |
82 </test> | |
83 </tests> | |
84 | |
85 <stdio> | |
86 <exit_code range="1:" level="fatal"/> | |
87 </stdio> | |
88 | |
89 <help> | |
90 | |
91 **Purpose** | |
92 | |
93 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments. | |
94 | |
95 ------ | |
96 | |
97 .. class:: warningmark | |
98 | |
99 **Warning on using this tool on BWA-MEM output** | |
100 | |
101 This tool will likely fail on BAM datasets generated by BWA MEM as it generates partial read alignemnts. | |
102 | |
103 @dataset_collections@ | |
104 | |
105 @description@ | |
106 | |
107 FILTER=Filter Filter. Required. Possible values: | |
108 includeAligned [OUTPUT SAM/BAM will contain aligned | |
109 reads only. (Note that *both* first and | |
110 second of paired reads must be aligned to be included | |
111 in the OUTPUT SAM or BAM)], | |
112 | |
113 excludeAligned [OUTPUT SAM/BAM will contain un-mapped reads only. | |
114 (Note that *both* first and second of pair must be aligned to be | |
115 excluded from the OUTPUT SAM or BAM)] | |
116 | |
117 includeReadList [OUTPUT SAM/BAM will contain reads | |
118 that are supplied in the READ_LIST_FILE file] | |
119 | |
120 excludeReadList [OUTPUT bam will contain | |
121 reads that are *not* supplied in the READ_LIST_FILE file]} | |
122 | |
123 READ_LIST_FILE=File | |
124 RLF=File Read List File containing reads that will be included or excluded from the OUTPUT SAM or | |
125 BAM file. Default value: null. | |
126 | |
127 @more_info@ | |
128 | |
129 </help> | |
130 </tool> | |
131 | |
132 |