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comparison picard_FilterSamReads.xml @ 13:7e6fd3d0f16e draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
author devteam
date Tue, 06 Dec 2016 10:04:41 -0500
parents 05087b27692a
children 465cbb0cf2eb
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12:05087b27692a 13:7e6fd3d0f16e
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 @java_options@ 8 @java_options@
9 9 @symlink_element_identifier@
10 ##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order 10 ##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order
11 11
12 picard 12 picard
13 SortSam 13 SortSam
14 INPUT="${inputFile}" 14 INPUT='$inputFile.element_identifier'
15 OUTPUT=query_sorted_bam.bam 15 OUTPUT=query_sorted_bam.bam
16 SORT_ORDER=queryname 16 SORT_ORDER=queryname
17 VALIDATION_STRINGENCY=LENIENT 17 VALIDATION_STRINGENCY=LENIENT
18 QUIET=true 18 QUIET=true
19 VERBOSITY=ERROR 19 VERBOSITY=ERROR
20 20
21 && 21 &&
22 22
23 picard 23 picard
24 FilterSamReads 24 FilterSamReads
25 INPUT=query_sorted_bam.bam 25 INPUT=query_sorted_bam.bam
26 FILTER="${filter_type.filter}" 26 FILTER="${filter_type.filter}"
27 27
28 #if ( str( $filter_type.filter ) == "includeReadList" or str( $filter_type.filter ) == "excludeReadList" ): 28 #if ( str( $filter_type.filter ) == "includeReadList" or str( $filter_type.filter ) == "excludeReadList" ):
29 READ_LIST_FILE="${filter_type.read_list_file}" 29 READ_LIST_FILE="${filter_type.read_list_file}"
30 #end if 30 #end if
31 31
32 OUTPUT="${outFile}" 32 OUTPUT="${outFile}"
33 SORT_ORDER=coordinate 33 SORT_ORDER=coordinate
34 VALIDATION_STRINGENCY="${validation_stringency}" 34 VALIDATION_STRINGENCY="${validation_stringency}"
35 QUIET=true 35 QUIET=true
36 VERBOSITY=ERROR 36 VERBOSITY=ERROR
37 37
38 ]]></command> 38 ]]></command>
39 <inputs> 39 <inputs>
40 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> 40 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
41 <conditional name="filter_type"> 41 <conditional name="filter_type">
42 <param name="filter" type="select" label="Select filtering type" help="FILTER; see Help for deatiled info"> 42 <param name="filter" type="select" label="Select filtering type" help="FILTER; see Help for deatiled info">
52 </when> 52 </when>
53 <when value="excludeReadList"> 53 <when value="excludeReadList">
54 <param name="read_list_file" type="data" format="tabular" label="Dataset containing read names that will be EXCLUDED in the output" help="READ_LIST_FILE"/> 54 <param name="read_list_file" type="data" format="tabular" label="Dataset containing read names that will be EXCLUDED in the output" help="READ_LIST_FILE"/>
55 </when> 55 </when>
56 </conditional> 56 </conditional>
57 57
58 <expand macro="VS" /> 58 <expand macro="VS" />
59 59
60 </inputs> 60 </inputs>
61 61
62 <outputs> 62 <outputs>
63 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: filtered BAM"/> 63 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: filtered BAM"/>
64 </outputs> 64 </outputs>
65 65
66 <tests> 66 <tests>
67 <test> 67 <test>
68 <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/> 68 <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/>
69 <param name="filter" value="includeReadList"/> 69 <param name="filter" value="includeReadList"/>
70 <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/> 70 <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/>
77 <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/> 77 <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/>
78 <param name="validation_stringency" value="LENIENT"/> 78 <param name="validation_stringency" value="LENIENT"/>
79 <output name="outFile" file="picard_FilterSamReads_exclude_reads_test2.bam" ftype="bam" lines_diff="4"/> 79 <output name="outFile" file="picard_FilterSamReads_exclude_reads_test2.bam" ftype="bam" lines_diff="4"/>
80 </test> 80 </test>
81 </tests> 81 </tests>
82 82
83 83
84 <help> 84 <help>
85 85
86 **Purpose** 86 **Purpose**
87 87
88 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments. 88 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
91 91
92 .. class:: warningmark 92 .. class:: warningmark
93 93
94 **Warning on using this tool on BWA-MEM output** 94 **Warning on using this tool on BWA-MEM output**
95 95
96 This tool will likely fail on BAM datasets generated by BWA MEM as it generates partial read alignemnts. 96 This tool will likely fail on BAM datasets generated by BWA MEM as it generates partial read alignemnts.
97 97
98 @dataset_collections@ 98 @dataset_collections@
99 99
100 @description@ 100 @description@
101 101
102 FILTER=Filter Filter. Required. Possible values: 102 FILTER=Filter Filter. Required. Possible values:
103 includeAligned [OUTPUT SAM/BAM will contain aligned 103 includeAligned [OUTPUT SAM/BAM will contain aligned
104 reads only. (Note that *both* first and 104 reads only. (Note that *both* first and
105 second of paired reads must be aligned to be included 105 second of paired reads must be aligned to be included
106 in the OUTPUT SAM or BAM)], 106 in the OUTPUT SAM or BAM)],
107 107
108 excludeAligned [OUTPUT SAM/BAM will contain un-mapped reads only. 108 excludeAligned [OUTPUT SAM/BAM will contain un-mapped reads only.
109 (Note that *both* first and second of pair must be aligned to be 109 (Note that *both* first and second of pair must be aligned to be
110 excluded from the OUTPUT SAM or BAM)] 110 excluded from the OUTPUT SAM or BAM)]
111 111
112 includeReadList [OUTPUT SAM/BAM will contain reads 112 includeReadList [OUTPUT SAM/BAM will contain reads
113 that are supplied in the READ_LIST_FILE file] 113 that are supplied in the READ_LIST_FILE file]
114 114
115 excludeReadList [OUTPUT bam will contain 115 excludeReadList [OUTPUT bam will contain
116 reads that are *not* supplied in the READ_LIST_FILE file]} 116 reads that are *not* supplied in the READ_LIST_FILE file]}
117 117
118 READ_LIST_FILE=File 118 READ_LIST_FILE=File
119 RLF=File Read List File containing reads that will be included or excluded from the OUTPUT SAM or 119 RLF=File Read List File containing reads that will be included or excluded from the OUTPUT SAM or
120 BAM file. Default value: null. 120 BAM file. Default value: null.
121 121
122 @more_info@ 122 @more_info@
123 123
124 </help> 124 </help>
125 </tool> 125 </tool>
126 126