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comparison picard_FilterSamReads.xml @ 33:3f254c5ced1d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author iuc
date Sun, 03 Mar 2024 16:06:11 +0000
parents f9242e01365a
children
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equal deleted inserted replaced
32:f9242e01365a 33:3f254c5ced1d
1 <tool name="FilterSamReads" id="picard_FilterSamReads" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="FilterSamReads" id="picard_FilterSamReads" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
2 <description>include or exclude aligned and unaligned reads and read lists</description> 2 <description>include or exclude aligned and unaligned reads and read lists</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 <token name="@WRAPPER_VERSION@">1</token> 5 <token name="@WRAPPER_VERSION@">0</token>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 @java_options@ 9 @java_options@
10 @symlink_element_identifier@ 10 @symlink_element_identifier@
11 ##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order 11 ##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order
12 12
13 picard 13 picard SortSam
14 SortSam 14 --INPUT '$escaped_element_identifier'
15 INPUT='$escaped_element_identifier' 15 --OUTPUT query_sorted_bam.bam
16 OUTPUT=query_sorted_bam.bam 16 --SORT_ORDER queryname
17 SORT_ORDER=queryname 17 --VALIDATION_STRINGENCY LENIENT
18 VALIDATION_STRINGENCY=LENIENT 18 --QUIET true
19 QUIET=true 19 --VERBOSITY ERROR
20 VERBOSITY=ERROR
21 20
22 && 21 &&
23 22
24 picard 23 picard FilterSamReads
25 FilterSamReads 24 --INPUT query_sorted_bam.bam
26 INPUT=query_sorted_bam.bam 25 --FILTER '${filter_type.filter}'
27 FILTER="${filter_type.filter}"
28 26
29 #if ( str( $filter_type.filter ) == "includeReadList" or str( $filter_type.filter ) == "excludeReadList" ): 27 #if ( str( $filter_type.filter ) == "includeReadList" or str( $filter_type.filter ) == "excludeReadList" ):
30 READ_LIST_FILE="${filter_type.read_list_file}" 28 --READ_LIST_FILE '${filter_type.read_list_file}'
31 #end if 29 #end if
32 30
33 OUTPUT="${outFile}" 31 --OUTPUT '${outFile}'
34 SORT_ORDER=coordinate 32 --SORT_ORDER coordinate
35 VALIDATION_STRINGENCY="${validation_stringency}" 33 --VALIDATION_STRINGENCY '${validation_stringency}'
36 QUIET=true 34 --QUIET true
37 VERBOSITY=ERROR 35 --VERBOSITY ERROR
38 36
39 ]]></command> 37 ]]></command>
40 <inputs> 38 <inputs>
41 <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"/> 39 <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"/>
42 <conditional name="filter_type"> 40 <conditional name="filter_type">
43 <param name="filter" type="select" label="Select filtering type" help="FILTER; see Help for deatiled info"> 41 <param name="filter" type="select" label="Select filtering type" help="FILTER; see Help for deatiled info">
44 <option value="includeAligned">Include aligned</option> 42 <option value="includeAligned">Include aligned</option>
45 <option value="excludeAligned">Exclude aligned</option> 43 <option value="excludeAligned">Exclude aligned</option>
46 <option value="includeReadList">Include read list</option> 44 <option value="includeReadList">Include read list</option>
47 <option value="excludeReadList">Exclude read list</option> 45 <option value="excludeReadList">Exclude read list</option>
48 </param> 46 </param>
49 <when value="includeAligned"/> <!-- do nothing --> 47 <when value="includeAligned"/>
50 <when value="excludeAligned"/> <!-- do nothing --> 48 <!-- do nothing -->
51 <when value="includeReadList"> 49 <when value="excludeAligned"/>
52 <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"/> 50 <!-- do nothing -->
53 </when> 51 <when value="includeReadList">
54 <when value="excludeReadList"> 52 <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"/>
55 <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"/> 53 </when>
56 </when> 54 <when value="excludeReadList">
57 </conditional> 55 <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"/>
58 56 </when>
59 <expand macro="VS" /> 57 </conditional>
60 58 <expand macro="VS"/>
61 </inputs> 59 </inputs>
62 60 <outputs>
63 <outputs> 61 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: filtered BAM"/>
64 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: filtered BAM"/> 62 </outputs>
65 </outputs> 63 <tests>
66 64 <test>
67 <tests> 65 <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/>
68 <test> 66 <param name="filter" value="includeReadList"/>
69 <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/> 67 <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/>
70 <param name="filter" value="includeReadList"/> 68 <param name="validation_stringency" value="LENIENT"/>
71 <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/> 69 <output name="outFile" file="picard_FilterSamReads_include_reads_test1.bam" ftype="bam" lines_diff="4"/>
72 <param name="validation_stringency" value="LENIENT"/> 70 </test>
73 <output name="outFile" file="picard_FilterSamReads_include_reads_test1.bam" ftype="bam" lines_diff="4"/> 71 <test>
74 </test> 72 <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/>
75 <test> 73 <param name="filter" value="excludeReadList"/>
76 <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/> 74 <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/>
77 <param name="filter" value="excludeReadList"/> 75 <param name="validation_stringency" value="LENIENT"/>
78 <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/> 76 <output name="outFile" file="picard_FilterSamReads_exclude_reads_test2.bam" ftype="bam" lines_diff="4"/>
79 <param name="validation_stringency" value="LENIENT"/> 77 </test>
80 <output name="outFile" file="picard_FilterSamReads_exclude_reads_test2.bam" ftype="bam" lines_diff="4"/> 78 </tests>
81 </test> 79 <help>
82 </tests>
83
84
85 <help>
86 80
87 **Purpose** 81 **Purpose**
88 82
89 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments. 83 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
90 84
121 BAM file. Default value: null. 115 BAM file. Default value: null.
122 116
123 @more_info@ 117 @more_info@
124 118
125 </help> 119 </help>
126 <expand macro="citations" /> 120 <expand macro="citations"/>
127 </tool> 121 </tool>