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comparison picard_FilterSamReads.xml @ 12:05087b27692a draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
author devteam
date Sun, 27 Nov 2016 15:11:50 -0500
parents 3a3234d7a2e8
children 7e6fd3d0f16e
comparison
equal deleted inserted replaced
11:efc56ee1ade4 12:05087b27692a
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 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command> 7 <command detect_errors="exit_code"><![CDATA[
8 @java_options@ 8 @java_options@
9 9
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 java -jar \$JAVA_JAR_PATH/picard.jar 12 picard
13 SortSam 13 SortSam
14 INPUT="${inputFile}" 14 INPUT="${inputFile}"
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 &amp;&amp; 21 &&
22 22
23 java -jar \$JAVA_JAR_PATH/picard.jar 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( $filter_type.filter ) == "excludeReadList" ):
33 SORT_ORDER=coordinate 33 SORT_ORDER=coordinate
34 VALIDATION_STRINGENCY="${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">
43 <option value="includeAligned">Include aligned</option> 43 <option value="includeAligned">Include aligned</option>
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"/>
71 <param name="validation_stringency" value="LENIENT"/> 71 <param name="validation_stringency" value="LENIENT"/>
72 <output name="outFile" file="picard_FilterSamReads_include_reads_test1.bam" ftype="bam" lines_diff="2"/> 72 <output name="outFile" file="picard_FilterSamReads_include_reads_test1.bam" ftype="bam" lines_diff="4"/>
73 </test> 73 </test>
74 <test> 74 <test>
75 <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/> 75 <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/>
76 <param name="filter" value="excludeReadList"/> 76 <param name="filter" value="excludeReadList"/>
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="2"/> 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 <stdio>
84 <exit_code range="1:" level="fatal"/>
85 </stdio>
86 83
87 <help> 84 <help>
88 85
89 **Purpose** 86 **Purpose**
90 87