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comparison picard_SortSam.xml @ 7:08f69add4d06 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 15:11:36 -0500
parents 2f3cdd537834
children e417b1d6288d
comparison
equal deleted inserted replaced
6:961236c5ec73 7:08f69add4d06
2 <description>sort SAM/BAM dataset</description> 2 <description>sort SAM/BAM dataset</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 #if $sort_order == "queryname":
9 #set $output = "output.sam"
10 ln -s '${outFile}' output.sam &&
11 #else:
12 #set $output = $outFile
13 #end if
8 @java_options@ 14 @java_options@
9 java -jar \$JAVA_JAR_PATH/picard.jar 15 picard
10 SortSam 16 SortSam
11 INPUT="${inputFile}" 17 INPUT="${inputFile}"
12 OUTPUT="${outFile}" 18 OUTPUT='${output}'
13 SORT_ORDER="${sort_order}" 19 SORT_ORDER="${sort_order}"
14 QUIET=true 20 QUIET=true
15 VERBOSITY=ERROR 21 VERBOSITY=ERROR
16 VALIDATION_STRINGENCY=${validation_stringency} 22 VALIDATION_STRINGENCY=${validation_stringency}
17 </command> 23 ]]></command>
18 24
19 <inputs> 25 <inputs>
20 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> 26 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
21 <param name="sort_order" type="select" display="radio" label="Sort order" help="SORT_ORDER; default=coordinate"> 27 <param name="sort_order" type="select" display="radio" label="Sort order" help="SORT_ORDER; default=coordinate. Selecting Queryname will output SAM file, as Galaxy does not support BAM files that are not coordinate sorted.">
22 <option value="coordinate" selected="True">Coordinate</option> 28 <option value="coordinate" selected="True">Coordinate</option>
23 <option value="queryname">Queryname</option> 29 <option value="queryname">Queryname</option>
24 </param> 30 </param>
25 <expand macro="VS" /> 31 <expand macro="VS" />
26 </inputs> 32 </inputs>
27 33
28 <outputs> 34 <outputs>
29 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM sorted in ${sort_order} order"> 35 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Alignment sorted in ${sort_order} order">
36 <change_format>
37 <when input="sort_order" value="queryname" format="sam"/>
38 </change_format>
30 </data> 39 </data>
31 </outputs> 40 </outputs>
32 41
33 <stdio> 42
34 <exit_code range="1:" level="fatal"/>
35 </stdio>
36
37 <tests> 43 <tests>
44 <!-- This test fails when setting metadata on non-coordinate sorted bam files.
45 This should be handled better in Galaxy (info as of release 16.0).
46 Workaroudn is to produce queryname sorted sam files.
38 <test> 47 <test>
39 <param name="inputFile" ftype="bam" value="picard_SortSam.bam" /> 48 <param name="inputFile" ftype="bam" value="picard_SortSam.bam" />
40 <param name="sort_order" value="queryname"/> 49 <param name="sort_order" value="queryname"/>
41 <output name="outFile" file="picard_SortSam_test1.bam" ftype="bam" lines_diff="2"/> 50 <output name="outFile" file="picard_SortSam_test1.bam" ftype="bam" lines_diff="4"/>
51 </test>
52 -->
53 <test>
54 <param name="inputFile" ftype="bam" value="picard_SortSam.bam" />
55 <param name="sort_order" value="queryname"/>
56 <output name="outFile" file="picard_SortSam_test1.sam" ftype="sam" lines_diff="4" compare="contains"/>
57 </test>
58 <test>
59 <param name="inputFile" ftype="bam" value="picard_SortSam.bam" />
60 <param name="sort_order" value="coordinate"/>
61 <output name="outFile" file="picard_SortSam_test1.bam" ftype="bam" lines_diff="4"/>
42 </test> 62 </test>
43 </tests> 63 </tests>
44 64
45 <help> 65 <help>
46 66
47 .. class:: infomark 67 .. class:: infomark
48 68
49 **Purpose** 69 **Purpose**
54 74
55 @description@ 75 @description@
56 76
57 SORT_ORDER=SortOrder 77 SORT_ORDER=SortOrder
58 SO=SortOrder Sort order of output file. You can either sort by queryname or by coordinate. 78 SO=SortOrder Sort order of output file. You can either sort by queryname or by coordinate.
59 79
60 @more_info@ 80 @more_info@
61 81
62 </help> 82 </help>
63 </tool> 83 </tool>