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comparison picard_SortSam.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 id="picard_SortSam" name="SortSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool id="picard_SortSam" name="SortSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
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 <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 #if $sort_order == "queryname": 9 #if $sort_order == "queryname":
10 #set $output = "output.sam" 10 #set $output = "output.sam"
11 ln -s '${outFile}' output.sam && 11 ln -sf '${outFile}' output.sam &&
12 #else: 12 #else:
13 #set $output = $outFile 13 #set $output = $outFile
14 #end if 14 #end if
15 @java_options@ 15 @java_options@
16 @symlink_element_identifier@ 16 @symlink_element_identifier@
17 picard 17 picard SortSam
18 SortSam 18 --INPUT '$escaped_element_identifier'
19 INPUT='$escaped_element_identifier' 19 --OUTPUT '${output}'
20 OUTPUT='${output}' 20 --SORT_ORDER '${sort_order}'
21 SORT_ORDER="${sort_order}" 21 --QUIET true
22 QUIET=true 22 --VERBOSITY ERROR
23 VERBOSITY=ERROR 23 --VALIDATION_STRINGENCY ${validation_stringency}
24 VALIDATION_STRINGENCY=${validation_stringency}
25 ]]></command> 24 ]]></command>
26 25 <inputs>
27 <inputs> 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"/>
28 <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"/> 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.">
29 <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."> 28 <option value="coordinate" selected="True">Coordinate</option>
30 <option value="coordinate" selected="True">Coordinate</option> 29 <option value="queryname">Queryname</option>
31 <option value="queryname">Queryname</option> 30 </param>
32 </param> 31 <expand macro="VS"/>
33 <expand macro="VS" /> 32 </inputs>
34 </inputs> 33 <outputs>
35 34 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Alignment sorted in ${sort_order} order">
36 <outputs> 35 <change_format>
37 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Alignment sorted in ${sort_order} order"> 36 <when input="sort_order" value="queryname" format="sam"/>
38 <change_format> 37 </change_format>
39 <when input="sort_order" value="queryname" format="sam"/> 38 </data>
40 </change_format> 39 </outputs>
41 </data> 40 <tests>
42 </outputs> 41 <!-- This test fails when setting metadata on non-coordinate sorted bam files.
43
44
45 <tests>
46 <!-- This test fails when setting metadata on non-coordinate sorted bam files.
47 This should be handled better in Galaxy (info as of release 16.0). 42 This should be handled better in Galaxy (info as of release 16.0).
48 Workaroudn is to produce queryname sorted sam files. 43 Workaroudn is to produce queryname sorted sam files.
49 <test> 44 <test>
50 <param name="inputFile" ftype="bam" value="picard_SortSam.bam" /> 45 <param name="inputFile" ftype="bam" value="picard_SortSam.bam" />
51 <param name="sort_order" value="queryname"/> 46 <param name="sort_order" value="queryname"/>
52 <output name="outFile" file="picard_SortSam_test1.bam" ftype="bam" lines_diff="4"/> 47 <output name="outFile" file="picard_SortSam_test1.bam" ftype="bam" lines_diff="4"/>
53 </test> 48 </test>
54 --> 49 -->
55 <test> 50 <test>
56 <param name="inputFile" ftype="bam" value="picard_SortSam.bam" /> 51 <param name="inputFile" ftype="bam" value="picard_SortSam.bam"/>
57 <param name="sort_order" value="queryname"/> 52 <param name="sort_order" value="queryname"/>
58 <output name="outFile" file="picard_SortSam_test1.sam" ftype="sam" lines_diff="4" compare="contains"/> 53 <output name="outFile" file="picard_SortSam_test1.sam" ftype="sam" lines_diff="4" compare="contains"/>
59 </test> 54 </test>
60 <test> 55 <test>
61 <param name="inputFile" ftype="bam" value="picard_SortSam.bam" /> 56 <param name="inputFile" ftype="bam" value="picard_SortSam.bam"/>
62 <param name="sort_order" value="coordinate"/> 57 <param name="sort_order" value="coordinate"/>
63 <output name="outFile" file="picard_SortSam_test1.bam" ftype="bam" lines_diff="4"/> 58 <output name="outFile" file="picard_SortSam_test1.bam" ftype="bam" lines_diff="4"/>
64 </test> 59 </test>
65 </tests> 60 </tests>
66 61 <help>
67 <help>
68 62
69 .. class:: infomark 63 .. class:: infomark
70 64
71 **Purpose** 65 **Purpose**
72 66
80 SO=SortOrder Sort order of output file. You can either sort by queryname or by coordinate. 74 SO=SortOrder Sort order of output file. You can either sort by queryname or by coordinate.
81 75
82 @more_info@ 76 @more_info@
83 77
84 </help> 78 </help>
85 <expand macro="citations" /> 79 <expand macro="citations"/>
86 </tool> 80 </tool>