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comparison picard_ReorderSam.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>reorder reads to match ordering in reference sequences</description> 2 <description>reorder reads to match ordering in reference sequences</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 #set $picard_dict = "localref.dict" 9 #set $picard_dict = "localref.dict"
10 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension 10 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension
11 11
12 ln -s "${reference_source.ref_file}" "${ref_fasta}" &amp;&amp; 12 ln -s "${reference_source.ref_file}" "${ref_fasta}" &&
13 13
14 #if str( $reference_source.reference_source_selector ) == "history": 14 #if str( $reference_source.reference_source_selector ) == "history":
15 15
16 java -jar \$JAVA_JAR_PATH/picard.jar CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" 16 picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
17 QUIET=true 17 QUIET=true
18 VERBOSITY=ERROR 18 VERBOSITY=ERROR
19 19
20 &amp;&amp; 20 &&
21 21
22 #else: 22 #else:
23 23
24 #set $ref_fasta = str( $reference_source.ref_file.fields.path ) 24 #set $ref_fasta = str( $reference_source.ref_file.fields.path )
25 25
26 #end if 26 #end if
27 27
28 java -jar \$JAVA_JAR_PATH/picard.jar 28 picard
29 ReorderSam 29 ReorderSam
30 INPUT="${inputFile}" 30 INPUT="${inputFile}"
31 OUTPUT="${outFile}" 31 OUTPUT="${outFile}"
32 REFERENCE="${ref_fasta}" 32 REFERENCE="${ref_fasta}"
33 ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}" 33 ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}"
35 35
36 VALIDATION_STRINGENCY="${validation_stringency}" 36 VALIDATION_STRINGENCY="${validation_stringency}"
37 QUIET=true 37 QUIET=true
38 VERBOSITY=ERROR 38 VERBOSITY=ERROR
39 39
40 </command> 40 ]]></command>
41 41
42 <inputs> 42 <inputs>
43 43
44 <conditional name="reference_source"> 44 <conditional name="reference_source">
45 <param name="reference_source_selector" type="select" label="Load reference genome from"> 45 <param name="reference_source_selector" type="select" label="Load reference genome from">
74 <param name="reference_source_selector" value="history" /> 74 <param name="reference_source_selector" value="history" />
75 <param name="ref_file" value="picard_ReorderSam_ref.fa" ftype="fasta" /> 75 <param name="ref_file" value="picard_ReorderSam_ref.fa" ftype="fasta" />
76 <param name="inputFile" value="picard_ReorderSam.bam" ftype="bam"/> 76 <param name="inputFile" value="picard_ReorderSam.bam" ftype="bam"/>
77 <param name="allow_incomplete_dict_concordance" value="false"/> 77 <param name="allow_incomplete_dict_concordance" value="false"/>
78 <param name="allow_contig_length_discordance" value="false"/> 78 <param name="allow_contig_length_discordance" value="false"/>
79 <output name="outFile" file="picard_ReorderSam_test1.bam" ftype="bam" lines_diff="2"/> 79 <output name="outFile" file="picard_ReorderSam_test1.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 .. class:: infomark 86 .. class:: infomark
90 87