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comparison picard_BedToIntervalList.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 52fdfc45590a
children e417b1d6288d
comparison
equal deleted inserted replaced
6:961236c5ec73 7:08f69add4d06
2 <description>convert coordinate data into picard interval list format</description> 2 <description>convert coordinate data into picard interval list format</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 #set $picard_dict = "localref.dict" 10 #set $picard_dict = "localref.dict"
11 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension 11 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension
12 12
13 ln -s "${reference_source.ref_file}" "${ref_fasta}" &amp;&amp; 13 ln -s "${reference_source.ref_file}" "${ref_fasta}" &&
14 14
15 #if str( $reference_source.reference_source_selector ) == "history": 15 #if str( $reference_source.reference_source_selector ) == "history":
16 16
17 java -jar \$JAVA_JAR_PATH/picard.jar CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" 17 picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
18 QUIET=true 18 QUIET=true
19 VERBOSITY=ERROR 19 VERBOSITY=ERROR
20 20
21 &amp;&amp; 21 &&
22 22
23 #else: 23 #else:
24 24
25 #set $ref_fasta = str( $reference_source.ref_file.fields.path ) ## getting path of reference fasta file (must end with .fa) 25 #set $ref_fasta = str( $reference_source.ref_file.fields.path ) ## getting path of reference fasta file (must end with .fa)
26 #set $picard_dict=$ref_fasta[:-2]+"dict" ## replacing .fa with .dict 26 #set $picard_dict=$ref_fasta[:-2]+"dict" ## replacing .fa with .dict
27 27
28 #end if 28 #end if
29 29
30 java -jar \$JAVA_JAR_PATH/picard.jar 30 picard
31 BedToIntervalList 31 BedToIntervalList
32 INPUT="${inputFile}" 32 INPUT="${inputFile}"
33 OUTPUT="${outFile}" 33 OUTPUT="${outFile}"
34 34
35 SEQUENCE_DICTIONARY="${picard_dict}" 35 SEQUENCE_DICTIONARY="${picard_dict}"
36 QUIET=true 36 QUIET=true
37 VERBOSITY=ERROR 37 VERBOSITY=ERROR
38 38
39 </command> 39 ]]></command>
40 40
41 <inputs> 41 <inputs>
42 42
43 <conditional name="reference_source"> 43 <conditional name="reference_source">
44 <param name="reference_source_selector" type="select" label="Load picard dictionary file from"> 44 <param name="reference_source_selector" type="select" label="Load picard dictionary file from">
69 <tests> 69 <tests>
70 <test> 70 <test>
71 <param name="reference_source_selector" value="history" /> 71 <param name="reference_source_selector" value="history" />
72 <param name="ref_file" value="picard_BedToIntervalList_ref.fa" ftype="fasta" /> 72 <param name="ref_file" value="picard_BedToIntervalList_ref.fa" ftype="fasta" />
73 <param name="inputFile" value="picard_BedToIntervalList.bed" ftype="bed"/> 73 <param name="inputFile" value="picard_BedToIntervalList.bed" ftype="bed"/>
74 <output name="outFile" file="picard_BedToIntervalList_test1.pif" ftype="picard_interval_list" lines_diff="2" /> 74 <output name="outFile" file="picard_BedToIntervalList_test1.pif" ftype="picard_interval_list" lines_diff="8" />
75 </test> 75 </test>
76 </tests> 76 </tests>
77 77
78 <stdio>
79 <exit_code range="1:" level="fatal"/>
80 </stdio>
81 78
82 <help> 79 <help>
83 80
84 .. class:: infomark 81 .. class:: infomark
85 82