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comparison picard_BedToIntervalList.xml @ 8:e417b1d6288d draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
author devteam
date Tue, 06 Dec 2016 10:04:26 -0500
parents 08f69add4d06
children 41b8d087a2d2
comparison
equal deleted inserted replaced
7:08f69add4d06 8:e417b1d6288d
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 detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 @java_options@ 8 @java_options@
9 9 @symlink_element_identifier@
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}" "${ref_fasta}" && 13 ln -s "${reference_source.ref_file}" "${ref_fasta}" &&
14 14
15 #if str( $reference_source.reference_source_selector ) == "history": 15 #if str( $reference_source.reference_source_selector ) == "history":
16 16
17 picard CreateSequenceDictionary REFERENCE="${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 && 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 picard 30 picard
31 BedToIntervalList 31 BedToIntervalList
32 INPUT="${inputFile}" 32 INPUT='$inputFile.element_identifier'
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">
45 <option value="cached">Local cache</option> 45 <option value="cached">Local cache</option>
46 <option value="history">History</option> 46 <option value="history">History</option>
47 </param> 47 </param>
52 <validator type="no_options" message="No indexes are available" /> 52 <validator type="no_options" message="No indexes are available" />
53 </options> 53 </options>
54 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> 54 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
55 </param> 55 </param>
56 </when> 56 </when>
57 <when value="history"> 57 <when value="history">
58 <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" /> 58 <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" />
59 </when> 59 </when>
60 </conditional> 60 </conditional>
61 61
62 <param format="bed" name="inputFile" type="data" label="Select coordinate dataset or dataset collection" help="This can be a bed or interval dataset" /> 62 <param format="bed" name="inputFile" type="data" label="Select coordinate dataset or dataset collection" help="This can be a bed or interval dataset" />
63 63
64 </inputs> 64 </inputs>
65 <outputs> 65 <outputs>
66 <data name="outFile" format="picard_interval_list" label="${tool.name} on ${on_string}: Picard interval list"> 66 <data name="outFile" format="picard_interval_list" label="${tool.name} on ${on_string}: Picard interval list">
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="8" /> 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 78
79 <help> 79 <help>
80 80
81 .. class:: infomark 81 .. class:: infomark
82 82
83 **Purpose** 83 **Purpose**