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comparison picard_BedToIntervalList.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
comparison
equal deleted inserted replaced
32:f9242e01365a 33:3f254c5ced1d
1 <tool name="BedToIntervalList" id="picard_BedToIntervalList" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="BedToIntervalList" id="picard_BedToIntervalList" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
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 <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 @java_options@ 9 @java_options@
10 @symlink_element_identifier@ 10 @symlink_element_identifier@
11 #set $picard_dict = "localref.dict" 11 #set $picard_dict = "localref.dict"
12 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension 12 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension
13 13
14 ln -s "${reference_source.ref_file}" "${ref_fasta}" && 14 ln -sf '${reference_source.ref_file}' '${ref_fasta}' &&
15 15
16 #if str( $reference_source.reference_source_selector ) == "history": 16 #if str( $reference_source.reference_source_selector ) == "history":
17 17
18 picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" 18 picard CreateSequenceDictionary
19 QUIET=true 19 -REFERENCE '${ref_fasta}'
20 VERBOSITY=ERROR 20 -OUTPUT '${picard_dict}'
21 -QUIET true
22 -VERBOSITY ERROR
21 23
22 && 24 &&
23 25
24 #else: 26 #else:
25 27
28 30
29 #end if 31 #end if
30 32
31 picard 33 picard
32 BedToIntervalList 34 BedToIntervalList
33 INPUT='$escaped_element_identifier' 35 --INPUT '$escaped_element_identifier'
34 OUTPUT="${outFile}" 36 --OUTPUT '${outFile}'
35 37
36 SEQUENCE_DICTIONARY="${picard_dict}" 38 --SEQUENCE_DICTIONARY '${picard_dict}'
37 QUIET=true 39 --QUIET true
38 VERBOSITY=ERROR 40 --VERBOSITY ERROR
39 41
40 ]]></command> 42 ]]></command>
41 43 <inputs>
42 <inputs> 44 <conditional name="reference_source">
43 45 <param name="reference_source_selector" type="select" label="Load picard dictionary file from">
44 <conditional name="reference_source"> 46 <option value="cached">Local cache</option>
45 <param name="reference_source_selector" type="select" label="Load picard dictionary file from"> 47 <option value="history">History</option>
46 <option value="cached">Local cache</option> 48 </param>
47 <option value="history">History</option> 49 <when value="cached">
48 </param> 50 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
49 <when value="cached"> 51 <options from_data_table="picard_indexes">
50 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list"> 52 <filter type="sort_by" column="2"/>
51 <options from_data_table="picard_indexes"> 53 <validator type="no_options" message="No indexes are available"/>
52 <filter type="sort_by" column="2" /> 54 </options>
53 <validator type="no_options" message="No indexes are available" /> 55 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
54 </options> 56 </param>
55 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> 57 </when>
56 </param> 58 <when value="history">
57 </when> 59 <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 <when value="history"> 60 </when>
59 <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" /> 61 </conditional>
60 </when> 62 <param format="bed" name="inputFile" type="data" label="Select coordinate dataset or dataset collection" help="This can be a bed or interval dataset"/>
61 </conditional> 63 </inputs>
62 64 <outputs>
63 <param format="bed" name="inputFile" type="data" label="Select coordinate dataset or dataset collection" help="This can be a bed or interval dataset" /> 65 <data name="outFile" format="picard_interval_list" label="${tool.name} on ${on_string}: Picard interval list">
64
65 </inputs>
66 <outputs>
67 <data name="outFile" format="picard_interval_list" label="${tool.name} on ${on_string}: Picard interval list">
68 </data> 66 </data>
69 </outputs> 67 </outputs>
70 <tests> 68 <tests>
71 <test> 69 <test>
72 <param name="reference_source_selector" value="history" /> 70 <param name="reference_source_selector" value="history"/>
73 <param name="ref_file" value="picard_BedToIntervalList_ref.fa" ftype="fasta" /> 71 <param name="ref_file" value="picard_BedToIntervalList_ref.fa" ftype="fasta"/>
74 <param name="inputFile" value="picard_BedToIntervalList.bed" ftype="bed"/> 72 <param name="inputFile" value="picard_BedToIntervalList.bed" ftype="bed"/>
75 <output name="outFile" file="picard_BedToIntervalList_test1.pif" ftype="picard_interval_list" lines_diff="8" /> 73 <output name="outFile" file="picard_BedToIntervalList_test1.pif" ftype="picard_interval_list" lines_diff="8"/>
76 </test> 74 </test>
77 </tests> 75 </tests>
78 76 <help>
79
80 <help>
81 77
82 .. class:: infomark 78 .. class:: infomark
83 79
84 **Purpose** 80 **Purpose**
85 81
95 file uploaded to history (right pane of the interface). 91 file uploaded to history (right pane of the interface).
96 92
97 93
98 @more_info@ 94 @more_info@
99 </help> 95 </help>
100 <expand macro="citations" /> 96 <expand macro="citations"/>
101 </tool> 97 </tool>