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comparison picard_ReorderSam.xml @ 13:7e6fd3d0f16e 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 10:04:41 -0500
parents 05087b27692a
children 465cbb0cf2eb
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equal deleted inserted replaced
12:05087b27692a 13:7e6fd3d0f16e
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 @symlink_element_identifier@
9 #set $picard_dict = "localref.dict" 10 #set $picard_dict = "localref.dict"
10 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension 11 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension
11 12
12 ln -s "${reference_source.ref_file}" "${ref_fasta}" && 13 ln -s "${reference_source.ref_file}" "${ref_fasta}" &&
13 14
14 #if str( $reference_source.reference_source_selector ) == "history": 15 #if str( $reference_source.reference_source_selector ) == "history":
15 16
16 picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" 17 picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
17 QUIET=true 18 QUIET=true
18 VERBOSITY=ERROR 19 VERBOSITY=ERROR
19 20
20 && 21 &&
21 22
22 #else: 23 #else:
23 24
24 #set $ref_fasta = str( $reference_source.ref_file.fields.path ) 25 #set $ref_fasta = str( $reference_source.ref_file.fields.path )
25 26
26 #end if 27 #end if
27 28
28 picard 29 picard
29 ReorderSam 30 ReorderSam
30 INPUT="${inputFile}" 31 INPUT='$inputFile.element_identifier'
31 OUTPUT="${outFile}" 32 OUTPUT="${outFile}"
32 REFERENCE="${ref_fasta}" 33 REFERENCE="${ref_fasta}"
33 ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}" 34 ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}"
34 ALLOW_CONTIG_LENGTH_DISCORDANCE="${allow_contig_length_discordance}" 35 ALLOW_CONTIG_LENGTH_DISCORDANCE="${allow_contig_length_discordance}"
35 36
36 VALIDATION_STRINGENCY="${validation_stringency}" 37 VALIDATION_STRINGENCY="${validation_stringency}"
37 QUIET=true 38 QUIET=true
38 VERBOSITY=ERROR 39 VERBOSITY=ERROR
39 40
40 ]]></command> 41 ]]></command>
41 42
42 <inputs> 43 <inputs>
43 44
44 <conditional name="reference_source"> 45 <conditional name="reference_source">
45 <param name="reference_source_selector" type="select" label="Load reference genome from"> 46 <param name="reference_source_selector" type="select" label="Load reference genome from">
46 <option value="cached">Local cache</option> 47 <option value="cached">Local cache</option>
47 <option value="history">History</option> 48 <option value="history">History</option>
48 </param> 49 </param>
53 <validator type="no_options" message="No indexes are available" /> 54 <validator type="no_options" message="No indexes are available" />
54 </options> 55 </options>
55 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> 56 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
56 </param> 57 </param>
57 </when> 58 </when>
58 <when value="history"> 59 <when value="history">
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" /> 60 <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" />
60 </when> 61 </when>
61 </conditional> 62 </conditional>
62 63
63 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> 64 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
64 <param name="allow_incomplete_dict_concordance" type="boolean" label="If true, then allows only a partial overlap of the BAM contigs with the new reference sequence contigs" help="ALLOW_INCOMPLETE_DICT_CONCORDANCE; By default, this tool requires a corresponding contig in the new reference for each read contig; default=False"/> 65 <param name="allow_incomplete_dict_concordance" type="boolean" label="If true, then allows only a partial overlap of the BAM contigs with the new reference sequence contigs" help="ALLOW_INCOMPLETE_DICT_CONCORDANCE; By default, this tool requires a corresponding contig in the new reference for each read contig; default=False"/>
65 <param name="allow_contig_length_discordance" type="boolean" label="If true, then permits mapping from a read contig to a new reference contig with the same name but a different length" help="ALLOW_CONTIG_LENGTH_DISCORDANCE; HIGHLY DANGEROUS! Only use if you know what you are doing; default=False"/> 66 <param name="allow_contig_length_discordance" type="boolean" label="If true, then permits mapping from a read contig to a new reference contig with the same name but a different length" help="ALLOW_CONTIG_LENGTH_DISCORDANCE; HIGHLY DANGEROUS! Only use if you know what you are doing; default=False"/>
66 <expand macro="VS" /> 67 <expand macro="VS" />
67 68
68 </inputs> 69 </inputs>
69 <outputs> 70 <outputs>
70 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Reordered BAM"/> 71 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Reordered BAM"/>
71 </outputs> 72 </outputs>
72 <tests> 73 <tests>
77 <param name="allow_incomplete_dict_concordance" value="false"/> 78 <param name="allow_incomplete_dict_concordance" value="false"/>
78 <param name="allow_contig_length_discordance" value="false"/> 79 <param name="allow_contig_length_discordance" value="false"/>
79 <output name="outFile" file="picard_ReorderSam_test1.bam" ftype="bam" lines_diff="4"/> 80 <output name="outFile" file="picard_ReorderSam_test1.bam" ftype="bam" lines_diff="4"/>
80 </test> 81 </test>
81 </tests> 82 </tests>
82 83
83 84
84 <help> 85 <help>
85 86
86 .. class:: infomark 87 .. class:: infomark
87 88
88 **Purpose** 89 **Purpose**
98 Not to be confused with **SortSam**. 99 Not to be confused with **SortSam**.
99 100
100 @description@ 101 @description@
101 102
102 ALLOW_INCOMPLETE_DICT_CONCORDANCE=Boolean 103 ALLOW_INCOMPLETE_DICT_CONCORDANCE=Boolean
103 S=Boolean If true, then allows only a partial overlap of the BAM contigs with the new reference 104 S=Boolean If true, then allows only a partial overlap of the BAM contigs with the new reference
104 sequence contigs. By default, this tool requires a corresponding contig in the new 105 sequence contigs. By default, this tool requires a corresponding contig in the new
105 reference for each read contig Default value: false. Possible values: {true, false} 106 reference for each read contig Default value: false. Possible values: {true, false}
106 107
107 ALLOW_CONTIG_LENGTH_DISCORDANCE=Boolean 108 ALLOW_CONTIG_LENGTH_DISCORDANCE=Boolean
108 U=Boolean If true, then permits mapping from a read contig to a new reference contig with the same 109 U=Boolean If true, then permits mapping from a read contig to a new reference contig with the same
109 name but a different length. Highly dangerous, only use if you know what you are doing. 110 name but a different length. Highly dangerous, only use if you know what you are doing.
110 Default value: false. Possible values: {true, false} 111 Default value: false. Possible values: {true, false}
111 112
112 @more_info@ 113 @more_info@
113 </help> 114 </help>
114 </tool> 115 </tool>
115 116