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comparison picard_ReorderSam.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="ReorderSam" id="picard_ReorderSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="ReorderSam" id="picard_ReorderSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
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 <token name="@WRAPPER_VERSION@">1</token> 5 <token name="@WRAPPER_VERSION@">0</token>
6 </macros> 6 </macros>
7 <xrefs> 7 <xrefs>
8 <xref type="bio.tools">picard_reordersam</xref> 8 <xref type="bio.tools">picard_reordersam</xref>
9 </xrefs> 9 </xrefs>
10 <expand macro="requirements" /> 10 <expand macro="requirements"/>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 @java_options@ 12 @java_options@
13 @symlink_element_identifier@ 13 @symlink_element_identifier@
14 #set $picard_dict = "localref.dict" 14 #set $picard_dict = "localref.dict"
15 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension 15 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension
16 16
17 ln -s "${reference_source.ref_file}" "${ref_fasta}" && 17 ln -sf '${reference_source.ref_file}' '${ref_fasta}' &&
18 18
19 #if str( $reference_source.reference_source_selector ) == "history": 19 #if str( $reference_source.reference_source_selector ) == "history":
20 20
21 picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" 21 picard CreateSequenceDictionary
22 QUIET=true 22 --REFERENCE '${ref_fasta}'
23 VERBOSITY=ERROR 23 --OUTPUT '${picard_dict}'
24 --QUIET true
25 --VERBOSITY ERROR
24 26
25 && 27 &&
26 28
27 #else: 29 #else:
28 30
30 32
31 #end if 33 #end if
32 34
33 picard 35 picard
34 ReorderSam 36 ReorderSam
35 INPUT='$escaped_element_identifier' 37 --INPUT '$escaped_element_identifier'
36 OUTPUT="${outFile}" 38 --OUTPUT '${outFile}'
37 REFERENCE="${ref_fasta}" 39 --SEQUENCE_DICTIONARY '${ref_fasta}'
38 ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}" 40 --ALLOW_INCOMPLETE_DICT_CONCORDANCE '${allow_incomplete_dict_concordance}'
39 ALLOW_CONTIG_LENGTH_DISCORDANCE="${allow_contig_length_discordance}" 41 --ALLOW_CONTIG_LENGTH_DISCORDANCE '${allow_contig_length_discordance}'
40 42
41 VALIDATION_STRINGENCY="${validation_stringency}" 43 --VALIDATION_STRINGENCY '${validation_stringency}'
42 QUIET=true 44 --QUIET true
43 VERBOSITY=ERROR 45 --VERBOSITY ERROR
44 46
45 ]]></command> 47 ]]></command>
46 48 <inputs>
47 <inputs> 49 <conditional name="reference_source">
48 50 <param name="reference_source_selector" type="select" label="Load reference genome from">
49 <conditional name="reference_source"> 51 <option value="cached">Local cache</option>
50 <param name="reference_source_selector" type="select" label="Load reference genome from"> 52 <option value="history">History</option>
51 <option value="cached">Local cache</option> 53 </param>
52 <option value="history">History</option> 54 <when value="cached">
53 </param> 55 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
54 <when value="cached"> 56 <options from_data_table="picard_indexes">
55 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list"> 57 <filter type="sort_by" column="2"/>
56 <options from_data_table="picard_indexes"> 58 <validator type="no_options" message="No indexes are available"/>
57 <filter type="sort_by" column="2" /> 59 </options>
58 <validator type="no_options" message="No indexes are available" /> 60 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
59 </options> 61 </param>
60 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> 62 </when>
61 </param> 63 <when value="history">
62 </when> 64 <param name="ref_file" type="data" format="fasta,bam,sam" label="Use the following dataset to create dictionary" help="You can upload sequences to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command"/>
63 <when value="history"> 65 </when>
64 <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" /> 66 </conditional>
65 </when> 67 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
66 </conditional> 68 <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"/>
67 69 <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"/>
68 <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"/> 70 <expand macro="VS"/>
69 <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"/> 71 </inputs>
70 <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"/> 72 <outputs>
71 <expand macro="VS" /> 73 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Reordered BAM"/>
72 74 </outputs>
73 </inputs> 75 <tests>
74 <outputs> 76 <test>
75 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Reordered BAM"/> 77 <param name="reference_source_selector" value="history"/>
76 </outputs> 78 <param name="ref_file" value="picard_ReorderSam_ref.fa" ftype="fasta"/>
77 <tests> 79 <param name="inputFile" value="picard_ReorderSam.bam" ftype="bam"/>
78 <test> 80 <param name="allow_incomplete_dict_concordance" value="false"/>
79 <param name="reference_source_selector" value="history" /> 81 <param name="allow_contig_length_discordance" value="false"/>
80 <param name="ref_file" value="picard_ReorderSam_ref.fa" ftype="fasta" /> 82 <output name="outFile" file="picard_ReorderSam_test1.bam" ftype="bam" lines_diff="4"/>
81 <param name="inputFile" value="picard_ReorderSam.bam" ftype="bam"/> 83 </test>
82 <param name="allow_incomplete_dict_concordance" value="false"/> 84 </tests>
83 <param name="allow_contig_length_discordance" value="false"/> 85 <help>
84 <output name="outFile" file="picard_ReorderSam_test1.bam" ftype="bam" lines_diff="4"/>
85 </test>
86 </tests>
87
88
89 <help>
90 86
91 .. class:: infomark 87 .. class:: infomark
92 88
93 **Purpose** 89 **Purpose**
94 90
114 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.
115 Default value: false. Possible values: {true, false} 111 Default value: false. Possible values: {true, false}
116 112
117 @more_info@ 113 @more_info@
118 </help> 114 </help>
119 <expand macro="citations" /> 115 <expand macro="citations"/>
120 </tool> 116 </tool>