Mercurial > repos > devteam > picard
annotate picard_ReorderSam.xml @ 24:b9fbec5ac6b2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9c268f08be6d363990a822fc941e031dd13be3f4
author | iuc |
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date | Fri, 31 May 2019 03:21:52 -0400 |
parents | 2a17c789e0a5 |
children | 881d7645d1bf |
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5053a18d9bc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
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1 <tool name="ReorderSam" id="picard_ReorderSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> |
5 | 2 <description>reorder reads to match ordering in reference sequences</description> |
3 <macros> | |
4 <import>picard_macros.xml</import> | |
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2a17c789e0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
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5 <token name="@WRAPPER_VERSION@">1</token> |
5 | 6 </macros> |
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3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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7 <expand macro="requirements" /> |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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8 <command detect_errors="exit_code"><![CDATA[ |
5 | 9 @java_options@ |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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10 @symlink_element_identifier@ |
5 | 11 #set $picard_dict = "localref.dict" |
12 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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13 |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
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14 ln -s "${reference_source.ref_file}" "${ref_fasta}" && |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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15 |
5 | 16 #if str( $reference_source.reference_source_selector ) == "history": |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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17 |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
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18 picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" |
5 | 19 QUIET=true |
20 VERBOSITY=ERROR | |
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2a17c789e0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
iuc
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21 @TMPDIR_OPTION@ |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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22 |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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23 && |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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24 |
5 | 25 #else: |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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26 |
5 | 27 #set $ref_fasta = str( $reference_source.ref_file.fields.path ) |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
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28 |
5 | 29 #end if |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
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30 |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
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31 picard |
5 | 32 ReorderSam |
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465cbb0cf2eb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
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33 INPUT='$escaped_element_identifier' |
5 | 34 OUTPUT="${outFile}" |
35 REFERENCE="${ref_fasta}" | |
36 ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}" | |
37 ALLOW_CONTIG_LENGTH_DISCORDANCE="${allow_contig_length_discordance}" | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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38 |
5 | 39 VALIDATION_STRINGENCY="${validation_stringency}" |
40 QUIET=true | |
41 VERBOSITY=ERROR | |
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2a17c789e0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
iuc
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42 @TMPDIR_OPTION@ |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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43 |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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44 ]]></command> |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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45 |
0 | 46 <inputs> |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
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47 |
5 | 48 <conditional name="reference_source"> |
49 <param name="reference_source_selector" type="select" label="Load reference genome from"> | |
50 <option value="cached">Local cache</option> | |
0 | 51 <option value="history">History</option> |
52 </param> | |
5 | 53 <when value="cached"> |
54 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list"> | |
55 <options from_data_table="picard_indexes"> | |
56 <filter type="sort_by" column="2" /> | |
57 <validator type="no_options" message="No indexes are available" /> | |
58 </options> | |
59 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> | |
0 | 60 </param> |
61 </when> | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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62 <when value="history"> |
5 | 63 <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" /> |
0 | 64 </when> |
65 </conditional> | |
5 | 66 |
67 <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"/> | |
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"/> | |
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"/> | |
70 <expand macro="VS" /> | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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71 |
0 | 72 </inputs> |
73 <outputs> | |
5 | 74 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Reordered BAM"/> |
0 | 75 </outputs> |
76 <tests> | |
77 <test> | |
5 | 78 <param name="reference_source_selector" value="history" /> |
79 <param name="ref_file" value="picard_ReorderSam_ref.fa" ftype="fasta" /> | |
80 <param name="inputFile" value="picard_ReorderSam.bam" ftype="bam"/> | |
81 <param name="allow_incomplete_dict_concordance" value="false"/> | |
82 <param name="allow_contig_length_discordance" value="false"/> | |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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83 <output name="outFile" file="picard_ReorderSam_test1.bam" ftype="bam" lines_diff="4"/> |
0 | 84 </test> |
85 </tests> | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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86 |
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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87 |
0 | 88 <help> |
89 | |
90 .. class:: infomark | |
91 | |
92 **Purpose** | |
93 | |
5 | 94 ReorderSam reorders reads in a SAM/BAM file to match the contig ordering in a provided reference file, as determined by exact name matching of contigs. Reads mapped to contigs absent in the new reference are dropped. |
0 | 95 |
5 | 96 @dataset_collections@ |
0 | 97 |
5 | 98 ---- |
0 | 99 |
100 .. class:: warningmark | |
101 | |
5 | 102 Not to be confused with **SortSam**. |
103 | |
104 @description@ | |
0 | 105 |
5 | 106 ALLOW_INCOMPLETE_DICT_CONCORDANCE=Boolean |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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107 S=Boolean If true, then allows only a partial overlap of the BAM contigs with the new reference |
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
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108 sequence contigs. By default, this tool requires a corresponding contig in the new |
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
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109 reference for each read contig Default value: false. Possible values: {true, false} |
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
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110 |
5 | 111 ALLOW_CONTIG_LENGTH_DISCORDANCE=Boolean |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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parents:
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112 U=Boolean If true, then permits mapping from a read contig to a new reference contig with the same |
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
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113 name but a different length. Highly dangerous, only use if you know what you are doing. |
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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114 Default value: false. Possible values: {true, false} |
0 | 115 |
5 | 116 @more_info@ |
0 | 117 </help> |
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5053a18d9bc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
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118 <expand macro="citations" /> |
0 | 119 </tool> |