Mercurial > repos > devteam > picard
annotate picard_ReorderSam.xml @ 14:465cbb0cf2eb draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
| author | devteam |
|---|---|
| date | Wed, 07 Dec 2016 14:56:30 -0500 |
| parents | 7e6fd3d0f16e |
| children | 5053a18d9bc8 |
| rev | line source |
|---|---|
|
8
3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
5
diff
changeset
|
1 <tool name="ReorderSam" id="picard_ReorderSam" version="@TOOL_VERSION@.0"> |
| 5 | 2 <description>reorder reads to match ordering in reference sequences</description> |
| 3 <macros> | |
| 4 <import>picard_macros.xml</import> | |
| 5 </macros> | |
|
8
3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
5
diff
changeset
|
6 <expand macro="requirements" /> |
|
12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
8
diff
changeset
|
7 <command detect_errors="exit_code"><![CDATA[ |
| 5 | 8 @java_options@ |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
9 @symlink_element_identifier@ |
| 5 | 10 #set $picard_dict = "localref.dict" |
| 11 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension | |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
12 |
|
12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
8
diff
changeset
|
13 ln -s "${reference_source.ref_file}" "${ref_fasta}" && |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
14 |
| 5 | 15 #if str( $reference_source.reference_source_selector ) == "history": |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
16 |
|
12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
8
diff
changeset
|
17 picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" |
| 5 | 18 QUIET=true |
| 19 VERBOSITY=ERROR | |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
20 |
|
12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
8
diff
changeset
|
21 && |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
22 |
| 5 | 23 #else: |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
24 |
| 5 | 25 #set $ref_fasta = str( $reference_source.ref_file.fields.path ) |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
26 |
| 5 | 27 #end if |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
28 |
|
12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
8
diff
changeset
|
29 picard |
| 5 | 30 ReorderSam |
|
14
465cbb0cf2eb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
devteam
parents:
13
diff
changeset
|
31 INPUT='$escaped_element_identifier' |
| 5 | 32 OUTPUT="${outFile}" |
| 33 REFERENCE="${ref_fasta}" | |
| 34 ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}" | |
| 35 ALLOW_CONTIG_LENGTH_DISCORDANCE="${allow_contig_length_discordance}" | |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
36 |
| 5 | 37 VALIDATION_STRINGENCY="${validation_stringency}" |
| 38 QUIET=true | |
| 39 VERBOSITY=ERROR | |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
40 |
|
12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
8
diff
changeset
|
41 ]]></command> |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
42 |
| 0 | 43 <inputs> |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
44 |
| 5 | 45 <conditional name="reference_source"> |
| 46 <param name="reference_source_selector" type="select" label="Load reference genome from"> | |
| 47 <option value="cached">Local cache</option> | |
| 0 | 48 <option value="history">History</option> |
| 49 </param> | |
| 5 | 50 <when value="cached"> |
| 51 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list"> | |
| 52 <options from_data_table="picard_indexes"> | |
| 53 <filter type="sort_by" column="2" /> | |
| 54 <validator type="no_options" message="No indexes are available" /> | |
| 55 </options> | |
| 56 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> | |
| 0 | 57 </param> |
| 58 </when> | |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
59 <when value="history"> |
| 5 | 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" /> |
| 0 | 61 </when> |
| 62 </conditional> | |
| 5 | 63 |
| 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"/> | |
| 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"/> | |
| 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"/> | |
| 67 <expand macro="VS" /> | |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
68 |
| 0 | 69 </inputs> |
| 70 <outputs> | |
| 5 | 71 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Reordered BAM"/> |
| 0 | 72 </outputs> |
| 73 <tests> | |
| 74 <test> | |
| 5 | 75 <param name="reference_source_selector" value="history" /> |
| 76 <param name="ref_file" value="picard_ReorderSam_ref.fa" ftype="fasta" /> | |
| 77 <param name="inputFile" value="picard_ReorderSam.bam" ftype="bam"/> | |
| 78 <param name="allow_incomplete_dict_concordance" value="false"/> | |
| 79 <param name="allow_contig_length_discordance" value="false"/> | |
|
12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
8
diff
changeset
|
80 <output name="outFile" file="picard_ReorderSam_test1.bam" ftype="bam" lines_diff="4"/> |
| 0 | 81 </test> |
| 82 </tests> | |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
83 |
|
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
84 |
| 0 | 85 <help> |
| 86 | |
| 87 .. class:: infomark | |
| 88 | |
| 89 **Purpose** | |
| 90 | |
| 5 | 91 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 | 92 |
| 5 | 93 @dataset_collections@ |
| 0 | 94 |
| 5 | 95 ---- |
| 0 | 96 |
| 97 .. class:: warningmark | |
| 98 | |
| 5 | 99 Not to be confused with **SortSam**. |
| 100 | |
| 101 @description@ | |
| 0 | 102 |
| 5 | 103 ALLOW_INCOMPLETE_DICT_CONCORDANCE=Boolean |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
104 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:
12
diff
changeset
|
105 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
parents:
12
diff
changeset
|
106 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
parents:
12
diff
changeset
|
107 |
| 5 | 108 ALLOW_CONTIG_LENGTH_DISCORDANCE=Boolean |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
109 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
parents:
12
diff
changeset
|
110 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
devteam
parents:
12
diff
changeset
|
111 Default value: false. Possible values: {true, false} |
| 0 | 112 |
| 5 | 113 @more_info@ |
| 0 | 114 </help> |
| 115 </tool> | |
| 116 | |
| 117 | |
| 118 | |
| 119 | |
| 120 | |
| 121 | |
| 122 | |
| 123 | |
| 124 | |
| 125 | |
| 126 | |
| 127 | |
| 5 | 128 |