picard: picard_ReorderSam.xml annotate

annotate picard_ReorderSam.xml @ 25:7d34178f2812 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a0fcbda330469051d130fd0802c55960ae948e3b

author	iuc
date	Tue, 11 Jun 2019 02:36:54 -0400
parents	2a17c789e0a5
children	881d7645d1bf

rev	line source
19 5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73 iuc parents: 14 diff changeset	1 <tool name="ReorderSam" id="picard_ReorderSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	2 <description>reorder reads to match ordering in reference sequences</description>
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	3 <macros>
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	4 <import>picard_macros.xml</import>
20 2a17c789e0a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a iuc parents: 19 diff changeset	5 <token name="@WRAPPER_VERSION@">1</token>
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	6 </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	7 <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	8 <command detect_errors="exit_code"><![CDATA[
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	9 @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	10 @symlink_element_identifier@
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	11 #set $picard_dict = "localref.dict"
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	12 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	13
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	14 ln -s "${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	15
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	16 #if str( $reference_source.reference_source_selector ) == "history":
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	17
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	18 picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	19 QUIET=true
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	20 VERBOSITY=ERROR
20 2a17c789e0a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a iuc parents: 19 diff changeset	21 @TMPDIR_OPTION@
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	22
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	23 &&
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 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	25 #else:
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 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	27 #set $ref_fasta = str( $reference_source.ref_file.fields.path )
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	28
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	29 #end if
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	30
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	31 picard
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	32 ReorderSam
14 465cbb0cf2eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f devteam parents: 13 diff changeset	33 INPUT='$escaped_element_identifier'
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	34 OUTPUT="${outFile}"
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	35 REFERENCE="${ref_fasta}"
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	36 ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}"
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	37 ALLOW_CONTIG_LENGTH_DISCORDANCE="${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	38
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	39 VALIDATION_STRINGENCY="${validation_stringency}"
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	40 QUIET=true
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	41 VERBOSITY=ERROR
20 2a17c789e0a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a iuc parents: 19 diff changeset	42 @TMPDIR_OPTION@
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	43
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	44 ]]></command>
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	45
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	46 <inputs>
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	47
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	48 <conditional name="reference_source">
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	49 <param name="reference_source_selector" type="select" label="Load reference genome from">
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	50 <option value="cached">Local cache</option>
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	51 <option value="history">History</option>
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	52 </param>
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	53 <when value="cached">
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	54 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	55 <options from_data_table="picard_indexes">
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	56 <filter type="sort_by" column="2" />
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	57 <validator type="no_options" message="No indexes are available" />
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	58 </options>
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	59 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	60 </param>
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	61 </when>
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	62 <when value="history">
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	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 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	64 </when>
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	65 </conditional>
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	66
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	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"/>
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	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"/>
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	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"/>
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	70 <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	71
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	72 </inputs>
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	73 <outputs>
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	74 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Reordered BAM"/>
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	75 </outputs>
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	76 <tests>
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	77 <test>
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	78 <param name="reference_source_selector" value="history" />
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	79 <param name="ref_file" value="picard_ReorderSam_ref.fa" ftype="fasta" />
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	80 <param name="inputFile" value="picard_ReorderSam.bam" ftype="bam"/>
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	81 <param name="allow_incomplete_dict_concordance" value="false"/>
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	82 <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	83 <output name="outFile" file="picard_ReorderSam_test1.bam" ftype="bam" lines_diff="4"/>
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	84 </test>
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	85 </tests>
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	86
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	87
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	88 <help>
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	89
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	90 .. class:: infomark
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	91
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	92 Purpose
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	93
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	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 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	95
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	96 @dataset_collections@
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	97
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	98 ----
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	99
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	100 .. class:: warningmark
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	101
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	102 Not to be confused with SortSam.
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	103
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	104 @description@
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	105
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	106 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	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: 12 diff changeset	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 parents: 12 diff changeset	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 parents: 12 diff changeset	110
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	111 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	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 parents: 12 diff changeset	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 devteam parents: 12 diff changeset	114 Default value: false. Possible values: {true, false}
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	115
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	116 @more_info@
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	117 </help>
19 5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73 iuc parents: 14 diff changeset	118 <expand macro="citations" />
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	119 </tool>

Mercurial > repos > devteam > picard

annotate picard_ReorderSam.xml @ 25:7d34178f2812 draft