picard: picard_AddOrReplaceReadGroups.xml annotate

annotate picard_AddOrReplaceReadGroups.xml @ 9:5eaa8a968300 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1

author	devteam
date	Fri, 09 Oct 2015 17:43:13 -0400
parents	3a3234d7a2e8
children	05087b27692a

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="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="@TOOL_VERSION@.0">
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	2 <description>add or replaces read group information</description>
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	3 <macros>
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	4 <import>picard_macros.xml</import>
8 3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty devteam parents: 5 diff changeset	5 <import>read_group_macros.xml</import>
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" />
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	8 <command>
8 3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty devteam parents: 5 diff changeset	9 @define_read_group_helpers@
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty devteam parents: 5 diff changeset	10 #set $rg_auto_name = $read_group_name_default($inputFile)
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty devteam parents: 5 diff changeset	11 @set_read_group_vars@
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	12 @java_options@
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	13 java -jar \$JAVA_JAR_PATH/picard.jar
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	14 AddOrReplaceReadGroups
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	15 INPUT="${inputFile}"
8 3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty devteam parents: 5 diff changeset	16 $format_read_group("RGLB=", $rg_lb, '"')
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty devteam parents: 5 diff changeset	17 $format_read_group("RGPL=", $rg_pl, '"')
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty devteam parents: 5 diff changeset	18 $format_read_group("RGPU=", $rg_pu, '"')
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty devteam parents: 5 diff changeset	19 $format_read_group("RGSM=", $rg_sm, '"')
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty devteam parents: 5 diff changeset	20 $format_read_group("RGID=", $rg_id, '"')
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty devteam parents: 5 diff changeset	21 $format_read_group("RGDS=", $rg_ds, '"')
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty devteam parents: 5 diff changeset	22 $format_read_group("RGPI=", $rg_pi, '"')
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty devteam parents: 5 diff changeset	23 $format_read_group("RGDT=", $rg_dt, '"')
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	24 VALIDATION_STRINGENCY="${validation_stringency}"
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	25 QUIET=true
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	26 VERBOSITY=ERROR
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	27 OUTPUT="${outFile}"
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	28
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	29 </command>
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	30
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	31 <inputs>
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	32 <param format="bam,sam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
8 3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty devteam parents: 5 diff changeset	33 <expand macro="read_group_inputs_picard" />
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	34 <expand macro="VS" />
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	35
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	36 </inputs>
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	37
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	38 <outputs>
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	39 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/>
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	40 </outputs>
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	41
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	42 <stdio>
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	43 <exit_code range="1:" level="fatal"/>
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	44 </stdio>
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	45
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	46 <tests>
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	47 <test>
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	48 <param name="inputFile" value="picard_ARRG.bam" />
8 3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty devteam parents: 5 diff changeset	49 <param name="LB" value="tumor-a" />
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty devteam parents: 5 diff changeset	50 <param name="PL" value="ILLUMINA" />
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty devteam parents: 5 diff changeset	51 <param name="PU" value="run-1" />
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty devteam parents: 5 diff changeset	52 <param name="SM" value="sample-a" />
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty devteam parents: 5 diff changeset	53 <param name="ID" value="id-1" />
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	54 <output name="outFile" file="picard_ARRG_test1.bam" ftype="bam" />
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	55 </test>
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	56 </tests>
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	57 <help>
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	58
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	59 .. class:: infomark
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	60
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	61 Purpose
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	62
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	63 Add or Replace Read Groups in an input BAM or SAM file.
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	64
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	65 @dataset_collections@
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	66
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	67 @RG@
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	68
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	69 @description@
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	70
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	71 INPUT=File
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	72 I=File Input file (bam or sam). Required.
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	73
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	74 OUTPUT=File
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	75 O=File Output file (bam or sam). Required.
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	76
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	77 SORT_ORDER=SortOrder
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	78 SO=SortOrder Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT.
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	79 Default value: null. Possible values: {unsorted, queryname, coordinate}
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	80
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	81 RGID=String
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	82 ID=String Read Group ID Default value: 1. This option can be set to 'null' to clear the default
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	83 value.
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	84
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	85 RGLB=String
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	86 LB=String Read Group Library Required.
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	87
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	88 RGPL=String
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	89 PL=String Read Group platform (e.g. illumina, solid) Required.
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	90
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	91 RGPU=String
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	92 PU=String Read Group platform unit (eg. run barcode) Required.
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	93
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	94 RGSM=String
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	95 SM=String Read Group sample name Required.
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	96
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	97 RGCN=String
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	98 CN=String Read Group sequencing center name Default value: null.
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	99
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	100 RGDS=String
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	101 DS=String Read Group description Default value: null.
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	102
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	103 RGDT=Iso8601Date
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	104 DT=Iso8601Date Read Group run date Default value: null.
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	105
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	106 RGPI=Integer
3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	107 PI=Integer Read Group predicted insert size Default value: null.
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	108
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	109 @more_info@
0 1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	110 </help>
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	111 </tool>
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	112
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	113
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	114
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	115
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	116
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	117
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	118
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	119
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	120
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	121
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	122
1cd7f3b42609 Uploaded tool. devteam parents: diff changeset	123
5 3d4f1fa26f0e Uploaded devteam parents: 2 diff changeset	124
8 3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty devteam parents: 5 diff changeset	125

Mercurial > repos > devteam > picard

annotate picard_AddOrReplaceReadGroups.xml @ 9:5eaa8a968300 draft