# HG changeset patch
# User refinery-platform
# Date 1512397386 18000
# Node ID 40d9376df6d6fb840afb4065ddbce072c5539fb8
planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
diff -r 000000000000 -r 40d9376df6d6 picard_MergeSamFiles.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_MergeSamFiles.xml Mon Dec 04 09:23:06 2017 -0500
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+ merges multiple SAM/BAM datasets into one
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+ picard_macros.xml
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+**Purpose**
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+Merges multiple SAM/BAM datasets into one.
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+@dataset_collections@
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+@description@
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+ ASSUME_SORTED=Boolean
+ AS=Boolean If true, assume that the input files are in the same sort order as the requested output
+ sort order, even if their headers say otherwise. Default value: false. This option can
+ be set to 'null' to clear the default value. Possible values: {true, false}
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+ MERGE_SEQUENCE_DICTIONARIES=Boolean
+ MSD=Boolean Merge the sequence dictionaries Default value: false. This option can be set to 'null'
+ to clear the default value. Possible values: {true, false}
+
+ COMMENT=String
+ CO=String Comment(s) to include in the merged output file's header. This option may be specified 0
+ or more times.
+
+
+@more_info@
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+
diff -r 000000000000 -r 40d9376df6d6 picard_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_macros.xml Mon Dec 04 09:23:06 2017 -0500
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+ 2.7.1
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+ picard
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+------
+
+**Additional information**
+
+Additional information about Picard tools is available from Picard web site at http://broadinstitute.github.io/picard/ .
+
+
+
+
+------
+
+**Inputs, outputs, and parameters**
+
+Either a SAM file or a BAM file must be supplied. Galaxy automatically coordinate-sorts all uploaded BAM files.
+
+From Picard documentation( http://broadinstitute.github.io/picard/)::
+
+
+
+-------
+
+**Read Groups are Important!**
+
+Setting read groups correctly from the start will simplify your life greatly because you can merge multiple BAM files into one significantly reducing the number of analysis steps. Below we provide an explanation of read groups fields taken from GATK FAQ webpage:
+
+.. csv-table::
+ :header-rows: 1
+
+ Tag,Importance,Definition,Meaning
+ "ID","Required","Read group identifier. Each @RG line must have a unique ID. The value of ID is used in the RG tags of alignment records. Must be unique among all read groups in header section. Read group IDs may be modified when merging SAM files in order to handle collisions.","Ideally, this should be a globally unique identify across all sequencing data in the world, such as the Illumina flowcell + lane name and number. Will be referenced by each read with the RG:Z field, allowing tools to determine the read group information associated with each read, including the sample from which the read came. Also, a read group is effectively treated as a separate run of the NGS instrument in tools like base quality score recalibration (a GATK component) -- all reads within a read group are assumed to come from the same instrument run and to therefore share the same error model."
+ "SM","Sample. Use pool name where a pool is being sequenced.","Required. As important as ID.","The name of the sample sequenced in this read group. GATK tools treat all read groups with the same SM value as containing sequencing data for the same sample. Therefore it's critical that the SM field be correctly specified, especially when using multi-sample tools like the Unified Genotyper (a GATK component)."
+ "PL","Platform/technology used to produce the read. Valid values: ILLUMINA, SOLID, LS454, HELICOS and PACBIO.","Important. Not currently used in the GATK, but was in the past, and may return. The only way to known the sequencing technology used to generate the sequencing data","It's a good idea to use this field."
+ "LB","DNA preparation library identify","Essential for MarkDuplicates","MarkDuplicates uses the LB field to determine which read groups might contain molecular duplicates, in case the same DNA library was sequenced on multiple lanes."
+
+**Example of Read Group usage**
+
+Support we have a trio of samples: MOM, DAD, and KID. Each has two DNA libraries prepared, one with 400 bp inserts and another with 200 bp inserts. Each of these libraries is run on two lanes of an illumina hiseq, requiring 3 x 2 x 2 = 12 lanes of data. When the data come off the sequencer, we would create 12 BAM files, with the following @RG fields in the header::
+
+ Dad's data:
+ @RG ID:FLOWCELL1.LANE1 PL:illumina LB:LIB-DAD-1 SM:DAD PI:200
+ @RG ID:FLOWCELL1.LANE2 PL:illumina LB:LIB-DAD-1 SM:DAD PI:200
+ @RG ID:FLOWCELL1.LANE3 PL:illumina LB:LIB-DAD-2 SM:DAD PI:400
+ @RG ID:FLOWCELL1.LANE4 PL:illumina LB:LIB-DAD-2 SM:DAD PI:400
+
+ Mom's data:
+ @RG ID:FLOWCELL1.LANE5 PL:illumina LB:LIB-MOM-1 SM:MOM PI:200
+ @RG ID:FLOWCELL1.LANE6 PL:illumina LB:LIB-MOM-1 SM:MOM PI:200
+ @RG ID:FLOWCELL1.LANE7 PL:illumina LB:LIB-MOM-2 SM:MOM PI:400
+ @RG ID:FLOWCELL1.LANE8 PL:illumina LB:LIB-MOM-2 SM:MOM PI:400
+
+ Kid's data:
+ @RG ID:FLOWCELL2.LANE1 PL:illumina LB:LIB-KID-1 SM:KID PI:200
+ @RG ID:FLOWCELL2.LANE2 PL:illumina LB:LIB-KID-1 SM:KID PI:200
+ @RG ID:FLOWCELL2.LANE3 PL:illumina LB:LIB-KID-2 SM:KID PI:400
+ @RG ID:FLOWCELL2.LANE4 PL:illumina LB:LIB-KID-2 SM:KID PI:400
+
+Note the hierarchical relationship between read groups (unique for each lane) to libraries (sequenced on two lanes) and samples (across four lanes, two lanes for each library).
+
+
+------
+
+**Dataset collections - processing large numbers of datasets at once**
+
+This tool accepts nested lists of .bam files to be merged. This type of structure is modeled in Galaxy as a `list:list` Dataset Collection.
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\ No newline at end of file
diff -r 000000000000 -r 40d9376df6d6 read_group_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/read_group_macros.xml Mon Dec 04 09:23:06 2017 -0500
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+
+
+
+#def identifier_or_name($input1)
+ #if hasattr($input1, 'element_identifier')
+ #return $input1.element_identifier
+ #else
+ #return $input1.name.rstrip('.gz').rstrip('.fastq').rstrip('.fq')
+ #end if
+#end def
+
+#def clean(name)
+ #import re
+ #set $name_clean = re.sub('[^\w\-_\.]', '_', $name)
+ #return $name_clean
+#end def
+
+#def read_group_name_default($input1, $input2=None)
+ #if $input2 is None
+ #return $clean($identifier_or_name($input1))
+ #else
+ #import itertools
+ #set $input_name1 = $clean($identifier_or_name($input1))
+ #set $input_name2 = $clean($identifier_or_name($input2))
+ #set $common_prefix = ''.join([c[0] for c in itertools.takewhile(lambda x: all(x[0] == y for y in x), itertools.izip(*[$input_name1, $input_name2]))])
+ #if len($common_prefix) > 3
+ #return $common_prefix
+ #else
+ #return $input_name1
+ #end if
+ #end if
+#end def
+
+#def format_read_group(prefix, value, quote='', arg='')
+ #if $value
+ #return $arg + $quote + $prefix + $value + $quote
+ #else
+ #return ''
+ #end if
+#end def
+
+#def rg_param(name)
+ #if $varExists("rg")
+ #return $rg.get($name, None)
+ #else
+ #return $getVar($name, None)
+ #end if
+#end def
+
+#set $use_rg = True
+
+
+
+#if $use_rg
+ #if $rg_param('read_group_id_conditional') is None
+ #set $rg_id = $rg_auto_name
+ #elif $rg_param('read_group_id_conditional').do_auto_name
+ #set $rg_id = $rg_auto_name
+ #else
+ #set $rg_id = str($rg_param('read_group_id_conditional').ID)
+ #end if
+
+ #if $rg_param('read_group_sm_conditional') is None
+ #set $rg_sm = ''
+ #elif $rg_param('read_group_sm_conditional').do_auto_name
+ #set $rg_sm = $rg_auto_name
+ #else
+ #set $rg_sm = str($rg_param('read_group_sm_conditional').SM)
+ #end if
+
+ #if $rg_param('PL')
+ #set $rg_pl = str($rg_param('PL'))
+ #else
+ #set $rg_pl = ''
+ #end if
+
+ #if $rg_param('read_group_lb_conditional') is None
+ #set $rg_lb = ''
+ #elif $rg_param('read_group_lb_conditional').do_auto_name
+ #set $rg_lb = $rg_auto_name
+ #else
+ #set $rg_lb = str($rg_param('read_group_lb_conditional').LB)
+ #end if
+
+ #if $rg_param('CN')
+ #set $rg_cn = str($rg_param('CN'))
+ #else
+ #set $rg_cn = ''
+ #end if
+
+ #if $rg_param("DS")
+ #set $rg_ds = str($rg_param("DS"))
+ #else
+ #set $rg_ds = ''
+ #end if
+
+ #if $rg_param("DT")
+ #set $rg_dt = str($rg_param("DT"))
+ #else
+ #set $rg_dt = ''
+ #end if
+
+ #if $rg_param("FO")
+ #set $rg_fo = str($rg_param("FO"))
+ #else
+ #set $rg_fo = ''
+ #end if
+
+ #if $rg_param("KS")
+ #set $rg_ks = str($rg_param("KS"))
+ #else
+ #set $rg_ks = ''
+ #end if
+
+ #if $rg_param("PG")
+ #set $rg_pg = str($rg_param("PG"))
+ #else
+ #set $rg_pg = ''
+ #end if
+
+ #if $rg_param("PI") != None
+ #set $rg_pi = str($rg_param("PI"))
+ #else
+ #set $rg_pi = ''
+ #end if
+
+ #if $rg_param("PU")
+ #set $rg_pu = str($rg_param("PU"))
+ #else
+ #set $rg_pu = ''
+ #end if
+#end if
+
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+#set $use_rg = str($rg.rg_selector) != "do_not_set"
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diff -r 000000000000 -r 40d9376df6d6 test-data/picard_MergeSamFiles_input1.bam
Binary file test-data/picard_MergeSamFiles_input1.bam has changed
diff -r 000000000000 -r 40d9376df6d6 test-data/picard_MergeSamFiles_input2.bam
Binary file test-data/picard_MergeSamFiles_input2.bam has changed
diff -r 000000000000 -r 40d9376df6d6 test-data/picard_MergeSamFiles_input3.bam
Binary file test-data/picard_MergeSamFiles_input3.bam has changed
diff -r 000000000000 -r 40d9376df6d6 test-data/picard_MergeSamFiles_test1.bam
Binary file test-data/picard_MergeSamFiles_test1.bam has changed
diff -r 000000000000 -r 40d9376df6d6 tool-data/picard_index.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/picard_index.loc.sample Mon Dec 04 09:23:06 2017 -0500
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+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Picard dict and associated files. You will need
+#to create these data files and then create a picard_index.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The picard_index.loc
+#file has this format (longer white space is the TAB character):
+#
+#
+#
+#So, for example, if you had hg18 indexed and stored in
+#/depot/data2/galaxy/srma/hg18/,
+#then the srma_index.loc entry would look like this:
+#
+#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa
+#
+#and your /depot/data2/galaxy/srma/hg18/ directory
+#would contain the following three files:
+#hg18.fa
+#hg18.dict
+#hg18.fa.fai
+#
+#The dictionary file for each reference (ex. hg18.dict) must be
+#created via Picard (http://picard.sourceforge.net). Note that
+#the dict file does not have the .fa extension although the
+#path list in the loc file does include it.
+#
diff -r 000000000000 -r 40d9376df6d6 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Mon Dec 04 09:23:06 2017 -0500
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