barcode_splitter: barcode_splitter.xml annotate

author	iuc
date	Wed, 29 May 2019 10:23:55 -0400
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children

rev	line source
0 5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	1 <tool id="barcode_splitter" name="Barcode Splitter" version="0.18.4.0">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	2 <description>Split sequence files using multiple sets of barcodes</description>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	3 <requirements>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	4 <requirement type="package" version="0.18.4">barcode_splitter</requirement>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	5 </requirements>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	6 <version_command>barcode_splitter --version</version_command>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	7 <command detect_errors="exit_code">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	8 <![CDATA[
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	9 mkdir split &&
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	10 barcode_splitter
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	11
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	12 --bcfile '$bcfile' --mismatches '$mismatches' --galaxy $barcodes_at_end --prefix 'split/'
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	13
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	14 #set $auto_split_all = $split_all
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	15 #set $format = ""
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	16 #set $paired_match = "0"
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	17 #set $num_index_files = 0
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	18
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	19 #if str($runinterface.run_type) == "flexible":
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	20
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	21 ## Determine the format based on the first input file's extension
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	22 ## #for $indf in $runinterface.seqfiles
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	23 ## #set $format = $indf.input.extension
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	24 ## #break
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	25 ## #end for
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	26 #set $format = $runinterface.seqfiles[0].input.extension
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	27
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	28 ## Add the sequence files, count the number of forward, reverse, and other non-index read names, and auto-set split_all
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	29 #set $numforwards = 0
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	30 #set $numreverses = 0
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	31 #for $sf in $runinterface.seqfiles
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	32 #if str($sf.nameinterface.readtype) == "forward" or str($sf.nameinterface.readtype) == "forwardindex":
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	33 #set $numforwards += 1
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	34 #elif str($sf.nameinterface.readtype) == "reverse" or str($sf.nameinterface.readtype) == "reverseindex":
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	35 #set $numreverses += 1
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	36 #end if
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	37 #if str($sf.nameinterface.readtype) == "singleindex" or str($sf.nameinterface.readtype) == "forwardindex" or str($sf.nameinterface.readtype) == "reverseindex":
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	38 #set $auto_split_all = "--split_all"
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	39 #end if
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	40 '${sf.input}'
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	41 #end for
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	42
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	43 ## Determine whether valid paired-end data exists
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	44 #if $numforwards == 1 and $numreverses == 1:
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	45 #set $paired_match = "1"
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	46 #end if
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	47
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	48 ##Add the relative file argument positions of the index files in the list included above
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	49 --idxread
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	50 #set $n = 0
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	51 #for $sf in $runinterface.seqfiles
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	52 #set $n += 1
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	53 #if str($sf.nameinterface.readtype) == 'index' or str($sf.nameinterface.readtype) == "singleindex" or str($sf.nameinterface.readtype) == "forwardindex" or str($sf.nameinterface.readtype) == "reverseindex":
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	54 #set $num_index_files += 1
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	55 '${n}'
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	56 #end if
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	57 #end for
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	58
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	59 #elif str($runinterface.run_type) == "single":
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	60
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	61 #set $format = $runinterface.snglinput.extension
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	62
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	63 ## Add the sequence files
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	64 '${runinterface.snglinput}'
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	65 #for $sf in $runinterface.idxfiles
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	66 '${sf.idxinput}'
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	67 #end for
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	68
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	69 ##Add the relative file argument positions of the index files
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	70 --idxread
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	71 #set $n = 1
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	72 #for $sf in $runinterface.idxfiles
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	73 #set $num_index_files += 1
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	74 #set $n += 1
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	75 '${n}'
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	76 #end for
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	77
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	78 #elif str($runinterface.run_type) == "paired":
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	79
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	80 #set $format = $runinterface.fwdinput.extension
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	81 #set $paired_match = "1"
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	82
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	83 ## Add the sequence files
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	84 '${runinterface.fwdinput}' '${runinterface.revinput}'
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	85 #for $sf in $runinterface.idxfiles
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	86 '${sf.idxinput}'
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	87 #end for
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	88
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	89 ##Add the relative file argument positions of the index files
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	90 --idxread
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	91 #set $n = 2
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	92 #for $sf in $runinterface.idxfiles
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	93 #set $num_index_files += 1
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	94 #set $n += 1
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	95 '${n}'
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	96 #end for
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	97
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	98 #end if
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	99
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	100 --format '${format}' --suffix '.${format}' $auto_split_all
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	101
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	102 > '$summary';
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	103
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	104 ## Determine validity of repeat params
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	105 #if $num_index_files == 0:
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	106 echo "ERROR: At least 1 read file must have a 'Read Type' selected as 'Index', 'Single-End with Index', 'Forward with index', or 'Reverse with Index')."
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	107 #end if
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	108
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	109 ## Give the output split file names the name specified by the user (to be turned into collection identifiers)
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	110 rc=0;
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	111 #set $n = 0
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	112
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	113 #if str($runinterface.run_type) == "flexible":
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	114
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	115 #for $repeat in $runinterface.seqfiles
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	116
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	117 #set $n += 1
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	118
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	119 #set $readname = "read-" + str($n)
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	120 #set $readtype = "index"
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	121 #if str($repeat.nameinterface.readtype) == "forward" or str($repeat.nameinterface.readtype) == "forwardindex":
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	122 #set $readname = "forward"
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	123 #set $readtype = "forward"
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	124 #elif str($repeat.nameinterface.readtype) == "reverse" or str($repeat.nameinterface.readtype) == "reverseindex":
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	125 #set $readname = "reverse"
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	126 #set $readtype = "reverse"
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	127 #else:
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	128 #if (str($repeat.nameinterface.readtype) == "single" or str($repeat.nameinterface.readtype) == "singleindex" or str($repeat.nameinterface.readtype) == "index") and str($repeat.nameinterface.readname) != "":
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	129 #set $readname = $repeat.nameinterface.readname
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	130 #end if
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	131 #if str($repeat.nameinterface.readtype) == "single" or str($repeat.nameinterface.readtype) == "singleindex":
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	132 #set $readtype = "single"
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	133 #end if
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	134 #end if
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	135
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	136 for f in split/*-read-'${n}'.'${format}';
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	137 do
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	138 if [ -e "\$f" ]; then
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	139 ## Space-delimited file name structure: "SAMPLE READNAME READTYPE MATCHEDPAIR.EXT"
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	140 mv "\$f" "\${f/-read-${n}/ ${readname} ${readtype} ${paired_match}}" \|\| rc=\$?;
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	141 fi;
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	142 done;
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	143 #end for
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	144
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	145 #elif str($runinterface.run_type) == "single":
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	146
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	147 #set $n = 1
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	148
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	149 ## Rename the single-end split read files
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	150 #set $readname = "read-" + str($n)
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	151 #set $readtype = 'single'
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	152 for f in split/*-read-'${n}'.'${format}';
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	153 do
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	154 mv "\$f" "\${f/-read-${n}/ ${readname} ${readtype} ${paired_match}}" \|\| rc=\$?;
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	155 done;
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	156
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	157 ## Rename the index read files
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	158 #set $readtype = "index"
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	159 #for $repeat in $runinterface.idxfiles
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	160 #set $n += 1
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	161
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	162 #set $readname = "read-" + str($n)
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	163 #if str($repeat.idxreadname) != "":
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	164 #set $readname = $repeat.idxreadname
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	165 #end if
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	166
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	167 for f in split/*-read-'${n}'.'${format}';
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	168 do
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	169 if [ -e "\$f" ]; then
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	170 ## Space-delimited file name structure: "SAMPLE READNAME READTYPE MATCHEDPAIR.EXT"
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	171 mv "\$f" "\${f/-read-${n}/ ${readname} ${readtype} ${paired_match}}" \|\| rc=\$?;
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	172 fi;
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	173 done;
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	174 #end for
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	175
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	176 #elif str($runinterface.run_type) == "paired":
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	177
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	178 #set $n = 1
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	179
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	180 ## Rename the forward split read files
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	181 #set $readname = "forward"
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	182 #set $readtype = "forward"
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	183 for f in split/*-read-'${n}'.'${format}';
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	184 do
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	185 mv "\$f" "\${f/-read-${n}/ ${readname} ${readtype} ${paired_match}}" \|\| rc=\$?;
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	186 done;
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	187
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	188 #set $n += 1
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	189
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	190 ## Rename the reverse split read files
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	191 #set $readname = "reverse"
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	192 #set $readtype = "reverse"
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	193 for f in split/*-read-'${n}'.'${format}';
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	194 do
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	195 mv "\$f" "\${f/-read-${n}/ ${readname} ${readtype} ${paired_match}}" \|\| rc=\$?;
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	196 done;
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	197
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	198 ## Rename the index read files
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	199 #set $readtype = "index"
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	200 #for $repeat in $runinterface.idxfiles
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	201 #set $n += 1
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	202
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	203 #set $readname = "read-" + str($n)
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	204 #if str($repeat.idxreadname) != "":
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	205 #set $readname = $repeat.idxreadname
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	206 #end if
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	207
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	208 for f in split/*-read-'${n}'.'${format}';
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	209 do
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	210 if [ -e "\$f" ]; then
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	211 ## Space-delimited file name structure: "SAMPLE READNAME READTYPE MATCHEDPAIR.EXT"
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	212 mv "\$f" "\${f/-read-${n}/ ${readname} ${readtype} ${paired_match}}" \|\| rc=\$?;
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	213 fi;
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	214 done;
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	215 #end for
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	216
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	217 #end if
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	218
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	219 ## Exit non-zero if rc is not 0
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	220 [ \$rc == 0 ];
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	221 ]]>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	222 </command>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	223
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	224 <inputs>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	225 <param name="bcfile" type="data" format="tabular" label="Barcode File" help="Tab-delimited text file where the first column is a sample ID and subsequent columns are barcodes. Note, files with indexes/barcode sequences must be supplied in the same order as the barcode columns in this file and their 'Read Type' must have 'Index'." />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	226
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	227 <conditional name="runinterface">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	228 <param label="Run Type" name="run_type" type="select">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	229 <option value="single" selected="true">Single-End</option>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	230 <option value="paired">Paired-End</option>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	231 <option value="flexible">Flexible</option>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	232 </param>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	233 <when value="single">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	234 <!-- Simplified interface for common use-case. Can still use "Flexible" for alternative single-end options. -->
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	235 <param name="snglinput" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Read File" help="Typically, 'Read 1'." />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	236 <repeat name="idxfiles" title="Index File(s)" min="1" default="1">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	237 <param name="idxinput" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Index File" help="Typically, 'Read 2 Index'." />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	238 <param name="idxreadname" type="text" label="Index Name" help="E.g. index1, index2, etc.. Letters and numbers only. No spaces. Default is 'read-x' where 'x' is a number corresponding to the order in which the file was supplied (including the read file above).">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	239 <sanitizer>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	240 <valid initial="string.ascii_letters,string.digits" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	241 </sanitizer>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	242 </param>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	243 </repeat>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	244 </when>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	245 <when value="paired">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	246 <!-- No embedded index allowed in the forward/reverse reads for simplicity. Can still use "Flexible" for that. -->
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	247 <param name="fwdinput" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Forward Read File" help="Typically, 'Read 1'." />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	248 <param name="revinput" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Reverse Read File" help="Typically, 'Read 3'." />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	249
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	250 <repeat name="idxfiles" title="Index Files" min="0" default="1">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	251 <param name="idxinput" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Index File" help="Typically, 'Read 2 Index' or 'Read 4 Index'." />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	252 <param name="idxreadname" type="text" label="Index Name" help="E.g. index1, index2, etc.. Letters and numbers only. No spaces. Default is 'read-x' where 'x' is a number corresponding to the order in which the file was supplied (including the forward and reverse files).">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	253 <sanitizer>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	254 <valid initial="string.ascii_letters,string.digits" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	255 </sanitizer>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	256 </param>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	257 </repeat>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	258 </when>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	259 <when value="flexible">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	260 <repeat name="seqfiles" title="Read Files" min="1" default="1">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	261 <param name="input" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Read File" help="Forward or single-end read files are typically named 'Read 1'. Index files are typically named 'Read 2 Index' or 'Read 4 Index'. Reverse read files are typically named 'Read 3'." />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	262 <conditional name="nameinterface">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	263 <param name="readtype" type="select" label="Read Type" help="E.g. If one file is 'Forward' and one is 'Reverse', split reads from those files will appear in an output paired collection. If your file has reads with barcodes embedded in them, select their 'with index' variant, e.g. 'Forward with Index'.">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	264 <option value="single" selected="true">Single-End</option>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	265 <option value="forward">Forward</option>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	266 <option value="reverse">Reverse</option>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	267 <option value="index">Index</option>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	268 <option value="singleindex">Single-End with Index</option>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	269 <option value="forwardindex">Forward with Index</option>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	270 <option value="reverseindex">Reverse with Index</option>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	271 </param>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	272 <when value="single">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	273 <param name="readname" type="text" label="Read Name" help="E.g. index1, index2, etc.. Ignored for paired-collections. Letters and numbers only. No spaces. Default is 'read-x' where 'x' is a number corresponding to the order in which the file was supplied.">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	274 <sanitizer>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	275 <valid initial="string.ascii_letters,string.digits" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	276 </sanitizer>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	277 </param>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	278 </when>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	279 <when value="singleindex">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	280 <param name="readname" type="text" label="Read Name" help="E.g. index1, index2, etc.. Ignored for paired-collections. Letters and numbers only. No spaces. Default is 'read-x' where 'x' is a number corresponding to the order in which the file was supplied.">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	281 <sanitizer>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	282 <valid initial="string.ascii_letters,string.digits" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	283 </sanitizer>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	284 </param>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	285 </when>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	286 <when value="index">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	287 <param name="readname" type="text" label="Read Name" help="E.g. index1, index2, etc.. Ignored for paired-collections. Letters and numbers only. No spaces. Default is 'read-x' where 'x' is a number corresponding to the order in which the file was supplied.">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	288 <sanitizer>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	289 <valid initial="string.ascii_letters,string.digits" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	290 </sanitizer>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	291 </param>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	292 </when>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	293 </conditional>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	294 </repeat>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	295 </when>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	296 </conditional>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	297
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	298 <param name="mismatches" type="integer" value="1" max="2" min="0" label="Number of allowed mismatches" help="An integer between 0 and 2 (inclusive). Warning: Make sure all your barcodes differ by at least double this value plus 1, otherwise sequences that match both barcodes equally well will be discarded as 'multimatched' reads." />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	299 <param argument="--barcodes_at_end" type="boolean" truevalue="--barcodes_at_end" falsevalue="" checked="false" label="Barcodes are at the end of all index sequences" help="Default is the beginning of all sequences" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	300 <param argument="--split_all" type="boolean" truevalue="--split_all" falsevalue="" checked="false" label="Split index files too" help="This creates an output collection for split files whose selected 'Read Type' is 'Index'." />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	301 </inputs>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	302
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	303 <outputs>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	304 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: Summary" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	305 <!-- Collection for single-end split reads, regardless of run_type -->
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	306 <collection name="split_output_single" type="list" format_source="input" label="${tool.name} on ${on_string}: single-end">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	307 <!-- run_type is single OR flexible and there's only 1 output read type -->
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	308 <filter>str(runinterface['run_type']) == "single" or (str(runinterface['run_type']) == "flexible" and len(list(filter(lambda x: str(x['nameinterface']['readtype']) != "index", runinterface['seqfiles']))) == 1)</filter>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	309 <discover_datasets pattern="(?P<identifier_0>\S+)\ \S+\ (single\|forward\|reverse) 0\.(?P<ext>.*)" directory="split" visible="false" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	310 </collection>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	311 <!-- Collection for paired-end split reads, regardless of run_type -->
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	312 <collection name="split_output_paired" type="list:paired" format_source="input" label="${tool.name} on ${on_string}: paired-end">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	313 <!-- run_type is paired OR flexible and there's 1 forward and 1 reverse readtype -->
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	314 <filter>str(runinterface['run_type']) == "paired" or (str(runinterface['run_type']) == "flexible" and len(list(filter(lambda x: str(x['nameinterface']['readtype']).startswith('forward'), runinterface['seqfiles']))) == 1 and len(list(filter(lambda x: str(x['nameinterface']['readtype']).startswith('reverse'), runinterface['seqfiles']))) == 1)</filter>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	315 <discover_datasets pattern="(?P<identifier_0>\S+)\ \S+\ (?P<identifier_1>forward\|reverse) 1\.(?P<ext>.*)" directory="split" visible="false" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	316 </collection>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	317 <!-- Collection for single-end split reads that sit alongside a paired-end collection -->
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	318 <collection name="split_output_paired_other" type="list" format_source="input" label="${tool.name} on ${on_string}: other-end">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	319 <!-- run_type is flexible, there are single-end reads, and there's a single valid read pair -->
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	320 <filter>str(runinterface['run_type']) == "flexible" and len(list(filter(lambda x: str(x['nameinterface']['readtype']).startswith('single'), runinterface['seqfiles']))) > 0 and len(list(filter(lambda x: str(x['nameinterface']['readtype']).startswith('forward'), runinterface['seqfiles']))) == 1 and len(list(filter(lambda x: str(x['nameinterface']['readtype']).startswith('reverse'), runinterface['seqfiles']))) == 1</filter>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	321 <discover_datasets pattern="(?P<identifier_0>\S+\ \S+)\ single 1\.(?P<ext>.*)" directory="split" visible="false" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	322 </collection>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	323 <!-- Collection for multi-end split reads -->
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	324 <collection name="split_output_multi" type="list" format_source="input" label="${tool.name} on ${on_string}: multi-end">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	325 <!-- run_type is flexible, there are multiple output split readtypes, and there's not a single valid read pair -->
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	326 <filter>str(runinterface['run_type']) == "flexible" and (len(runinterface['seqfiles']) - len(list(filter(lambda x: str(x['nameinterface']['readtype']) == "index", runinterface['seqfiles'])))) > 1 and (len(list(filter(lambda x: str(x['nameinterface']['readtype']).startswith('forward'), runinterface['seqfiles']))) != 1 or len(list(filter(lambda x: str(x['nameinterface']['readtype']).startswith('reverse'), runinterface['seqfiles']))) != 1)</filter>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	327 <discover_datasets pattern="(?P<identifier_0>\S+ \S+) (single (0\|1)\|(forward\|reverse) 0)\.(?P<ext>.*)" directory="split" visible="false" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	328 </collection>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	329 <!-- Collection for split_all index-only reads -->
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	330 <collection name="index_only" type="list" format_source="input" label="${tool.name} on ${on_string}: indexes">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	331 <!-- split_all is true and ((run_type is not flexible and there are index only files) or (run_type is flexible and there are index only files)) -->
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	332 <filter>split_all and ((str(runinterface['run_type']) != "flexible" and len(runinterface['idxfiles']) > 0) or (str(runinterface['run_type']) == "flexible" and len(list(filter(lambda x: str(x['nameinterface']['readtype']) == "index", runinterface['seqfiles']))) > 0))</filter>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	333 <discover_datasets pattern="(?P<identifier_0>.?) index (0\|1)\.(?P<ext>.)" directory="split" visible="false" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	334 </collection>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	335 </outputs>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	336
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	337 <tests>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	338 <test>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	339 <!-- single end with 1 index -->
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	340 <param name="run_type" value="single" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	341 <param name="bcfile" value="barcode_splitter_barcodes.txt" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	342 <param name="mismatches" value="2" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	343 <param name="barcodes_at_end" value="" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	344 <param name="split_all" value="False" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	345 <param name="snglinput" value="barcode_splitter1.fastq" ftype="fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	346
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	347 <repeat name="idxfiles">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	348 <param name="idxinput" value="barcode_splitter_index.fastq" ftype="fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	349 <param name="idxreadname" value="read" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	350 </repeat>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	351
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	352 <output name="summary" file="test_1_summary.out" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	353 <output_collection name="split_output_single" type="list">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	354 <element name="BC1" ftype="fastq" file="test_1_BC1-read-1.out" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	355 <element name="BC2" ftype="fastq" file="test_1_BC2-read-1.out" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	356 <element name="BC3" ftype="fastq" file="test_1_BC3-read-1.out" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	357 <element name="BC4" ftype="fastq" file="test_1_BC4-read-1.out" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	358 <element name="unmatched" ftype="fastq" file="test_1_unmatched-read-1.out" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	359 <element name="multimatched" ftype="fastq" file="test_1_multimatched-read-1.out" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	360 </output_collection>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	361 </test>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	362 <test>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	363 <!-- single end with 1 index and split all -->
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	364 <param name="run_type" value="single" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	365 <param name="bcfile" value="barcode_splitter_barcodes_dual.txt" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	366 <param name="mismatches" value="2" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	367 <param name="barcodes_at_end" value="" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	368 <param name="split_all" value="True" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	369 <param name="snglinput" value="barcode_splitter1.fastq" ftype="fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	370
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	371 <repeat name="idxfiles">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	372 <param name="idxinput" value="barcode_splitter_index.fastq" ftype="fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	373 <param name="idxreadname" value="index1" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	374 </repeat>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	375 <repeat name="idxfiles">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	376 <param name="idxinput" value="barcode_splitter_index_2.fastq" ftype="fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	377 <param name="idxreadname" value="index2" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	378 </repeat>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	379
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	380 <output name="summary" file="test_2_summary.out" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	381 <output_collection name="split_output_single" type="list">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	382 <element name="BC1" ftype="fastq" file="test_2_BC1-read-1.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	383 <element name="BC2" ftype="fastq" file="test_2_BC2-read-1.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	384 <element name="BC3" ftype="fastq" file="test_2_BC3-read-1.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	385 <element name="BC4" ftype="fastq" file="test_2_BC4-read-1.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	386 <element name="unmatched" ftype="fastq" file="test_2_unmatched-read-1.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	387 <element name="multimatched" ftype="fastq" file="test_2_multimatched-read-1.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	388 </output_collection>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	389 <output_collection name="index_only" type="list">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	390 <element name="BC1 index1" ftype="fastq" file="test_2_BC1_index1.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	391 <element name="BC2 index1" ftype="fastq" file="test_2_BC2_index1.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	392 <element name="BC3 index1" ftype="fastq" file="test_2_BC3_index1.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	393 <element name="BC4 index1" ftype="fastq" file="test_2_BC4_index1.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	394 <element name="unmatched index1" ftype="fastq" file="test_2_unmatched_index1.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	395 <element name="multimatched index1" ftype="fastq" file="test_2_multimatched_index1.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	396 <element name="BC1 index2" ftype="fastq" file="test_2_BC1_index2.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	397 <element name="BC2 index2" ftype="fastq" file="test_2_BC2_index2.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	398 <element name="BC3 index2" ftype="fastq" file="test_2_BC3_index2.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	399 <element name="BC4 index2" ftype="fastq" file="test_2_BC4_index2.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	400 <element name="unmatched index2" ftype="fastq" file="test_2_unmatched_index2.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	401 <element name="multimatched index2" ftype="fastq" file="test_2_multimatched_index2.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	402 </output_collection>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	403 </test>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	404 <test>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	405 <!-- paired end with one index -->
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	406 <param name="run_type" value="paired" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	407 <param name="bcfile" value="barcode_splitter_barcodes.txt" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	408 <param name="mismatches" value="2" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	409 <param name="barcodes_at_end" value="" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	410 <param name="split_all" value="False" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	411 <param name="fwdinput" value="barcode_splitter1.fastq" ftype="fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	412 <param name="revinput" value="barcode_splitter_index_2.fastq" ftype="fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	413
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	414 <repeat name="idxfiles">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	415 <param name="idxinput" value="barcode_splitter_index.fastq" ftype="fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	416 <param name="idxreadname" value="index" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	417 </repeat>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	418
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	419 <output name="summary" file="test_1_summary.out" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	420 <output_collection name="split_output_paired" type="list:paired">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	421 <element name="BC1">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	422 <element name="forward" ftype="fastq" file="test_3_BC1-forward.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	423 <element name="reverse" ftype="fastq" file="test_3_BC1-reverse.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	424 </element>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	425 <element name="BC2">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	426 <element name="forward" ftype="fastq" file="test_3_BC2-forward.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	427 <element name="reverse" ftype="fastq" file="test_3_BC2-reverse.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	428 </element>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	429 <element name="BC3">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	430 <element name="forward" ftype="fastq" file="test_3_BC3-forward.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	431 <element name="reverse" ftype="fastq" file="test_3_BC3-reverse.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	432 </element>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	433 <element name="BC4">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	434 <element name="forward" ftype="fastq" file="test_3_BC4-forward.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	435 <element name="reverse" ftype="fastq" file="test_3_BC4-reverse.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	436 </element>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	437 <element name="unmatched">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	438 <element name="forward" ftype="fastq" file="test_3_unmatched-forward.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	439 <element name="reverse" ftype="fastq" file="test_3_unmatched-reverse.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	440 </element>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	441 <element name="multimatched">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	442 <element name="forward" ftype="fastq" file="test_3_multimatched-forward.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	443 <element name="reverse" ftype="fastq" file="test_3_multimatched-reverse.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	444 </element>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	445 </output_collection>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	446 </test>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	447 <test>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	448 <!-- paired end 2 indexes and split_all -->
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	449 <param name="run_type" value="paired" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	450 <param name="bcfile" value="barcode_splitter_barcodes_dual.txt" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	451 <param name="mismatches" value="2" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	452 <param name="barcodes_at_end" value="" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	453 <param name="split_all" value="True" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	454 <param name="fwdinput" value="barcode_splitter1.fastq" ftype="fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	455 <param name="revinput" value="barcode_splitter_index_2.fastq" ftype="fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	456
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	457 <repeat name="idxfiles">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	458 <param name="idxinput" value="barcode_splitter_index.fastq" ftype="fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	459 <param name="idxreadname" value="index1" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	460 </repeat>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	461 <repeat name="idxfiles">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	462 <param name="idxinput" value="barcode_splitter_index_2.fastq" ftype="fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	463 <param name="idxreadname" value="index2" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	464 </repeat>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	465
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	466 <output name="summary" file="test_2_summary.out" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	467 <output_collection name="split_output_paired" type="list:paired">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	468 <element name="BC1">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	469 <element name="forward" ftype="fastq" file="test_3_BC1-forward.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	470 <element name="reverse" ftype="fastq" file="test_3_BC1-reverse.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	471 </element>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	472 <element name="BC2">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	473 <element name="forward" ftype="fastq" file="test_3_BC2-forward.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	474 <element name="reverse" ftype="fastq" file="test_3_BC2-reverse.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	475 </element>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	476 <element name="BC3">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	477 <element name="forward" ftype="fastq" file="test_3_BC3-forward.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	478 <element name="reverse" ftype="fastq" file="test_3_BC3-reverse.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	479 </element>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	480 <element name="BC4">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	481 <element name="forward" ftype="fastq" file="test_3_BC4-forward.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	482 <element name="reverse" ftype="fastq" file="test_3_BC4-reverse.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	483 </element>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	484 <element name="unmatched">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	485 <element name="forward" ftype="fastq" file="test_3_unmatched-forward.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	486 <element name="reverse" ftype="fastq" file="test_3_unmatched-reverse.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	487 </element>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	488 <element name="multimatched">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	489 <element name="forward" ftype="fastq" file="test_3_multimatched-forward.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	490 <element name="reverse" ftype="fastq" file="test_3_multimatched-reverse.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	491 </element>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	492 </output_collection>
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	493 <output_collection name="index_only" type="list">
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	494 <element name="BC1 index1" ftype="fastq" file="test_2_BC1_index1.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	495 <element name="BC2 index1" ftype="fastq" file="test_2_BC2_index1.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	496 <element name="BC3 index1" ftype="fastq" file="test_2_BC3_index1.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	497 <element name="BC4 index1" ftype="fastq" file="test_2_BC4_index1.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	498 <element name="unmatched index1" ftype="fastq" file="test_2_unmatched_index1.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	499 <element name="multimatched index1" ftype="fastq" file="test_2_multimatched_index1.fastq" />
5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10 iuc parents: diff changeset	500 <element name="BC1 index2" ftype="fastq" file="test_2_BC1_index2.fastq" />

0

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

1 <tool id="barcode_splitter" name="Barcode Splitter" version="0.18.4.0">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

2 <description>Split sequence files using multiple sets of barcodes</description>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

3 <requirements>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

4 <requirement type="package" version="0.18.4">barcode_splitter</requirement>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

5 </requirements>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

6 <version_command>barcode_splitter --version</version_command>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

7 <command detect_errors="exit_code">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

8 <![CDATA[

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

9 mkdir split &&

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

10 barcode_splitter

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

11

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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12 --bcfile '$bcfile' --mismatches '$mismatches' --galaxy $barcodes_at_end --prefix 'split/'

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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13

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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14 #set $auto_split_all = $split_all

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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15 #set $format = ""

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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16 #set $paired_match = "0"

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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17 #set $num_index_files = 0

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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18

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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19 #if str($runinterface.run_type) == "flexible":

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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20

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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21 ## Determine the format based on the first input file's extension

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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22 ## #for $indf in $runinterface.seqfiles

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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23 ## #set $format = $indf.input.extension

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

24 ## #break

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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25 ## #end for

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

26 #set $format = $runinterface.seqfiles[0].input.extension

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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27

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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28 ## Add the sequence files, count the number of forward, reverse, and other non-index read names, and auto-set split_all

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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29 #set $numforwards = 0

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

30 #set $numreverses = 0

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

31 #for $sf in $runinterface.seqfiles

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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32 #if str($sf.nameinterface.readtype) == "forward" or str($sf.nameinterface.readtype) == "forwardindex":

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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33 #set $numforwards += 1

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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34 #elif str($sf.nameinterface.readtype) == "reverse" or str($sf.nameinterface.readtype) == "reverseindex":

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

35 #set $numreverses += 1

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

36 #end if

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

37 #if str($sf.nameinterface.readtype) == "singleindex" or str($sf.nameinterface.readtype) == "forwardindex" or str($sf.nameinterface.readtype) == "reverseindex":

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

38 #set $auto_split_all = "--split_all"

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

39 #end if

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

40 '${sf.input}'

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

41 #end for

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

42

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

43 ## Determine whether valid paired-end data exists

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

44 #if $numforwards == 1 and $numreverses == 1:

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

45 #set $paired_match = "1"

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

46 #end if

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

47

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

48 ##Add the relative file argument positions of the index files in the list included above

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

49 --idxread

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

50 #set $n = 0

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

51 #for $sf in $runinterface.seqfiles

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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52 #set $n += 1

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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53 #if str($sf.nameinterface.readtype) == 'index' or str($sf.nameinterface.readtype) == "singleindex" or str($sf.nameinterface.readtype) == "forwardindex" or str($sf.nameinterface.readtype) == "reverseindex":

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

54 #set $num_index_files += 1

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

55 '${n}'

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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parents:

diff changeset

56 #end if

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

57 #end for

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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diff changeset

58

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

59 #elif str($runinterface.run_type) == "single":

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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diff changeset

60

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

61 #set $format = $runinterface.snglinput.extension

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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diff changeset

62

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

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63 ## Add the sequence files

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

64 '${runinterface.snglinput}'

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

65 #for $sf in $runinterface.idxfiles

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

66 '${sf.idxinput}'

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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67 #end for

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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diff changeset

68

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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69 ##Add the relative file argument positions of the index files

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

70 --idxread

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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71 #set $n = 1

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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diff changeset

72 #for $sf in $runinterface.idxfiles

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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73 #set $num_index_files += 1

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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74 #set $n += 1

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

75 '${n}'

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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diff changeset

76 #end for

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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diff changeset

77

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

78 #elif str($runinterface.run_type) == "paired":

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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79

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

80 #set $format = $runinterface.fwdinput.extension

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

81 #set $paired_match = "1"

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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diff changeset

82

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

83 ## Add the sequence files

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

84 '${runinterface.fwdinput}' '${runinterface.revinput}'

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

85 #for $sf in $runinterface.idxfiles

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

86 '${sf.idxinput}'

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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87 #end for

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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diff changeset

88

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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89 ##Add the relative file argument positions of the index files

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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diff changeset

90 --idxread

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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91 #set $n = 2

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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diff changeset

92 #for $sf in $runinterface.idxfiles

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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93 #set $num_index_files += 1

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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94 #set $n += 1

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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diff changeset

95 '${n}'

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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96 #end for

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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97

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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diff changeset

98 #end if

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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99

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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diff changeset

100 --format '${format}' --suffix '.${format}' $auto_split_all

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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101

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102 > '$summary';

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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103

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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104 ## Determine validity of repeat params

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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105 #if $num_index_files == 0:

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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106 echo "ERROR: At least 1 read file must have a 'Read Type' selected as 'Index', 'Single-End with Index', 'Forward with index', or 'Reverse with Index')."

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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diff changeset

107 #end if

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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108

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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109 ## Give the output split file names the name specified by the user (to be turned into collection identifiers)

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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110 rc=0;

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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111 #set $n = 0

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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112

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113 #if str($runinterface.run_type) == "flexible":

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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114

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115 #for $repeat in $runinterface.seqfiles

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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116

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117 #set $n += 1

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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118

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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119 #set $readname = "read-" + str($n)

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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120 #set $readtype = "index"

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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121 #if str($repeat.nameinterface.readtype) == "forward" or str($repeat.nameinterface.readtype) == "forwardindex":

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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122 #set $readname = "forward"

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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123 #set $readtype = "forward"

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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124 #elif str($repeat.nameinterface.readtype) == "reverse" or str($repeat.nameinterface.readtype) == "reverseindex":

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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125 #set $readname = "reverse"

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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126 #set $readtype = "reverse"

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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127 #else:

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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parents:

diff changeset

128 #if (str($repeat.nameinterface.readtype) == "single" or str($repeat.nameinterface.readtype) == "singleindex" or str($repeat.nameinterface.readtype) == "index") and str($repeat.nameinterface.readname) != "":

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

129 #set $readname = $repeat.nameinterface.readname

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

130 #end if

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

131 #if str($repeat.nameinterface.readtype) == "single" or str($repeat.nameinterface.readtype) == "singleindex":

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

132 #set $readtype = "single"

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

133 #end if

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

134 #end if

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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parents:

diff changeset

135

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

136 for f in split/*-read-'${n}'.'${format}';

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

137 do

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

138 if [ -e "\$f" ]; then

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

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139 ## Space-delimited file name structure: "SAMPLE READNAME READTYPE MATCHEDPAIR.EXT"

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

140 mv "\$f" "\${f/-read-${n}/ ${readname} ${readtype} ${paired_match}}" || rc=\$?;

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

141 fi;

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

142 done;

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

143 #end for

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

144

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

145 #elif str($runinterface.run_type) == "single":

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

146

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

147 #set $n = 1

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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148

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

149 ## Rename the single-end split read files

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

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150 #set $readname = "read-" + str($n)

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

151 #set $readtype = 'single'

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

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152 for f in split/*-read-'${n}'.'${format}';

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

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153 do

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

154 mv "\$f" "\${f/-read-${n}/ ${readname} ${readtype} ${paired_match}}" || rc=\$?;

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

155 done;

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

156

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

157 ## Rename the index read files

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

158 #set $readtype = "index"

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

159 #for $repeat in $runinterface.idxfiles

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

160 #set $n += 1

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

161

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

162 #set $readname = "read-" + str($n)

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

163 #if str($repeat.idxreadname) != "":

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

164 #set $readname = $repeat.idxreadname

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

165 #end if

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

166

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

167 for f in split/*-read-'${n}'.'${format}';

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

168 do

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

169 if [ -e "\$f" ]; then

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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170 ## Space-delimited file name structure: "SAMPLE READNAME READTYPE MATCHEDPAIR.EXT"

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

171 mv "\$f" "\${f/-read-${n}/ ${readname} ${readtype} ${paired_match}}" || rc=\$?;

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

172 fi;

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

173 done;

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

174 #end for

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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diff changeset

175

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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diff changeset

176 #elif str($runinterface.run_type) == "paired":

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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diff changeset

177

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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diff changeset

178 #set $n = 1

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iuc

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diff changeset

179

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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180 ## Rename the forward split read files

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

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181 #set $readname = "forward"

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

182 #set $readtype = "forward"

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

183 for f in split/*-read-'${n}'.'${format}';

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

184 do

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

185 mv "\$f" "\${f/-read-${n}/ ${readname} ${readtype} ${paired_match}}" || rc=\$?;

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

186 done;

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

187

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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188 #set $n += 1

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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diff changeset

189

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

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190 ## Rename the reverse split read files

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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191 #set $readname = "reverse"

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

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192 #set $readtype = "reverse"

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

193 for f in split/*-read-'${n}'.'${format}';

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

194 do

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

195 mv "\$f" "\${f/-read-${n}/ ${readname} ${readtype} ${paired_match}}" || rc=\$?;

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

196 done;

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

197

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

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198 ## Rename the index read files

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

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199 #set $readtype = "index"

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

200 #for $repeat in $runinterface.idxfiles

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

201 #set $n += 1

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

202

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

203 #set $readname = "read-" + str($n)

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

204 #if str($repeat.idxreadname) != "":

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

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205 #set $readname = $repeat.idxreadname

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

206 #end if

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

207

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

208 for f in split/*-read-'${n}'.'${format}';

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

209 do

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

210 if [ -e "\$f" ]; then

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

211 ## Space-delimited file name structure: "SAMPLE READNAME READTYPE MATCHEDPAIR.EXT"

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

212 mv "\$f" "\${f/-read-${n}/ ${readname} ${readtype} ${paired_match}}" || rc=\$?;

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

213 fi;

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

214 done;

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

215 #end for

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

216

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

217 #end if

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

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218

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219 ## Exit non-zero if rc is not 0

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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220 [ \$rc == 0 ];

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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221 ]]>

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222 </command>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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223

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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224 <inputs>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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225 <param name="bcfile" type="data" format="tabular" label="Barcode File" help="Tab-delimited text file where the first column is a sample ID and subsequent columns are barcodes. Note, files with indexes/barcode sequences must be supplied in the same order as the barcode columns in this file and their 'Read Type' must have 'Index'." />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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226

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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227 <conditional name="runinterface">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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228 <param label="Run Type" name="run_type" type="select">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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229 <option value="single" selected="true">Single-End</option>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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230 <option value="paired">Paired-End</option>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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231 <option value="flexible">Flexible</option>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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232 </param>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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233 <when value="single">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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234

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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235 <param name="snglinput" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Read File" help="Typically, 'Read 1'." />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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236 <repeat name="idxfiles" title="Index File(s)" min="1" default="1">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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237 <param name="idxinput" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Index File" help="Typically, 'Read 2 Index'." />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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238 <param name="idxreadname" type="text" label="Index Name" help="E.g. index1, index2, etc.. Letters and numbers only. No spaces. Default is 'read-x' where 'x' is a number corresponding to the order in which the file was supplied (including the read file above).">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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239 <sanitizer>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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240 <valid initial="string.ascii_letters,string.digits" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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241 </sanitizer>

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242 </param>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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243 </repeat>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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244 </when>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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245 <when value="paired">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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246

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247 <param name="fwdinput" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Forward Read File" help="Typically, 'Read 1'." />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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248 <param name="revinput" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Reverse Read File" help="Typically, 'Read 3'." />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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249

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250 <repeat name="idxfiles" title="Index Files" min="0" default="1">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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251 <param name="idxinput" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Index File" help="Typically, 'Read 2 Index' or 'Read 4 Index'." />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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252 <param name="idxreadname" type="text" label="Index Name" help="E.g. index1, index2, etc.. Letters and numbers only. No spaces. Default is 'read-x' where 'x' is a number corresponding to the order in which the file was supplied (including the forward and reverse files).">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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253 <sanitizer>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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254 <valid initial="string.ascii_letters,string.digits" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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255 </sanitizer>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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256 </param>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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257 </repeat>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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258 </when>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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259 <when value="flexible">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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260 <repeat name="seqfiles" title="Read Files" min="1" default="1">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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261 <param name="input" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Read File" help="Forward or single-end read files are typically named 'Read 1'. Index files are typically named 'Read 2 Index' or 'Read 4 Index'. Reverse read files are typically named 'Read 3'." />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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262 <conditional name="nameinterface">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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263 <param name="readtype" type="select" label="Read Type" help="E.g. If one file is 'Forward' and one is 'Reverse', split reads from those files will appear in an output paired collection. If your file has reads with barcodes embedded in them, select their 'with index' variant, e.g. 'Forward with Index'.">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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264 <option value="single" selected="true">Single-End</option>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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265 <option value="forward">Forward</option>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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266 <option value="reverse">Reverse</option>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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267 <option value="index">Index</option>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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268 <option value="singleindex">Single-End with Index</option>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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269 <option value="forwardindex">Forward with Index</option>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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270 <option value="reverseindex">Reverse with Index</option>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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271 </param>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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272 <when value="single">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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273 <param name="readname" type="text" label="Read Name" help="E.g. index1, index2, etc.. Ignored for paired-collections. Letters and numbers only. No spaces. Default is 'read-x' where 'x' is a number corresponding to the order in which the file was supplied.">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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274 <sanitizer>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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275 <valid initial="string.ascii_letters,string.digits" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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276 </sanitizer>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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277 </param>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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278 </when>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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279 <when value="singleindex">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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280 <param name="readname" type="text" label="Read Name" help="E.g. index1, index2, etc.. Ignored for paired-collections. Letters and numbers only. No spaces. Default is 'read-x' where 'x' is a number corresponding to the order in which the file was supplied.">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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281 <sanitizer>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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282 <valid initial="string.ascii_letters,string.digits" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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283 </sanitizer>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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284 </param>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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285 </when>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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286 <when value="index">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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287 <param name="readname" type="text" label="Read Name" help="E.g. index1, index2, etc.. Ignored for paired-collections. Letters and numbers only. No spaces. Default is 'read-x' where 'x' is a number corresponding to the order in which the file was supplied.">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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288 <sanitizer>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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289 <valid initial="string.ascii_letters,string.digits" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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290 </sanitizer>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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291 </param>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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292 </when>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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293 </conditional>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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294 </repeat>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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295 </when>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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296 </conditional>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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297

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298 <param name="mismatches" type="integer" value="1" max="2" min="0" label="Number of allowed mismatches" help="An integer between 0 and 2 (inclusive). Warning: Make sure all your barcodes differ by at least double this value plus 1, otherwise sequences that match both barcodes equally well will be discarded as 'multimatched' reads." />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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299 <param argument="--barcodes_at_end" type="boolean" truevalue="--barcodes_at_end" falsevalue="" checked="false" label="Barcodes are at the end of all index sequences" help="Default is the beginning of all sequences" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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300 <param argument="--split_all" type="boolean" truevalue="--split_all" falsevalue="" checked="false" label="Split index files too" help="This creates an output collection for split files whose selected 'Read Type' is 'Index'." />

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301 </inputs>

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302

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303 <outputs>

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304 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: Summary" />

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305

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306 <collection name="split_output_single" type="list" format_source="input" label="${tool.name} on ${on_string}: single-end">

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307

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308 <filter>str(runinterface['run_type']) == "single" or (str(runinterface['run_type']) == "flexible" and len(list(filter(lambda x: str(x['nameinterface']['readtype']) != "index", runinterface['seqfiles']))) == 1)</filter>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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309 <discover_datasets pattern="(?P<identifier_0>\S+)\ \S+\ (single|forward|reverse) 0\.(?P<ext>.*)" directory="split" visible="false" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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310 </collection>

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311

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312 <collection name="split_output_paired" type="list:paired" format_source="input" label="${tool.name} on ${on_string}: paired-end">

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313

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314 <filter>str(runinterface['run_type']) == "paired" or (str(runinterface['run_type']) == "flexible" and len(list(filter(lambda x: str(x['nameinterface']['readtype']).startswith('forward'), runinterface['seqfiles']))) == 1 and len(list(filter(lambda x: str(x['nameinterface']['readtype']).startswith('reverse'), runinterface['seqfiles']))) == 1)</filter>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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315 <discover_datasets pattern="(?P<identifier_0>\S+)\ \S+\ (?P<identifier_1>forward|reverse) 1\.(?P<ext>.*)" directory="split" visible="false" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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316 </collection>

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317

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318 <collection name="split_output_paired_other" type="list" format_source="input" label="${tool.name} on ${on_string}: other-end">

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319

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320 <filter>str(runinterface['run_type']) == "flexible" and len(list(filter(lambda x: str(x['nameinterface']['readtype']).startswith('single'), runinterface['seqfiles']))) > 0 and len(list(filter(lambda x: str(x['nameinterface']['readtype']).startswith('forward'), runinterface['seqfiles']))) == 1 and len(list(filter(lambda x: str(x['nameinterface']['readtype']).startswith('reverse'), runinterface['seqfiles']))) == 1</filter>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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321 <discover_datasets pattern="(?P<identifier_0>\S+\ \S+)\ single 1\.(?P<ext>.*)" directory="split" visible="false" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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322 </collection>

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323

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324 <collection name="split_output_multi" type="list" format_source="input" label="${tool.name} on ${on_string}: multi-end">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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325

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326 <filter>str(runinterface['run_type']) == "flexible" and (len(runinterface['seqfiles']) - len(list(filter(lambda x: str(x['nameinterface']['readtype']) == "index", runinterface['seqfiles'])))) > 1 and (len(list(filter(lambda x: str(x['nameinterface']['readtype']).startswith('forward'), runinterface['seqfiles']))) != 1 or len(list(filter(lambda x: str(x['nameinterface']['readtype']).startswith('reverse'), runinterface['seqfiles']))) != 1)</filter>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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327 <discover_datasets pattern="(?P<identifier_0>\S+ \S+) (single (0|1)|(forward|reverse) 0)\.(?P<ext>.*)" directory="split" visible="false" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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328 </collection>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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329

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330 <collection name="index_only" type="list" format_source="input" label="${tool.name} on ${on_string}: indexes">

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331

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332 <filter>split_all and ((str(runinterface['run_type']) != "flexible" and len(runinterface['idxfiles']) > 0) or (str(runinterface['run_type']) == "flexible" and len(list(filter(lambda x: str(x['nameinterface']['readtype']) == "index", runinterface['seqfiles']))) > 0))</filter>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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333 <discover_datasets pattern="(?P<identifier_0>.*?) index (0|1)\.(?P<ext>.*)" directory="split" visible="false" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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334 </collection>

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335 </outputs>

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336

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337 <tests>

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338 <test>

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339

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340 <param name="run_type" value="single" />

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341 <param name="bcfile" value="barcode_splitter_barcodes.txt" />

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342 <param name="mismatches" value="2" />

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343 <param name="barcodes_at_end" value="" />

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344 <param name="split_all" value="False" />

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345 <param name="snglinput" value="barcode_splitter1.fastq" ftype="fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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346

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347 <repeat name="idxfiles">

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348 <param name="idxinput" value="barcode_splitter_index.fastq" ftype="fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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349 <param name="idxreadname" value="read" />

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350 </repeat>

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351

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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352 <output name="summary" file="test_1_summary.out" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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353 <output_collection name="split_output_single" type="list">

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354 <element name="BC1" ftype="fastq" file="test_1_BC1-read-1.out" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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355 <element name="BC2" ftype="fastq" file="test_1_BC2-read-1.out" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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356 <element name="BC3" ftype="fastq" file="test_1_BC3-read-1.out" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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357 <element name="BC4" ftype="fastq" file="test_1_BC4-read-1.out" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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358 <element name="unmatched" ftype="fastq" file="test_1_unmatched-read-1.out" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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359 <element name="multimatched" ftype="fastq" file="test_1_multimatched-read-1.out" />

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360 </output_collection>

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361 </test>

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362 <test>

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363

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364 <param name="run_type" value="single" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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365 <param name="bcfile" value="barcode_splitter_barcodes_dual.txt" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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366 <param name="mismatches" value="2" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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367 <param name="barcodes_at_end" value="" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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368 <param name="split_all" value="True" />

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369 <param name="snglinput" value="barcode_splitter1.fastq" ftype="fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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370

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371 <repeat name="idxfiles">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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372 <param name="idxinput" value="barcode_splitter_index.fastq" ftype="fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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373 <param name="idxreadname" value="index1" />

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374 </repeat>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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375 <repeat name="idxfiles">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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376 <param name="idxinput" value="barcode_splitter_index_2.fastq" ftype="fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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377 <param name="idxreadname" value="index2" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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378 </repeat>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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379

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diff changeset

380 <output name="summary" file="test_2_summary.out" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

381 <output_collection name="split_output_single" type="list">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

382 <element name="BC1" ftype="fastq" file="test_2_BC1-read-1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

383 <element name="BC2" ftype="fastq" file="test_2_BC2-read-1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

384 <element name="BC3" ftype="fastq" file="test_2_BC3-read-1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

385 <element name="BC4" ftype="fastq" file="test_2_BC4-read-1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

386 <element name="unmatched" ftype="fastq" file="test_2_unmatched-read-1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

387 <element name="multimatched" ftype="fastq" file="test_2_multimatched-read-1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

388 </output_collection>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

389 <output_collection name="index_only" type="list">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

390 <element name="BC1 index1" ftype="fastq" file="test_2_BC1_index1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

391 <element name="BC2 index1" ftype="fastq" file="test_2_BC2_index1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

392 <element name="BC3 index1" ftype="fastq" file="test_2_BC3_index1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

393 <element name="BC4 index1" ftype="fastq" file="test_2_BC4_index1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

394 <element name="unmatched index1" ftype="fastq" file="test_2_unmatched_index1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

395 <element name="multimatched index1" ftype="fastq" file="test_2_multimatched_index1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

396 <element name="BC1 index2" ftype="fastq" file="test_2_BC1_index2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

397 <element name="BC2 index2" ftype="fastq" file="test_2_BC2_index2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

398 <element name="BC3 index2" ftype="fastq" file="test_2_BC3_index2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

399 <element name="BC4 index2" ftype="fastq" file="test_2_BC4_index2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

400 <element name="unmatched index2" ftype="fastq" file="test_2_unmatched_index2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

401 <element name="multimatched index2" ftype="fastq" file="test_2_multimatched_index2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

402 </output_collection>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

403 </test>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

404 <test>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

405

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

406 <param name="run_type" value="paired" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

407 <param name="bcfile" value="barcode_splitter_barcodes.txt" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

408 <param name="mismatches" value="2" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

409 <param name="barcodes_at_end" value="" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

410 <param name="split_all" value="False" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

411 <param name="fwdinput" value="barcode_splitter1.fastq" ftype="fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

412 <param name="revinput" value="barcode_splitter_index_2.fastq" ftype="fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

413

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

414 <repeat name="idxfiles">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

415 <param name="idxinput" value="barcode_splitter_index.fastq" ftype="fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

416 <param name="idxreadname" value="index" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

417 </repeat>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

418

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

419 <output name="summary" file="test_1_summary.out" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

420 <output_collection name="split_output_paired" type="list:paired">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

421 <element name="BC1">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

422 <element name="forward" ftype="fastq" file="test_3_BC1-forward.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

423 <element name="reverse" ftype="fastq" file="test_3_BC1-reverse.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

424 </element>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

425 <element name="BC2">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

426 <element name="forward" ftype="fastq" file="test_3_BC2-forward.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

427 <element name="reverse" ftype="fastq" file="test_3_BC2-reverse.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

428 </element>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

429 <element name="BC3">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

430 <element name="forward" ftype="fastq" file="test_3_BC3-forward.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

431 <element name="reverse" ftype="fastq" file="test_3_BC3-reverse.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

432 </element>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

433 <element name="BC4">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

434 <element name="forward" ftype="fastq" file="test_3_BC4-forward.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

435 <element name="reverse" ftype="fastq" file="test_3_BC4-reverse.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

436 </element>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

437 <element name="unmatched">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

438 <element name="forward" ftype="fastq" file="test_3_unmatched-forward.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

439 <element name="reverse" ftype="fastq" file="test_3_unmatched-reverse.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

440 </element>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

441 <element name="multimatched">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

442 <element name="forward" ftype="fastq" file="test_3_multimatched-forward.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

443 <element name="reverse" ftype="fastq" file="test_3_multimatched-reverse.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

444 </element>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

445 </output_collection>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

446 </test>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

447 <test>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

448

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

449 <param name="run_type" value="paired" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

450 <param name="bcfile" value="barcode_splitter_barcodes_dual.txt" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

451 <param name="mismatches" value="2" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

452 <param name="barcodes_at_end" value="" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

453 <param name="split_all" value="True" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

454 <param name="fwdinput" value="barcode_splitter1.fastq" ftype="fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

455 <param name="revinput" value="barcode_splitter_index_2.fastq" ftype="fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

456

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

457 <repeat name="idxfiles">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

458 <param name="idxinput" value="barcode_splitter_index.fastq" ftype="fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

459 <param name="idxreadname" value="index1" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

460 </repeat>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

461 <repeat name="idxfiles">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

462 <param name="idxinput" value="barcode_splitter_index_2.fastq" ftype="fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

463 <param name="idxreadname" value="index2" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

464 </repeat>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

465

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

466 <output name="summary" file="test_2_summary.out" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

467 <output_collection name="split_output_paired" type="list:paired">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

468 <element name="BC1">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

469 <element name="forward" ftype="fastq" file="test_3_BC1-forward.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

470 <element name="reverse" ftype="fastq" file="test_3_BC1-reverse.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

471 </element>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

472 <element name="BC2">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

473 <element name="forward" ftype="fastq" file="test_3_BC2-forward.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

474 <element name="reverse" ftype="fastq" file="test_3_BC2-reverse.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

475 </element>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

476 <element name="BC3">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

477 <element name="forward" ftype="fastq" file="test_3_BC3-forward.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

478 <element name="reverse" ftype="fastq" file="test_3_BC3-reverse.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

479 </element>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

480 <element name="BC4">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

481 <element name="forward" ftype="fastq" file="test_3_BC4-forward.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

482 <element name="reverse" ftype="fastq" file="test_3_BC4-reverse.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

483 </element>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

484 <element name="unmatched">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

485 <element name="forward" ftype="fastq" file="test_3_unmatched-forward.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

486 <element name="reverse" ftype="fastq" file="test_3_unmatched-reverse.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

487 </element>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

488 <element name="multimatched">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

489 <element name="forward" ftype="fastq" file="test_3_multimatched-forward.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

490 <element name="reverse" ftype="fastq" file="test_3_multimatched-reverse.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

491 </element>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

492 </output_collection>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

493 <output_collection name="index_only" type="list">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

494 <element name="BC1 index1" ftype="fastq" file="test_2_BC1_index1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

495 <element name="BC2 index1" ftype="fastq" file="test_2_BC2_index1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

496 <element name="BC3 index1" ftype="fastq" file="test_2_BC3_index1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

497 <element name="BC4 index1" ftype="fastq" file="test_2_BC4_index1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

498 <element name="unmatched index1" ftype="fastq" file="test_2_unmatched_index1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

499 <element name="multimatched index1" ftype="fastq" file="test_2_multimatched_index1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

500 <element name="BC1 index2" ftype="fastq" file="test_2_BC1_index2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

501 <element name="BC2 index2" ftype="fastq" file="test_2_BC2_index2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

502 <element name="BC3 index2" ftype="fastq" file="test_2_BC3_index2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

503 <element name="BC4 index2" ftype="fastq" file="test_2_BC4_index2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

504 <element name="unmatched index2" ftype="fastq" file="test_2_unmatched_index2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

505 <element name="multimatched index2" ftype="fastq" file="test_2_multimatched_index2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

506 </output_collection>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

507 </test>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

508 <test>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

509

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

510 <param name="bcfile" value="barcode_splitter_barcodes.txt" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

511 <param name="mismatches" value="2" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

512 <param name="barcodes_at_end" value="" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

513 <param name="split_all" value="False" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

514

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

515 <conditional name="runinterface">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

516 <param name="run_type" value="flexible" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

517 <repeat name="seqfiles">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

518 <param name="input" ftype="fastq" value="barcode_splitter1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

519 <conditional name="nameinterface">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

520 <param name="readtype" value="singleindex" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

521 <param name="readname" value="read" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

522 </conditional>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

523 </repeat>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

524 </conditional>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

525

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

526 <output name="summary" file="test_5_summary.out" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

527 <output_collection name="split_output_single" type="list">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

528 <element name="BC1" ftype="fastq" file="test_1_BC1-read-1.out" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

529 <element name="BC2" ftype="fastq" file="test_1_BC2-read-1.out" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

530 <element name="BC3" ftype="fastq" file="test_1_BC3-read-1.out" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

531 <element name="BC4" ftype="fastq" file="test_5_BC4-read-1.out" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

532 <element name="unmatched" ftype="fastq" file="test_5_unmatched-read-1.out" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

533 <element name="multimatched" ftype="fastq" file="test_1_multimatched-read-1.out" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

534 </output_collection>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

535 </test>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

536 <test>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

537

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

538 <param name="bcfile" value="barcode_splitter_barcodes_dual.txt" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

539 <param name="mismatches" value="2" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

540 <param name="barcodes_at_end" value="" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

541 <param name="split_all" value="True" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

542

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

543 <conditional name="runinterface">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

544 <param name="run_type" value="flexible" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

545 <repeat name="seqfiles">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

546 <param name="input" ftype="fastq" value="barcode_splitter1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

547 <conditional name="nameinterface">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

548 <param name="readtype" value="single" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

549 <param name="readname" value="read1" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

550 </conditional>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

551 </repeat>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

552 <repeat name="seqfiles">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

553 <param name="input" ftype="fastq" value="barcode_splitter_index.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

554 <conditional name="nameinterface">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

555 <param name="readtype" value="singleindex" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

556 <param name="readname" value="read2" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

557 </conditional>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

558 </repeat>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

559 <repeat name="seqfiles">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

560 <param name="input" ftype="fastq" value="barcode_splitter_index_2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

561 <conditional name="nameinterface">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

562 <param name="readtype" value="index" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

563 <param name="readname" value="index2" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

564 </conditional>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

565 </repeat>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

566 </conditional>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

567

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

568 <output name="summary" file="test_6_summary.out" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

569 <output_collection name="split_output_multi" type="list">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

570 <element name="BC1 read1" ftype="fastq" file="test_6_BC1_read1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

571 <element name="BC2 read1" ftype="fastq" file="test_6_BC2_read1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

572 <element name="BC3 read1" ftype="fastq" file="test_6_BC3_read1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

573 <element name="BC4 read1" ftype="fastq" file="test_6_BC4_read1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

574 <element name="unmatched read1" ftype="fastq" file="test_6_unmatched_read1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

575 <element name="multimatched read1" ftype="fastq" file="test_6_multimatched_read1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

576 <element name="BC1 read2" ftype="fastq" file="test_6_BC1_read2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

577 <element name="BC2 read2" ftype="fastq" file="test_6_BC2_read2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

578 <element name="BC3 read2" ftype="fastq" file="test_6_BC3_read2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

579 <element name="BC4 read2" ftype="fastq" file="test_6_BC4_read2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

580 <element name="unmatched read2" ftype="fastq" file="test_6_unmatched_read2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

581 <element name="multimatched read2" ftype="fastq" file="test_6_multimatched_read2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

582 </output_collection>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

583 <output_collection name="index_only" type="list">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

584 <element name="BC1 index2" ftype="fastq" file="test_6_BC1_index2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

585 <element name="BC2 index2" ftype="fastq" file="test_6_BC2_index2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

586 <element name="BC3 index2" ftype="fastq" file="test_6_BC3_index2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

587 <element name="BC4 index2" ftype="fastq" file="test_6_BC4_index2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

588 <element name="unmatched index2" ftype="fastq" file="test_6_unmatched_index2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

589 <element name="multimatched index2" ftype="fastq" file="test_6_multimatched_index2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

590 </output_collection>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

591 </test>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

592 <test>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

593

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

594 <param name="bcfile" value="barcode_splitter_barcodes.txt" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

595 <param name="mismatches" value="2" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

596 <param name="barcodes_at_end" value="" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

597 <param name="split_all" value="False" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

598

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

599 <conditional name="runinterface">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

600 <param name="run_type" value="flexible" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

601 <repeat name="seqfiles">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

602 <param name="input" ftype="fastq" value="barcode_splitter1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

603 <conditional name="nameinterface">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

604 <param name="readtype" value="forward" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

605 <param name="readname" value="" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

606 </conditional>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

607 </repeat>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

608 <repeat name="seqfiles">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

609 <param name="input" ftype="fastq" value="barcode_splitter_index.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

610 <conditional name="nameinterface">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

611 <param name="readtype" value="index" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

612 <param name="readname" value="index" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

613 </conditional>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

614 </repeat>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

615 <repeat name="seqfiles">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

616 <param name="input" ftype="fastq" value="barcode_splitter_index_2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

617 <conditional name="nameinterface">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

618 <param name="readtype" value="reverse" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

619 <param name="readname" value="" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

620 </conditional>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

621 </repeat>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

622 </conditional>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

623

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

624 <output name="summary" file="test_1_summary.out" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

625 <output_collection name="split_output_paired" type="list:paired">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

626 <element name="BC1">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

627 <element name="forward" ftype="fastq" file="test_3_BC1-forward.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

628 <element name="reverse" ftype="fastq" file="test_3_BC1-reverse.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

629 </element>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

630 <element name="BC2">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

631 <element name="forward" ftype="fastq" file="test_3_BC2-forward.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

632 <element name="reverse" ftype="fastq" file="test_3_BC2-reverse.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

633 </element>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

634 <element name="BC3">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

635 <element name="forward" ftype="fastq" file="test_3_BC3-forward.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

636 <element name="reverse" ftype="fastq" file="test_3_BC3-reverse.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

637 </element>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

638 <element name="BC4">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

639 <element name="forward" ftype="fastq" file="test_3_BC4-forward.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

640 <element name="reverse" ftype="fastq" file="test_3_BC4-reverse.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

641 </element>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

642 <element name="unmatched">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

643 <element name="forward" ftype="fastq" file="test_3_unmatched-forward.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

644 <element name="reverse" ftype="fastq" file="test_3_unmatched-reverse.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

645 </element>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

646 <element name="multimatched">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

647 <element name="forward" ftype="fastq" file="test_3_multimatched-forward.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

648 <element name="reverse" ftype="fastq" file="test_3_multimatched-reverse.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

649 </element>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

650 </output_collection>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

651 </test>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

652 <test>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

653

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

654 <param name="bcfile" value="barcode_splitter_barcodes_dual.txt" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

655 <param name="mismatches" value="2" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

656 <param name="barcodes_at_end" value="" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

657 <param name="split_all" value="False" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

658

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

659 <conditional name="runinterface">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

660 <param name="run_type" value="flexible" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

661 <repeat name="seqfiles">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

662 <param name="input" ftype="fastq" value="barcode_splitter1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

663 <conditional name="nameinterface">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

664 <param name="readtype" value="forward" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

665 <param name="readname" value="" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

666 </conditional>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

667 </repeat>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

668 <repeat name="seqfiles">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

669 <param name="input" ftype="fastq" value="barcode_splitter1.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

670 <conditional name="nameinterface">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

671 <param name="readtype" value="single" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

672 <param name="readname" value="read" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

673 </conditional>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

674 </repeat>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

675 <repeat name="seqfiles">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

676 <param name="input" ftype="fastq" value="barcode_splitter_index_2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

677 <conditional name="nameinterface">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

678 <param name="readtype" value="index" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

679 <param name="readname" value="index" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

680 </conditional>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

681 </repeat>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

682 <repeat name="seqfiles">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

683 <param name="input" ftype="fastq" value="barcode_splitter_index_2.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

684 <conditional name="nameinterface">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

685 <param name="readtype" value="reverseindex" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

686 <param name="readname" value="" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

687 </conditional>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

688 </repeat>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

689 </conditional>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

690

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

691 <output name="summary" file="test_2_summary.out" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

692 <output_collection name="split_output_paired" type="list:paired">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

693 <element name="BC1">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

694 <element name="forward" ftype="fastq" file="test_3_BC1-forward.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

695 <element name="reverse" ftype="fastq" file="test_3_BC1-reverse.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

696 </element>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

697 <element name="BC2">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

698 <element name="forward" ftype="fastq" file="test_3_BC2-forward.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

699 <element name="reverse" ftype="fastq" file="test_3_BC2-reverse.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

700 </element>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

701 <element name="BC3">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

702 <element name="forward" ftype="fastq" file="test_3_BC3-forward.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

703 <element name="reverse" ftype="fastq" file="test_3_BC3-reverse.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

704 </element>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

705 <element name="BC4">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

706 <element name="forward" ftype="fastq" file="test_3_BC4-forward.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

707 <element name="reverse" ftype="fastq" file="test_3_BC4-reverse.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

708 </element>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

709 <element name="unmatched">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

710 <element name="forward" ftype="fastq" file="test_3_unmatched-forward.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

711 <element name="reverse" ftype="fastq" file="test_3_unmatched-reverse.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

712 </element>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

713 <element name="multimatched">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

714 <element name="forward" ftype="fastq" file="test_3_multimatched-forward.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

715 <element name="reverse" ftype="fastq" file="test_3_multimatched-reverse.fastq" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

716 </element>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

717 </output_collection>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

718 <output_collection name="split_output_paired_other" type="list">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

iuc

parents:

diff changeset

719 <element name="BC1 read" ftype="fastq" file="test_1_BC1-read-1.out" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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720 <element name="BC2 read" ftype="fastq" file="test_1_BC2-read-1.out" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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721 <element name="BC3 read" ftype="fastq" file="test_1_BC3-read-1.out" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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722 <element name="BC4 read" ftype="fastq" file="test_1_BC4-read-1.out" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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723 <element name="unmatched read" ftype="fastq" file="test_1_unmatched-read-1.out" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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diff changeset

724 <element name="multimatched read" ftype="fastq" file="test_1_multimatched-read-1.out" />

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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diff changeset

725 </output_collection>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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diff changeset

726 </test>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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diff changeset

727 </tests>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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728

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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diff changeset

729 <help>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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730 <![CDATA[

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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731 **What it does**

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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732

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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733 This tool splits a FASTQ file into several files, using barcodes as the split criteria. Barcodes in one file can be used to split multiple sorted files. Multiple sets of barcodes, each located in a different file, can be used.

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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734

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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735 --------

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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736

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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737 **How it works**

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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738

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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739 Given a number of allowed mismatches, all possible mismatching barcode combinations are pre-computed and stored in a hash lookup table. Each barcode column in the barcode file (--bcfile) adds another level to the hash table data structure. For each read group (e.g. forward, reverse, index1, and index2), the index sequence(s) are used to look up the sample they belong to. No pattern matching takes place - it's a simple hash table lookup where the keys being looked up are taken from the sequences in the index files. Barcode collisions are detected during the construction of the hash table before any sequences are processed, which results in warnings and/or errors and reads that match collided barcodes end up in a "multimatched" file. (A barcode collision is when 2 barcodes can match each other when each has an allowed number of mismatches).

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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740

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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741 The length of the barcode sequences in the barcodes file must be less than or equal to the length of the sequences in the corresponding index files and all barcodes in 1 column must be the same length (though the lengths of the barcodes between columns may differ).

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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742

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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743 There can only be 1 number of mismatches and it is applied per barcode. E.g. If the number of mismatches is set to 1, and there are 2 barcode columns, then two barcodes on the same row may each have 1 mismatch. There is no way (currently) to set a different number of mismatches for different barcode columns.

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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744

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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745 If there are 2 barcode columns, the output summary table can have multiple rows where a single sample could not be identified. Ignoring multimatched and error states for the moment, the following 4 rows are possible, but only those with counts greater than 0 will be included in the summary table:

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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746

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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747 unmatched unmatched unmatched 1

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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748 unmatched matched unmatched 2

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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749 unmatched unmatched matched 3

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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750 unmatched matched matched 4

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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751

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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752 The first column is the ID, which is 'unmatched' in all cases (except the error row). Here's what each row means in the above example:

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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753

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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754 1. For 1 read group, neither of the index sequences matched any barcodes in either barcode column.

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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755 2. For 2 read groups, a barcode in the first barcode column matched but none from the second were matched.

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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756 3. For 3 read groups, no barcodes in the first column matched but a barcode in the second barcode column did match.

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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757 4. For 4 read groups, a barcode from each column matched, but they were not in the same row.

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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758

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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759 If you encounter large counts in case 4, then barcodes are likely not paired correctly in the barcodes file.

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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760

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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761 Two other states can also be reported: multimatched & error. Read groups with 'multimatch' in one or more columns means that with the allowed number of mismatches, the affected index read can match multiple barcodes in the corresponding column. A multimatch will only be reported if the number of mismatches in the 2 matched barcodes are the same. If they are different, barcode_splitter will assign the read group to the better match. If you have any multimatch barcodes or barcode collision warnings, then the barcode design should be improved. The number of differences between any pair of barcodes in a single column should be greater than double the number of allowed mismatches, or else you may end up with numerous multimatch scenarios. A match in another barcode column will not resolve a multimatch in a different column.

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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762

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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763 **Barcode file Format**

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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764

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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765 Barcode files are simple text files.

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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766 Each line should contain an identifier (descriptive name for the barcode), and at least 1 barcode, separated by TAB characters. Multiple columns of barcodes are supported (each corresponding to a separate barcoded read file), though there's usually just 1. An example of the usage of multiple sets of barcodes could be the first set of barcodes can denote user and the second set can be each user's sample barcodes.

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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767 Example::

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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768

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769 #This line is a comment (starts with a 'number' sign)

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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770 BC1 GATCT TTGCAT

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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771 BC2 ATCGT GCGCAT

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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772 BC3 GTGAT AGGTCA

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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773 BC4 TGTCT CTTTGG

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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774

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775 For each barcode, a new FASTQ file will be created (with the barcodes' identifier as part of the file name).

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776 Sequences matching the barcodes in a row will be stored in the appropriate file.

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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777

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778 The first sequence file submitted must contain sequences with the barcodes in the first column of the barcode file. The second sequence file must contain sequences with the barcodes in the second column, and so on. The Number of Index Files supplied must match the number of actual columns in the barcode file and the order in which they are supplied must match the order of the barcode columns as well.

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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779

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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780 As many as 2 additional FASTQ output files will be created for each read/index file: the 'unmatched' file and the 'multimatched' file, where sequences not matching any barcode or matching more than 1 barcode (when mismatches are taken into account) will be stored.

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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781

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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782 The output of this tool is a summary table displaying the split counts for each barcode identifier and the percentage of the total reads those represent.

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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783 In addition, each FASTQ file produced will be loaded into the galaxy history as part of a collection list.

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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784 ]]>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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785 </help>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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786 <citations>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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787 <citation type="bibtex">

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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788 @misc{paired_sequence_utils,

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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789 title = {{Barcode}-{Splitter}},

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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790 url = {https://bitbucket.org/princeton_genomics/barcode_splitter/},

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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791 author = "Parsons, Lance and Leach, Robert"

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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792 }

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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793 </citation>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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794 </citations>

5f2897da293a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter commit 8f4f88267b8adfa035539230eab3d8eea6896e10

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795 </tool>

Mercurial > repos > iuc > barcode_splitter

annotate barcode_splitter.xml @ 0:5f2897da293a draft default tip