ragtag: ragtag.xml annotate

annotate ragtag.xml @ 0:a04e64efa43a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"

author	iuc
date	Wed, 10 Nov 2021 23:33:13 +0000
parents
children	d110a4141898

rev	line source
0 a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	1 <tool id='ragtag' name='RagTag' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' profile='20.01'>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	2 <description>reference-guided scaffolding of draft genomes</description>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	3 <macros>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	4 <import>macros.xml</import>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	5 </macros>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	6 <expand macro='xrefs' />
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	7 <expand macro='requirements' />
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	8 <command detect_errors='exit_code'><![CDATA[
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	9 #if $mode_conditional.mode_option != 'merge'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	10 #if $mode_conditional.advanced_options.mapping_conditional.mapping_option == 'nucmer'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	11 #set $nucmer_params = '%s -l %s -c %s' % ($mode_conditional.advanced_options.mapping_conditional.anchor_mode,
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	12 $mode_conditional.advanced_options.mapping_conditional.l,
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	13 $mode_conditional.advanced_options.mapping_conditional.c)
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	14 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	15 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	16 #if $mode_conditional.mode_option == 'merge'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	17 #set $input_files = list()
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	18 mkdir merge_files &&
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	19 #for $i, $j in enumerate($mode_conditional.scaffold_files)
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	20 #set $out_file = './merge_files/scaffold_%s.agp' % $i
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	21 ln -s '${j}' $out_file &&
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	22 $input_files.append($out_file)
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	23 #end for
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	24 #set $merge_files = " ".join($input_files)
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	25 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	26 ragtag.py $mode_conditional.mode_option -u
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	27 #if $mode_conditional.mode_option == 'correct'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	28 @INPUTS@
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	29 @COMMON_PARAMETERS@
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	30 #if $mode_conditional.validation_conditional.validation_option == 'true'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	31 -R '${mode_conditional.validation_conditional.R}'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	32 -T $mode_conditional.validation_conditional.read_type
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	33 -v $mode_conditional.validation_conditional.v
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	34 #if $mode_conditional.validation_conditional.max_cov
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	35 --max-cov $mode_conditional.validation_conditional.max_cov
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	36 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	37 #if $mode_conditional.validation_conditional.min_cov
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	38 --min-cov $mode_conditional.validation_conditional.min_cov
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	39 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	40 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	41 -b $mode_conditional.advanced_options.b
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	42 #if $mode_conditional.advanced_options.missasembly_break
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	43 $mode_conditional.advanced_options.missasembly_break
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	44 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	45 #if $mode_conditional.advanced_options.gff
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	46 --gff '${mode_conditional.advanced_options.gff}'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	47 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	48 --read-aligner 'minimap2' ## it is the only allowed
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	49 #else if $mode_conditional.mode_option == 'scaffold'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	50 @INPUTS@
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	51 @COMMON_PARAMETERS@
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	52 -i $mode_conditional.advanced_options.i
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	53 -a $mode_conditional.advanced_options.a
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	54 -s $mode_conditional.advanced_options.s
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	55 #if $mode_conditional.advanced_options.gap_conditional.gap_option == 'true'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	56 -r
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	57 -g '${mode_conditional.advanced_options.gap_conditional.g}'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	58 -m '${mode_conditional.advanced_options.gap_conditional.m}'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	59 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	60 #if $mode_conditional.advanced_options.unplaced_conditional.unplaced_option == 'true'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	61 -C
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	62 #if $mode_conditional.advanced_options.unplaced_conditional.J
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	63 -J '${mode_conditional.advanced_options.unplaced_conditional.J}'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	64 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	65 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	66 #else if $mode_conditional.mode_option == 'patch'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	67 @INPUTS@
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	68 @COMMON_PARAMETERS@
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	69 -s $mode_conditional.advanced_options.s
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	70 -i $mode_conditional.advanced_options.i
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	71 #if $mode_conditional.advanced_options.patching_mode
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	72 $mode_conditional.advanced_options.patching_mode
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	73 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	74 #else
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	75 $assembly_fasta
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	76 #if $mode_conditional.scaffold_files
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	77 $merge_files
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	78 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	79 #if $mode_conditional.merging_options.j
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	80 -j $mode_conditional.merging_options.j
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	81 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	82 -l $mode_conditional.merging_options.l
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	83 -e $mode_conditional.merging_options.e
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	84 --gap-func $mode_conditional.merging_options.function_merging
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	85 #if $mode_conditional.hic_options.b
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	86 -b $mode_conditional.hic_options.b
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	87 -r $mode_conditional.hic_options.r
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	88 -p $mode_conditional.hic_options.p
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	89 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	90 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	91 -o ./
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	92 #if $mode_conditional.mode_option != 'merge'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	93 -t \${GALAXY_SLOTS:-2}
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	94 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	95 #if $mode_conditional.mode_option == 'patch'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	96 && mv ragtag.patch.asm.paf.log ragtag.patch.log
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	97 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	98 ]]> </command>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	99 <inputs>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	100 <conditional name="mode_conditional">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	101 <param name="mode_option" type="select" label="Operation mode">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	102 <option value="correct">Correct: homology-based missasembly correction</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	103 <option value="scaffold">Scaffold: homology-based assebly scaffolding</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	104 <option value="patch">Patch: homology-based assembly patching</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	105 <option value="merge">Merge: scaffolding merging</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	106 </param>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	107 <when value="correct">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	108 <expand macro="input_options"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	109 <conditional name="validation_conditional">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	110 <param name="validation_option" type="select" label="Use validation reads">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	111 <option value="true">Enabled</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	112 <option value="false" selected="true">Disabled</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	113 </param>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	114 <when value="true">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	115 <param argument="-R" type="data" format="fastq,fastqsanger" label="Validation reads"
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	116 help="Without validation, the module will break at any point of reference discordance as defined by the 'correction options'.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	117 With validation, RagTag maps reads to the query assembly and verifies putative break points if they are near regions of
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	118 exceptionally low or high coverage. The reads used for validation should come from the same genotype as the query
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	119 assembly to ensure that coverage abnormalities don't arise from true biological variation" />
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	120 <param name="read_type" type="select" label="Read type">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	121 <option value="sr">Illumina</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	122 <option value="ont">Nanopore</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	123 <option value="corr">Error corrected long-reads</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	124 </param>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	125 <param argument="-v" type="integer" min="0" value="10000" label="Coverage validation window size"
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	126 help="This parameter specifies the window around the putative misassembly break point that RagTag examines
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	127 for exceptionally low or high read coverage. The larger this window size, the more likely
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	128 it is to find an unrelated coverage abnormality"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	129 <param argument="--max-cov" type="integer" min="0" value="" optional="true" label="Break sequences at regions at or above this coverage level"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	130 <param argument="--min-cov" type="integer" min="0" value="" optional="true" label="Break sequences at regions at or below this coverage level"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	131 </when>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	132 <when value="false"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	133 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	134 <section name="advanced_options" title="Advanced options">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	135 <expand macro="common_parameters"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	136 <param argument="-b" type="integer" min="0" value="5000" label="Minimum break distance from contig ends"
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	137 help="Breaks will not be made within -b bp of query sequence termini"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	138 <param name="missasembly_break" type="select" optional="true" label="Break misassebly option"
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	139 help="One can also direct RagTag to only break misassemblies between (--inter, query maps to >1 reference sequence) or within
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	140 (--intra, query maps discordantly to 1 reference sequence) reference sequences">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	141 <option value="--inter">Only break misassemblies between reference sequences (--inter)</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	142 <option value="--intra">Only break missasemblies within reference sequences (--intra)</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	143 </param>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	144 <param argument="--gff" type="data" format="gff" optional="true" label="Don't break sequences within GFF intervals"
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	145 help=" If one has annotations associated with the query assembly, provide them with the --gff option to ensure that the query assembly
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	146 is never broken within annotation intervals. "/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	147 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	148 <param name="output_correct" type="select" multiple="true" label="Output files">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	149 <option value="fasta" selected="true">The corrected query assembly in FASTA format</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	150 <option value="agp" selected="true">The AGP file defining the exact coordinates of query sequence breaks</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	151 <option value="paf">The description of the approximate mapping positions between two set of sequences in PAF format</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	152 <option value="log">Log file</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	153 </param>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	154 </when>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	155 <when value="scaffold">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	156 <expand macro="input_options"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	157 <section name="advanced_options" title="advanced options">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	158 <expand macro="common_parameters"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	159 <param argument="-i" type="float" min="0" max="1" value="0.2" label="Minimum grouping confidence score"
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	160 help="The grouping confidence score is the number of base pairs a contig covered in its assigned reference chromosome
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	161 divided by the total number of covered base pairs in the entire reference genome"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	162 <param argument="-a" type="float" min="0" max="1" value="0" label="Minimum location confidence score"
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	163 help="To create a metric associated with contig ordering confidence, Ragtag define a location confidence. First, the smallest
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	164 and largest alignment positions, with respect to the reference, between a contig and its assigned reference chromosome are found.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	165 The location confidence is then calculated as the number of covered base pairs in this range divided by the total number of
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	166 base pairs in the range"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	167 <param argument="-s" type="float" min="0" max="1" value="0" label="Minimum orientation confidence score"
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	168 help="To calculate the orientation confidence, each base pair in each alignment between a contig and its assigned reference chromosome
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	169 casts a vote for the orientation of its alignment. The orientation confidence is the number of votes for the assigned orientation of
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	170 the contig divided by the total number of votes"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	171 <conditional name="gap_conditional">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	172 <param name="gap_option" type="select" label="Infer gap sizes" help="When disabled, all gaps are 100 bp (-r)">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	173 <option value="true" selected="true">Enabled</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	174 <option value="false">Disabled</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	175 </param>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	176 <when value="true">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	177 <param argument="-g" type="integer" min="0" value="100" label="Minimum infered gap size" />
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	178 <param argument="-m" type="integer" min="0" value="100000" label="Maximum inferred gap size"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	179 </when>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	180 <when value="false"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	181 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	182 <conditional name="unplaced_conditional">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	183 <param name="unplaced_option" type="select" label="Concatenate unplaced contigs and make 'chr0' (-C)">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	184 <option value="true">Enabled</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	185 <option value="false" selected="true">Disabled</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	186 </param>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	187 <when value="true">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	188 <param argument="-J" type="data" format="txt" optional="true" label="List of query headers to leave unplaceds and exclude form 'chr0'"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	189 </when>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	190 <when value="false"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	191 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	192 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	193 <param name="output_scaffold" type="select" multiple="true" label="Output files">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	194 <option value="fasta" selected="true">The scaffolds in FASTA format, defined by the ordering and orientations of the sequences containted in the AGP file</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	195 <option value="agp" selected="true">The ordering and orientations of query sequences in AGP format</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	196 <option value="paf">The description of the approximate mapping positions between two set of sequences in PAF format</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	197 <option value="confidence">Confidence score values</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	198 <option value="stats">Summary statistics for the scaffolding process</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	199 <option value="log">Log file</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	200 </param>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	201 </when>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	202 <when value="patch">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	203 <expand macro="input_options"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	204 <section name="advanced_options" title="advanced options">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	205 <expand macro="common_parameters"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	206 <param argument="-s" type="integer" min="0" value="50000" label="Minimum merged alignment length"
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	207 help="After merging, alignments less than -s bp long will be removed"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	208 <param argument="-i" type="float" min="0" max="1" value="0.05" label="Maximum merged alignment distance"
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	209 help="Maximum merged alignment distance from sequence terminus as fraction of the sequence length. Alignments must
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	210 be within -i bp of a target sequence terminus or gap to be considered for patchin "/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	211 <param name="patching_mode" type="select" optional="true" label="Patching mode">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	212 <option value="--fill-only">Only fill existing target gaps. Do not join target sequences</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	213 <option value="--join_only">Only join and patch target sequences. DO not fill existing gaps</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	214 </param>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	215 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	216 <param name="output_patch" type="select" multiple="true" label="Output files">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	217 <option value="final_fasta" selected="true">The final FASTA file containing the patched assembly</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	218 <option value="final_agp" selected="true">The final AGP file defining how final FASTA is built</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	219 <option value="assembly_file" selected="true">Assembly alignment files</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	220 <option value="split_assembly">The split target assembly and the renamed query assembly combined into one FASTA file</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	221 <option value="split_description">An AGP file defining how the target assembly was split at gaps</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	222 <option value="target_gaps">The target assembly split at gaps</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	223 <option value="agp_renamed">An AGP file defining the new names for query sequences</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	224 <option value="fasta_renamed">A FASTA file with the original query sequence, but with new names</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	225 <option value="log">Log file</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	226 </param>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	227 </when>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	228 <when value="merge">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	229 <param name="assembly_fasta" type="data" format="fasta" label="Assembly FASTA file"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	230 <param name="scaffold_files" type="data" format="agp" multiple="true" optional="true" label="Scaffold AGP files"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	231 <section name="merging_options" title="Merging options">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	232 <param argument="-j" type="data" format="txt" optional="true" label="List of query headers to leave unplaced"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	233 <param argument="-l" type="integer" min="0" value="100000" label="Minimum assembly sequence length"
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	234 help="Assembly sequences shorter than -l will also be left unplaced."/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	235 <param argument="-e" type="float" min="0" value="0" label="Minimum edge weight"
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	236 help="The edges in the merging graph represent scaffolding adjacencies. If an AGP file supports a particular adjacency,
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	237 its weight is added to the edge weight. Any edges with a weight lower than the minimum edge weigth will be removed from the graph"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	238 <param name="function_merging" type="select" label="Function for merging gap lengths"
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	239 help="Scaffold gaps can differ between input AGP files. For example, a Hi-C derived AGP file might place 100 bp gaps between sequences
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	240 while a reference-guided AGP file might infer gap sizes based on a reference genome. Use this parameter to specify how gap sizes
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	241 should be computed from the supporting AGP files (--gap-func)">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	242 <option value="min" selected="true">Min</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	243 <option value="max">Max</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	244 <option value="mean">Mean</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	245 </param>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	246 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	247 <section name="hic_options" title="HI-C options">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	248 <param argument="-b" type="data" format="bam" optional="true" label="Hi-C alignments" help="Sorted by read name"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	249 <param argument="-r" type="text" value="" optional="true" label="Restriction enzymes/sites or 'DNase'" help="List of restrction enzimes/sites or 'DNase', separated by comma. E.g. GATC,GACC">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	250 <sanitizer invalid_char="">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	251 <valid initial="string.letters,string.digits">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	252 <add value="," />
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	253 <add value="[" />
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	254 <add value="]" />
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	255 </valid>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	256 </sanitizer>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	257 <validator type="regex">[0-9a-zA-Z,\]\[]+</validator>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	258 </param>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	259 <param argument="-p" type="float" min="0" max="1" value="1" optional="true" label="Portion of the sequence termini to consider for links"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	260 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	261 </when>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	262 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	263 </inputs>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	264 <outputs>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	265 <!--Correct mode outputs-->
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	266 <data format="paf" name="correct_paf" from_work_dir="ragtag.correct.asm.paf" label="${tool.name} on ${on_string}: PAF">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	267 <filter>mode_conditional["mode_option"] == "correct" and "paf" in mode_conditional["output_correct"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	268 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	269 <data format="agp" name="correct_agp" from_work_dir="ragtag.correct.agp" label="${tool.name} on ${on_string}: AGP">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	270 <filter>mode_conditional["mode_option"] == "correct" and "agp" in mode_conditional["output_correct"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	271 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	272 <data format="fasta" name="correct_fasta" from_work_dir="ragtag.correct.fasta" label="${tool.name} on ${on_string}: FASTA">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	273 <filter>mode_conditional["mode_option"] == "correct" and "fasta" in mode_conditional["output_correct"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	274 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	275 <data format="txt" name="correct_log" from_work_dir="ragtag.correct.asm.paf.log" label="${tool.name} on ${on_string}: log">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	276 <filter>mode_conditional["mode_option"] == "correct" and "log" in mode_conditional["output_correct"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	277 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	278 <!--Scaffold mode outputs-->
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	279 <data format="paf" name="scaffold_paf" from_work_dir="ragtag.scaffold.asm.paf" label="${tool.name} on ${on_string}: PAF">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	280 <filter>mode_conditional["mode_option"] == "scaffold" and "paf" in mode_conditional["output_scaffold"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	281 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	282 <data format="agp" name="scaffold_agp" from_work_dir="ragtag.scaffold.agp" label="${tool.name} on ${on_string}: AGP">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	283 <filter>mode_conditional["mode_option"] == "scaffold" and "agp" in mode_conditional["output_scaffold"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	284 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	285 <data format="fasta" name="scaffold_fasta" from_work_dir="ragtag.scaffold.fasta" label="${tool.name} on ${on_string}: FASTA">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	286 <filter>mode_conditional["mode_option"] == "scaffold" and "fasta" in mode_conditional["output_scaffold"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	287 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	288 <data format="txt" name="scaffold_log" from_work_dir="ragtag.scaffold.asm.paf.log" label="${tool.name} on ${on_string}: log">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	289 <filter>mode_conditional["mode_option"] == "scaffold" and "log" in mode_conditional["output_scaffold"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	290 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	291 <data format="tabular" name="scaffold_stats" from_work_dir="ragtag.scaffold.stats" label="${tool.name} on ${on_string}: stats">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	292 <filter>mode_conditional["mode_option"] == "scaffold" and "stats" in mode_conditional["output_scaffold"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	293 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	294 <data format="tabular" name="scaffold_confidence" from_work_dir="ragtag.scaffold.confidence.txt" label="${tool.name} on ${on_string}: confidence">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	295 <filter>mode_conditional["mode_option"] == "scaffold" and "confidence" in mode_conditional["output_scaffold"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	296 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	297 <!--Patch mode outputs-->
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	298 <data format="agp" name="patch_agp" from_work_dir="ragtag.patch.agp" label="${tool.name} on ${on_string}: final AGP">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	299 <filter>mode_conditional["mode_option"] == "patch" and "final_agp" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	300 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	301 <data format="paf" name="patch_paf" from_work_dir="ragtag.patch.asm.paf" label="${tool.name} on ${on_string}: final PAF">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	302 <filter>mode_conditional["mode_option"] == "patch" and "assembly_file" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	303 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	304 <data format="txt" name="patch_log" from_work_dir="ragtag.patch.log" label="${tool.name} on ${on_string}: log">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	305 <filter>mode_conditional["mode_option"] == "patch" and "log" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	306 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	307 <data format="fasta" name="patch_comps_fasta" from_work_dir="ragtag.patch.comps.fasta" label="${tool.name} on ${on_string}: components FASTA">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	308 <filter>mode_conditional["mode_option"] == "patch" and "split_assembly" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	309 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	310 <data format="agp" name="patch_ctg_agp" from_work_dir="ragtag.patch.ctg.agp" label="${tool.name} on ${on_string}: contigs AGP">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	311 <filter>mode_conditional["mode_option"] == "patch" and "split_description" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	312 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	313 <data format="fasta" name="patch_ctg_fasta" from_work_dir="ragtag.patch.ctg.fasta" label="${tool.name} on ${on_string}: contigs FASTA">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	314 <filter>mode_conditional["mode_option"] == "patch" and "target_gaps" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	315 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	316 <data format="fasta" name="patch_fasta" from_work_dir="ragtag.patch.fasta" label="${tool.name} on ${on_string}: final FASTA">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	317 <filter>mode_conditional["mode_option"] == "patch" and "final_fasta" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	318 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	319 <data format="agp" name="patch_rename_agp" from_work_dir="ragtag.patch.rename.agp" label="${tool.name} on ${on_string}: renamed AGP">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	320 <filter>mode_conditional["mode_option"] == "patch" and "agp_renamed" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	321 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	322 <data format="fasta" name="patch_rename_fasta" from_work_dir="ragtag.patch.rename.fasta" label="${tool.name} on ${on_string}: renamed FASTA">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	323 <filter>mode_conditional["mode_option"] == "patch" and "fasta_renamed" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	324 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	325 <!-- Merge mode outputs-->
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	326 <data format="agp" name="merge_agp" from_work_dir="ragtag.merge.agp" label="${tool.name} on ${on_string}: merged AGP">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	327 <filter>mode_conditional["mode_option"] == "merge"</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	328 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	329 <data format="fasta" name="merge_fasta" from_work_dir="ragtag.merge.fasta" label="${tool.name} on ${on_string}: merged FASTA">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	330 <filter>mode_conditional["mode_option"] == "merge"</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	331 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	332 </outputs>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	333 <tests>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	334 <test expect_num_outputs="4">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	335 <!--Test 01 correct mode minimap2-->
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	336 <conditional name="mode_conditional">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	337 <param name="mode_option" value="correct"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	338 <param name="reference" value="genome.fna"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	339 <param name="query" value="contigs.fna"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	340 <param name="output_correct" value="fasta,agp,paf,log"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	341 <section name="advanced_options">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	342 <param name="e" value="reference_headers_skip.txt"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	343 <param name="j" value="query_headers_skip.txt"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	344 <param name="f" value="1000"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	345 <conditional name="mapping_conditional">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	346 <param name="mapping_option" value="minimap2"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	347 <param name="mm2_params" value="asm5"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	348 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	349 <param name="remove_small" value="false"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	350 <param name="q" value="10"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	351 <param name="d" value="100000"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	352 <param name="b" value="5000"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	353 <param name="missasembly_break" value="--inter"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	354 <param name="gff" value="annotation.gff"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	355 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	356 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	357 <output name="correct_paf" file="correct_paf_01.paf" ftype="paf"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	358 <output name="correct_agp" file="correct_agp_01.agp" ftype="agp"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	359 <output name="correct_fasta" file="correct_fasta_01.fasta" ftype="fasta"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	360 <output name="correct_log" file="correct_log_01.txt" ftype="txt" lines_diff="20"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	361 </test>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	362 <!--Test 02 correct mode nucmer-->
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	363 <test expect_num_outputs="2">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	364 <conditional name="mode_conditional">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	365 <param name="mode_option" value="correct"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	366 <param name="reference" value="genome.fna"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	367 <param name="query" value="contigs.fna"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	368 <param name="output_correct" value="fasta,agp"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	369 <section name="advanced_options">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	370 <param name="f" value="1000"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	371 <conditional name="mapping_conditional">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	372 <param name="mapping_option" value="nucmer"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	373 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	374 <param name="remove_small" value="true"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	375 <param name="q" value="10"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	376 <param name="d" value="100000"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	377 <param name="b" value="5000"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	378 <param name="missasembly_break" value="--inter"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	379 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	380 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	381 <output name="correct_fasta" file="correct_fasta_02.fasta" ftype="fasta"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	382 <output name="correct_agp" file="correct_agp_02.agp" ftype="agp"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	383
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	384 </test>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	385 <!--Test 03 scaffold mode-->
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	386 <test expect_num_outputs="6">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	387 <conditional name="mode_conditional">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	388 <param name="mode_option" value="scaffold"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	389 <param name="reference" value="genome.fna"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	390 <param name="query" value="contigs.fna"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	391 <param name="output_scaffold" value="fasta,agp,paf,confidence,log,stats"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	392 <section name="advanced_options">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	393 <param name="f" value="1000"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	394 <param name="remove_small" value="true"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	395 <param name="q" value="10"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	396 <param name="d" value="100000"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	397 <param name="i" value="0.2"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	398 <param name="a" value="0"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	399 <param name="s" value="0"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	400 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	401 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	402 <output name="scaffold_paf" file="scaffold_paf_03.paf" ftype="paf"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	403 <output name="scaffold_agp" file="scaffold_apg.03.agp" ftype="agp"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	404 <output name="scaffold_fasta" file="scaffold_fasta_03.fasta" ftype="fasta"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	405 <output name="scaffold_log" file="scaffold_log_03.txt" ftype="txt" lines_diff="20"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	406 <output name="scaffold_stats" file="scaffold_stats_03.tabular" ftype="tabular"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	407 <output name="scaffold_confidence" file="scaffold_confidence_03.tabular" ftype="tabular"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	408 </test>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	409 <!--Test 04 patch mode-->
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	410 <test expect_num_outputs="9">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	411 <conditional name="mode_conditional">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	412 <param name="mode_option" value="patch"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	413 <param name="reference" value="genome.fna"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	414 <param name="query" value="contigs.fna"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	415 <param name="output_patch" value="final_fasta,final_agp,assembly_file,split_assembly,split_description,target_gaps,agp_renamed,fasta_renamed,log"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	416 <section name="advanced_options">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	417 <param name="s" value="50000"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	418 <param name="i" value="0.05"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	419 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	420 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	421 <output name="patch_agp" file="patch_agp_04.agp" ftype="agp"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	422 <output name="patch_paf" file="patch_paf_04.paf" ftype="paf"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	423 <output name="patch_log" file="patch_log_04.txt" ftype="txt" lines_diff="20"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	424 <output name="patch_comps_fasta" ftype="fasta">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	425 <assert_contents>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	426 <has_size value="603691" delta="100" />
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	427 </assert_contents>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	428 </output>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	429 <output name="patch_ctg_fasta" file="patch_ctg_fasta_04.fasta" ftype="fasta"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	430 <output name="patch_ctg_agp" file="patch_ctg_fasta_04.agp" ftype="agp"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	431 <output name="patch_fasta" file="patch_fasta_04.fasta" ftype="fasta"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	432 <output name="patch_rename_agp" file="patch_rename_agp.agp" ftype="agp"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	433 <output name="patch_rename_fasta" file="patch_rename_fasta.fasta" ftype="fasta"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	434 </test>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	435 <test expect_num_outputs="2">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	436 <!-- Test 05 merge mode-->
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	437 <conditional name="mode_conditional">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	438 <param name="mode_option" value="merge"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	439 <param name="assembly_fasta" value="correct_fasta_01.fasta"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	440 <param name="scaffold_files" value="correct_agp_01.agp,correct_agp_02.agp"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	441 <section name="merging_options">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	442 <param name="l" value="100000"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	443 <param name="e" value="0"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	444 <param name="function_merging" value="min"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	445 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	446 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	447 <output name="merge_agp" file="merge_agp_05.agp" ftype="agp"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	448 <output name="merge_fasta" file="merge_fasta_05.fasta" ftype="fasta"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	449 </test>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	450 </tests>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	451 <help><![CDATA[
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	452 .. class:: infomark
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	453
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	454 Purpose
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	455
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	456 RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include:
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	457
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	458 - Homology-based misassembly correction
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	459 - Homology-based assembly scaffolding and patching
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	460 - Scaffold merging
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	461
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	462 ----
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	463
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	464 .. class:: infomark
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	465
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	466 Correct mode
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	467
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	468 RagTag offers a correction module that uses a reference genome to identify and correct potential misassemblies in a query assembly.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	469 RagTag also provides the option to verify putative misassemblies by aligning reads (from the same genotype) to the query assembly
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	470 and observing read coverage near misassembly break points. In all cases, sequence is never added or subtracted. Query sequences
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	471 are only broken at points of putative misassembly.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	472
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	473 Misassemblies vs true variation
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	474
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	475 Reference-guided misassembly signatures are sometimes caused by true biological structural variation if the reference and query assemblies
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	476 represent distinct genotypes (or haplotypes). The read validation feature should help to avoid some of these misassembly false positives,
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	477 and the validation sensitivity can be tuned with command line parameters. However, it is ultimately up to the discretion of the user to decide
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	478 if misassembly correction is appropriate. One should validate all RagTag results with independent data (usually physical, optical, or genetic
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	479 maps), when possible.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	480
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	481 ----
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	482
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	483 .. class:: infomark
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	484
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	485 Scaffold mode
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	486
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	487 Scaffolding is the process of ordering and orienting draft assembly (query) sequences into longer sequences. Gaps (stretches of "N" characters)
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	488 are placed between adjacent query sequences to indicate the presence of unknown sequence. RagTag uses whole-genome alignments to a reference
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	489 assembly to scaffold query sequences. RagTag does not alter input query sequence in any way and only orders and orients sequences, joining them with gaps.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	490
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	491 ----
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	492
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	493 .. class:: infomark
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	494
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	495 Patch mode
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	496
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	497 This mode uses one genome assembly to patch another genome assembly. We define two types of patches:
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	498
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	499 - Fills are patches that fill assembly gaps. This process is like traditional gap-filling, though it uses an assembly instead of WGS sequencing reads.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	500 - Joins are patches that join distinct contigs. This is essentially scaffolding and gap-filling in a single step.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	501
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	502 ----
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	503
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	504 .. class:: infomark
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	505
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	506 Merge mode
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	507
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	508 Draft genome assemblies are often scaffolded multiple times using different approaches. For example, one might scaffold an assembly using different genome
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	509 maps (physical, linkage, Hi-C, etc.), different methods, or different method parameters. RagTag merge is a tool to merge and reconcile different scaffoldings
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	510 of the same assembly. In this way, one can leverage the advantages of multiple techniques to synergistically improve scaffolding.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	511
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	512 Most tools write scaffolding results in the AGP file format, which encodes adjacency and gap information in a plain text file. To run RagTag merge,
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	513 one must supply the assembly in FASTA format and at least two AGP files that define a scaffolding of the assembly. Each AGP file can optionally be
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	514 assigned a weight, allowing users to assign the relative influence of each AGP on the final result.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	515
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	516 If available, users can supply Hi-C alignments to the draft assembly to resolve conflicts in the merging graph. In this scenario, the input AGP
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	517 files are used to build the initial graph, but then Hi-C alignments are used to re-weight the graph before computing the scaffolding solution.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	518
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	519
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	520 List of accepted restriction enzymes
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	521
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	522 List of all accepted restriction enzymes and their restriction sites:
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	523
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	524 - HindIII: AAGCTT
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	525 - Sau3AI: GATC
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	526 - MboI: GATC
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	527 - DpnII: GATC
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	528 - HinfI: GA[ATCG]TC
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	529 - DdeI: CT[ATCG]AG
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	530 - MseI: TTAA
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	531
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	532 For RagTag, use a comma separated list of enzymes or sites (or a mix). For example:
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	533
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	534 - Arima Hi-C v1.0: Sau3AI,HinfI or GATC,GA[ATCG]TC
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	535 - Arima Hi-C v2.0: Sau3AI,HinfI,DdeI,MseI or GATC,GA[ATCG]TC,CT[ATCG]AG,TTAA
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	536
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	537 Note that for restriction sites, wildcards are represented with python regex syntax, not IUPAC ambiguity codes. e.g. '[ATCG]' instead of 'N'.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	538
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	539 Restriction enzymes are not necessarily the enzyme used for sample prep. Each is only a enzyme that cuts at the corresponding restriction site.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	540
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	541 ]]> </help>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	542 <expand macro="citations" />
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	543 </tool>

Mercurial > repos > iuc > ragtag

annotate ragtag.xml @ 0:a04e64efa43a draft