ragtag: ragtag.xml annotate

annotate ragtag.xml @ 2:b3c3217c0cbc draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 5b09d46d1096109a68a41ccd63813469ec8ea675

author	iuc
date	Fri, 14 Oct 2022 13:35:18 +0000
parents	d110a4141898
children

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
1 d110a4141898 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 6add25f561c83df53d3e1302a7067ff33409b071 iuc parents: 0 diff changeset	26
d110a4141898 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 6add25f561c83df53d3e1302a7067ff33409b071 iuc parents: 0 diff changeset	27 ## symlink reference because a .fai file is created
d110a4141898 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 6add25f561c83df53d3e1302a7067ff33409b071 iuc parents: 0 diff changeset	28 #if $mode_conditional.mode_option in ['correct', 'scaffold', 'patch']
d110a4141898 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 6add25f561c83df53d3e1302a7067ff33409b071 iuc parents: 0 diff changeset	29 ln -s '$mode_conditional.reference' reference.fa &&
d110a4141898 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 6add25f561c83df53d3e1302a7067ff33409b071 iuc parents: 0 diff changeset	30 ln -s '$mode_conditional.query' query.fa &&
d110a4141898 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 6add25f561c83df53d3e1302a7067ff33409b071 iuc parents: 0 diff changeset	31 #else
d110a4141898 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 6add25f561c83df53d3e1302a7067ff33409b071 iuc parents: 0 diff changeset	32 ln -s '$assembly_fasta' assembly.fa &&
d110a4141898 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 6add25f561c83df53d3e1302a7067ff33409b071 iuc parents: 0 diff changeset	33 #end if
d110a4141898 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 6add25f561c83df53d3e1302a7067ff33409b071 iuc parents: 0 diff changeset	34
0 a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	35 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	36 #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	37 @INPUTS@
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	38 @COMMON_PARAMETERS@
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	39 #if $mode_conditional.validation_conditional.validation_option == 'true'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	40 -R '${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	41 -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	42 -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	43 #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	44 --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	45 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	46 #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	47 --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	48 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	49 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	50 -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	51 #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	52 $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	53 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	54 #if $mode_conditional.advanced_options.gff
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	55 --gff '${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	56 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	57 --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	58 #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	59 @INPUTS@
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	60 @COMMON_PARAMETERS@
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	61 -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	62 -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	63 -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	64 #if $mode_conditional.advanced_options.gap_conditional.gap_option == 'true'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	65 -r
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	66 -g '${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	67 -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	68 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	69 #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	70 -C
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	71 #if $mode_conditional.advanced_options.unplaced_conditional.J
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	72 -J '${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	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 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	75 #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	76 @INPUTS@
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	77 @COMMON_PARAMETERS@
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	78 -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	79 -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	80 #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	81 $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	82 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	83 #else
1 d110a4141898 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 6add25f561c83df53d3e1302a7067ff33409b071 iuc parents: 0 diff changeset	84 assembly.fa
0 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.scaffold_files
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	86 $merge_files
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	87 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	88 #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	89 -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	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 -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	92 -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	93 --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	94 #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	95 -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	96 -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	97 -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	98 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	99 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	100 -o ./
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	101 #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	102 -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	103 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	104 #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	105 && 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	106 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	107 ]]> </command>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	108 <inputs>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	109 <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	110 <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	111 <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	112 <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	113 <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	114 <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	115 </param>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	116 <when value="correct">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	117 <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	118 <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	119 <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	120 <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	121 <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	122 </param>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	123 <when value="true">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	124 <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	125 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	126 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	127 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	128 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	129 <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	130 <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	131 <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	132 <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	133 </param>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	134 <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	135 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	136 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	137 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	138 <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	139 <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	140 </when>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	141 <when value="false"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	142 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	143 <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	144 <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	145 <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	146 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	147 <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	148 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	149 (--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	150 <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	151 <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	152 </param>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	153 <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	154 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	155 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	156 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	157 <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	158 <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	159 <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	160 <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	161 <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	162 </param>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	163 </when>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	164 <when value="scaffold">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	165 <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	166 <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	167 <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	168 <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	169 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	170 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	171 <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	172 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	173 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	174 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	175 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	176 <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	177 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	178 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	179 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	180 <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	181 <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	182 <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	183 <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	184 </param>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	185 <when value="true">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	186 <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	187 <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	188 </when>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	189 <when value="false"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	190 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	191 <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	192 <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	193 <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	194 <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	195 </param>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	196 <when value="true">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	197 <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	198 </when>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	199 <when value="false"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	200 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	201 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	202 <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	203 <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	204 <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	205 <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	206 <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	207 <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	208 <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	209 </param>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	210 </when>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	211 <when value="patch">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	212 <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	213 <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	214 <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	215 <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	216 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	217 <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	218 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	219 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	220 <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	221 <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	222 <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	223 </param>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	224 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	225 <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	226 <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	227 <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	228 <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	229 <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	230 <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	231 <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	232 <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	233 <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	234 <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	235 </param>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	236 </when>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	237 <when value="merge">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	238 <param name="assembly_fasta" type="data" format="fasta" label="Assembly FASTA file"/>
2 b3c3217c0cbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 5b09d46d1096109a68a41ccd63813469ec8ea675 iuc parents: 1 diff changeset	239 <param name="scaffold_files" type="data" format="agp" multiple="true" min="2" label="Scaffold AGP files" help="At least two AGP files are required."/>
0 a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	240 <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	241 <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	242 <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	243 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	244 <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	245 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	246 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	247 <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	248 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	249 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	250 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	251 <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	252 <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	253 <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	254 </param>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	255 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	256 <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	257 <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	258 <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	259 <sanitizer invalid_char="">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	260 <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	261 <add value="," />
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	262 <add value="[" />
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	263 <add value="]" />
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	264 </valid>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	265 </sanitizer>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	266 <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	267 </param>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	268 <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	269 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	270 </when>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	271 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	272 </inputs>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	273 <outputs>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	274 <!--Correct mode outputs-->
2 b3c3217c0cbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 5b09d46d1096109a68a41ccd63813469ec8ea675 iuc parents: 1 diff changeset	275 <data format="paf" name="correct_paf" from_work_dir="ragtag.correct.asm.paf" label="${tool.name} on ${on_string}: correct PAF">
0 a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	276 <filter>mode_conditional["mode_option"] == "correct" and "paf" in mode_conditional["output_correct"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	277 </data>
2 b3c3217c0cbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 5b09d46d1096109a68a41ccd63813469ec8ea675 iuc parents: 1 diff changeset	278 <data format="agp" name="correct_agp" from_work_dir="ragtag.correct.agp" label="${tool.name} on ${on_string}: correct AGP">
0 a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	279 <filter>mode_conditional["mode_option"] == "correct" and "agp" in mode_conditional["output_correct"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	280 </data>
2 b3c3217c0cbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 5b09d46d1096109a68a41ccd63813469ec8ea675 iuc parents: 1 diff changeset	281 <data format="fasta" name="correct_fasta" from_work_dir="ragtag.correct.fasta" label="${tool.name} on ${on_string}: correct FASTA">
0 a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	282 <filter>mode_conditional["mode_option"] == "correct" and "fasta" in mode_conditional["output_correct"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	283 </data>
2 b3c3217c0cbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 5b09d46d1096109a68a41ccd63813469ec8ea675 iuc parents: 1 diff changeset	284 <data format="txt" name="correct_log" from_work_dir="ragtag.correct.asm.paf.log" label="${tool.name} on ${on_string}: correct log">
0 a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	285 <filter>mode_conditional["mode_option"] == "correct" and "log" in mode_conditional["output_correct"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	286 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	287 <!--Scaffold mode outputs-->
2 b3c3217c0cbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 5b09d46d1096109a68a41ccd63813469ec8ea675 iuc parents: 1 diff changeset	288 <data format="paf" name="scaffold_paf" from_work_dir="ragtag.scaffold.asm.paf" label="${tool.name} on ${on_string}: scaffold PAF">
0 a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	289 <filter>mode_conditional["mode_option"] == "scaffold" and "paf" in mode_conditional["output_scaffold"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	290 </data>
2 b3c3217c0cbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 5b09d46d1096109a68a41ccd63813469ec8ea675 iuc parents: 1 diff changeset	291 <data format="agp" name="scaffold_agp" from_work_dir="ragtag.scaffold.agp" label="${tool.name} on ${on_string}: scaffold AGP">
0 a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	292 <filter>mode_conditional["mode_option"] == "scaffold" and "agp" in mode_conditional["output_scaffold"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	293 </data>
2 b3c3217c0cbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 5b09d46d1096109a68a41ccd63813469ec8ea675 iuc parents: 1 diff changeset	294 <data format="fasta" name="scaffold_fasta" from_work_dir="ragtag.scaffold.fasta" label="${tool.name} on ${on_string}: scaffold FASTA">
0 a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	295 <filter>mode_conditional["mode_option"] == "scaffold" and "fasta" in mode_conditional["output_scaffold"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	296 </data>
2 b3c3217c0cbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 5b09d46d1096109a68a41ccd63813469ec8ea675 iuc parents: 1 diff changeset	297 <data format="txt" name="scaffold_log" from_work_dir="ragtag.scaffold.asm.paf.log" label="${tool.name} on ${on_string}: scaffold log">
0 a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	298 <filter>mode_conditional["mode_option"] == "scaffold" and "log" in mode_conditional["output_scaffold"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	299 </data>
2 b3c3217c0cbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 5b09d46d1096109a68a41ccd63813469ec8ea675 iuc parents: 1 diff changeset	300 <data format="tabular" name="scaffold_stats" from_work_dir="ragtag.scaffold.stats" label="${tool.name} on ${on_string}: scaffold stats">
0 a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	301 <filter>mode_conditional["mode_option"] == "scaffold" and "stats" in mode_conditional["output_scaffold"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	302 </data>
2 b3c3217c0cbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 5b09d46d1096109a68a41ccd63813469ec8ea675 iuc parents: 1 diff changeset	303 <data format="tabular" name="scaffold_confidence" from_work_dir="ragtag.scaffold.confidence.txt" label="${tool.name} on ${on_string}: scaffold confidence">
0 a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	304 <filter>mode_conditional["mode_option"] == "scaffold" and "confidence" in mode_conditional["output_scaffold"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	305 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	306 <!--Patch mode outputs-->
2 b3c3217c0cbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 5b09d46d1096109a68a41ccd63813469ec8ea675 iuc parents: 1 diff changeset	307 <data format="agp" name="patch_agp" from_work_dir="ragtag.patch.agp" label="${tool.name} on ${on_string}: patch final AGP">
0 a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	308 <filter>mode_conditional["mode_option"] == "patch" and "final_agp" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	309 </data>
2 b3c3217c0cbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 5b09d46d1096109a68a41ccd63813469ec8ea675 iuc parents: 1 diff changeset	310 <data format="paf" name="patch_paf" from_work_dir="ragtag.patch.asm.paf" label="${tool.name} on ${on_string}: patch final PAF">
0 a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	311 <filter>mode_conditional["mode_option"] == "patch" and "assembly_file" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	312 </data>
2 b3c3217c0cbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 5b09d46d1096109a68a41ccd63813469ec8ea675 iuc parents: 1 diff changeset	313 <data format="txt" name="patch_log" from_work_dir="ragtag.patch.log" label="${tool.name} on ${on_string}: patch log">
0 a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	314 <filter>mode_conditional["mode_option"] == "patch" and "log" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	315 </data>
2 b3c3217c0cbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 5b09d46d1096109a68a41ccd63813469ec8ea675 iuc parents: 1 diff changeset	316 <data format="fasta" name="patch_comps_fasta" from_work_dir="ragtag.patch.comps.fasta" label="${tool.name} on ${on_string}: patch components FASTA">
0 a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	317 <filter>mode_conditional["mode_option"] == "patch" and "split_assembly" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	318 </data>
2 b3c3217c0cbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 5b09d46d1096109a68a41ccd63813469ec8ea675 iuc parents: 1 diff changeset	319 <data format="agp" name="patch_ctg_agp" from_work_dir="ragtag.patch.ctg.agp" label="${tool.name} on ${on_string}: patch contigs AGP">
0 a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	320 <filter>mode_conditional["mode_option"] == "patch" and "split_description" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	321 </data>
2 b3c3217c0cbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 5b09d46d1096109a68a41ccd63813469ec8ea675 iuc parents: 1 diff changeset	322 <data format="fasta" name="patch_ctg_fasta" from_work_dir="ragtag.patch.ctg.fasta" label="${tool.name} on ${on_string}: patch contigs FASTA">
0 a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	323 <filter>mode_conditional["mode_option"] == "patch" and "target_gaps" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	324 </data>
2 b3c3217c0cbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 5b09d46d1096109a68a41ccd63813469ec8ea675 iuc parents: 1 diff changeset	325 <data format="fasta" name="patch_fasta" from_work_dir="ragtag.patch.fasta" label="${tool.name} on ${on_string}: patch final FASTA">
0 a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	326 <filter>mode_conditional["mode_option"] == "patch" and "final_fasta" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	327 </data>
2 b3c3217c0cbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 5b09d46d1096109a68a41ccd63813469ec8ea675 iuc parents: 1 diff changeset	328 <data format="agp" name="patch_rename_agp" from_work_dir="ragtag.patch.rename.agp" label="${tool.name} on ${on_string}: patch renamed AGP">
0 a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	329 <filter>mode_conditional["mode_option"] == "patch" and "agp_renamed" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	330 </data>
2 b3c3217c0cbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 5b09d46d1096109a68a41ccd63813469ec8ea675 iuc parents: 1 diff changeset	331 <data format="fasta" name="patch_rename_fasta" from_work_dir="ragtag.patch.rename.fasta" label="${tool.name} on ${on_string}: patch renamed FASTA">
0 a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	332 <filter>mode_conditional["mode_option"] == "patch" and "fasta_renamed" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	333 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	334 <!-- Merge mode outputs-->
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	335 <data format="agp" name="merge_agp" from_work_dir="ragtag.merge.agp" label="${tool.name} on ${on_string}: merged AGP">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	336 <filter>mode_conditional["mode_option"] == "merge"</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	337 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	338 <data format="fasta" name="merge_fasta" from_work_dir="ragtag.merge.fasta" label="${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	339 <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	340 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	341 </outputs>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	342 <tests>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	343 <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	344 <!--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	345 <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	346 <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	347 <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	348 <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	349 <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	350 <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	351 <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	352 <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	353 <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	354 <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	355 <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	356 <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	357 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	358 <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	359 <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	360 <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	361 <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	362 <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	363 <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	364 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	365 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	366 <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	367 <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	368 <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	369 <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	370 </test>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	371 <!--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	372 <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	373 <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	374 <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	375 <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	376 <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	377 <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	378 <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	379 <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	380 <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	381 <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	382 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	383 <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	384 <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	385 <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	386 <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	387 <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	388 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	389 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	390 <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	391 <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	392
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	393 </test>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	394 <!--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	395 <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	396 <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	397 <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	398 <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	399 <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	400 <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	401 <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	402 <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	403 <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	404 <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	405 <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	406 <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	407 <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	408 <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	409 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	410 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	411 <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	412 <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	413 <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	414 <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	415 <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	416 <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	417 </test>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	418 <!--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	419 <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	420 <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	421 <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	422 <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	423 <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	424 <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	425 <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	426 <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	427 <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	428 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	429 </conditional>
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_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	431 <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	432 <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	433 <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	434 <assert_contents>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	435 <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	436 </assert_contents>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	437 </output>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	438 <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	439 <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	440 <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	441 <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	442 <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	443 </test>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	444 <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	445 <!-- 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	446 <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	447 <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	448 <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	449 <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	450 <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	451 <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	452 <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	453 <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	454 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	455 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	456 <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	457 <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	458 </test>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	459 </tests>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	460 <help><![CDATA[
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	461 .. class:: infomark
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 Purpose
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	464
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	465 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	466
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	467 - 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	468 - 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	469 - Scaffold merging
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	470
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	471 ----
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 .. class:: infomark
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 Correct mode
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	476
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	477 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	478 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	479 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	480 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	481
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	482 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	483
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	484 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	485 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	486 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	487 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	488 maps), when possible.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	489
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 .. class:: infomark
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	493
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	494 Scaffold mode
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	495
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	496 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	497 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	498 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	499
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	500 ----
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 .. class:: infomark
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 Patch mode
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 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	507
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	508 - 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	509 - 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	510
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
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	513 .. class:: infomark
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	514
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	515 Merge mode
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	516
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	517 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	518 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	519 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	520
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	521 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	522 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	523 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	524
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	525 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	526 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	527
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	528
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	529 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	530
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	531 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	532
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	533 - HindIII: AAGCTT
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	534 - Sau3AI: GATC
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	535 - MboI: GATC
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	536 - DpnII: GATC
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	537 - 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	538 - 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	539 - MseI: TTAA
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 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	542
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	543 - 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	544 - 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	545
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	546 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	547
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	548 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	549
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	550 ]]> </help>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035" iuc parents: diff changeset	551 <expand macro="citations" />
2 b3c3217c0cbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 5b09d46d1096109a68a41ccd63813469ec8ea675 iuc parents: 1 diff changeset	552 </tool>

Mercurial > repos > iuc > ragtag

annotate ragtag.xml @ 2:b3c3217c0cbc draft default tip