map_damage: map_damage.xml annotate

annotate map_damage.xml @ 1:761b6fdcac6e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 1fc6a1ce5483f15ea5366a534529025781311200

author	iuc
date	Wed, 16 Jul 2025 08:09:11 +0000
parents	3db999d4e0c1
children	0287e2f82b64

rev	line source
0 3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	1 <tool id="map_damage" name="mapDamage" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	2
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	3 <description>Tracks and quantifies damage patterns in ancient DNA sequences</description>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	4
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	5 <macros>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	6 <token name="@TOOL_VERSION@">2.2.2</token>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	7 <token name="@VERSION_SUFFIX@">0</token>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	8 </macros>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	9
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	10 <xrefs>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	11 <xref type="bio.tools">mapdamage</xref>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	12 </xrefs>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	13
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	14 <requirements>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	15 <requirement type="package" version="@TOOL_VERSION@">mapdamage2</requirement>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	16 </requirements>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	17
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	18 <version_command><![CDATA[mapDamage --version]]></version_command>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	19
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	20 <command detect_errors="aggressive"><![CDATA[
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	21
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	22 ln -s '$sbam_file' alignment.$sbam_file.ext &&
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	23
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	24 #if $reference.ref_source == 'history':
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	25 ln -s '$reference.history_reference' reference.fa &&
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	26 #end if
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	27
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	28 ## MAIN COMMAND LINE
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	29
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	30 mapDamage
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	31
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	32 ## INPUT / OUTPUT PARAMETERS
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	33
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	34 --input alignment.$sbam_file.ext
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	35
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	36 #if $reference.ref_source == 'builtin':
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	37 --reference '$reference.builtin_reference.fields.path'
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	38 #elif $reference.ref_source == 'history':
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	39 --reference reference.fa
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	40 #end if
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	41
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	42 --folder 'mapDamage_results'
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	43
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	44 ## GENERAL OPTIONS
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	45
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	46 $merge_reference_sequences
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	47
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	48 #if $downsampling.downsampling.downsampling_type != 'no_downsampling':
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	49 --downsample $downsampling.downsampling.downsample
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	50 #if $downsampling.downsampling.downsample_seed:
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	51 --downsample-seed $downsampling.downsampling.downsample_seed
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	52 #end if
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	53 #end if
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	54
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	55 --length $window_size.length
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	56 --around $window_size.around
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	57 --min-basequal $min_basequal
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	58 $fasta
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	59
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	60 ## GRAPHICS OPTIONS
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	61
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	62 --ymax $graphics.ymax
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	63 --readplot $graphics.readplot
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	64 --refplot $graphics.refplot
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	65
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	66 #if str($graphics.title):
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	67 --title '$graphics.title'
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	68 #end if
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	69
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	70 $graphics.theme_bw
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	71
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	72 ## STATISTICS OPTIONS
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	73
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	74 #if $statistics.stats.no_stats:
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	75 $statistics.stats.no_stats
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	76 #else:
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	77 --rand $statistics.stats.rand
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	78 --burn $statistics.stats.burn
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	79 --adjust $statistics.stats.adjust
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	80 --iter $statistics.stats.iter
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	81 $statistics.stats.ends.ends_to_process
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	82
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	83 #if not $statistics.stats.ends.ends_to_process:
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	84 $statistics.stats.ends.diff_hangs
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	85 #end if
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	86
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	87 --seq-length $statistics.stats.seq_length
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	88 $statistics.stats.var_disp
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	89 $statistics.stats.mutation_model
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	90 $statistics.stats.nick_vector
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	91 #end if
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	92
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	93 ## RESCALING OPTIONS
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	94
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	95 #if $rescale.rescaling.rescale:
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	96 --rescale
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	97 #if $rescale.rescaling.rescale_length_5p:
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	98 --rescale-length-5p $rescale.rescaling.rescale_length_5p
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	99 #end if
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	100 #if $rescale.rescaling.rescale_length_3p:
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	101 --rescale-length-3p $rescale.rescaling.rescale_length_3p
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	102 #end if
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	103 #end if
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	104
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	105 ]]></command>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	106
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	107 <inputs>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	108
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	109 <!--INPUT FILES-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	110
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	111 <param name="sbam_file" argument="--input" type="data" format="sam,bam" label="SAM / BAM input file of aligned reads to be analyzed." help="Must contain a valid header."/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	112
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	113 <conditional name="reference">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	114 <param name="ref_source" type="select" label="Use a built-in FASTA reference or retrieve one from your history?">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	115 <option value="builtin" selected="true">Built-in reference FASTA file</option>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	116 <option value="history">From your history</option>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	117 </param>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	118 <when value="builtin">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	119 <param name="builtin_reference" type="select" label="FASTA genome to use as a reference in order to assess DNA damage" help="Contact your Galaxy team in order to add a reference">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	120 <options from_data_table="all_fasta"></options>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	121 <validator type="no_options" message="No FASTA references are available, please contact your Galaxy administrators."/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	122 </param>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	123 </when>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	124 <when value="history">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	125 <param name="history_reference" type="data" format="fasta" label="FASTA genome to use as a reference in order to use DNA damage"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	126 </when>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	127 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	128
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	129 <!--GENERAL OPTIONS-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	130
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	131 <param argument="--merge-reference-sequences" type="boolean" truevalue="--merge-reference-sequences" falsevalue="" label="Merge reference sequences in result files?" help="Useful for memory usage."/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	132
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	133 <param argument="--min-basequal" type="integer" min="0" max="93" value="0" label="Minimum PHRED score for base to be considered" help="(assumes PHRED+33 score)"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	134
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	135 <param argument="--fasta" type="boolean" checked="false" truevalue="--fasta" falsevalue="" label="Output alignments in FASTA format?"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	136
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	137 <section name="downsampling" title="Downsampling">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	138 <conditional name="downsampling">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	139 <param name="downsampling_type" type="select" label="Type of downsampling" help="Downsample using a percentage or a number of reads?">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	140 <option value="no_downsampling" selected="true">No downsampling</option>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	141 <option value="p">Percentage of reads</option>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	142 <option value="n">Number of reads</option>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	143 </param>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	144 <when value="no_downsampling"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	145 <when value="p">
1 761b6fdcac6e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 1fc6a1ce5483f15ea5366a534529025781311200 iuc parents: 0 diff changeset	146 <param argument="--downsample" type="float" min="0" max="1" value="0.8" label="Percentage of reads to sample" help="Must be between 0 and 1 (0 and 1 not included)">
0 3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	147 <validator type="in_range" min="0" exclude_min="true" max="1" exclude_max="true" message="Percentage of reads to downsample must be > 0 and < 1"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	148 </param>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	149 <param argument="--downsample-seed" type="integer" optional="true" label="Downsampling seed" help="Seed (integer) used to randomly select reads for downsampling. Useful for reproducibility."/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	150 </when>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	151 <when value="n">
1 761b6fdcac6e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 1fc6a1ce5483f15ea5366a534529025781311200 iuc parents: 0 diff changeset	152 <param argument="--downsample" type="integer" min="1" value="1000" label="Number of reads to sample" help="Must be superior or equal to 1"/>
0 3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	153 <param argument="--downsample-seed" type="integer" optional="true" label="Downsampling seed" help="Seed (integer) used to randomly select reads for downsampling. Useful for reproducibility."/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	154 </when>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	155 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	156
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	157 </section>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	158
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	159 <section name="window_size" title="Analysis Window Size">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	160 <param argument="--length" type="integer" min="1" value="70" label="Number of nucleotides to process, starting from 5p and 3p end of read" help="(Bases which are located further than this from one of the two read ends will not be analyzed)"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	161 <param argument="--around" type="integer" min="0" value="10" label="Number of nucleotides to retrieve before and after read" help="(This is used in order to look at purine enrichment before strand breaks)"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	162 </section>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	163
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	164 <!--GRAPHICS OPTIONS-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	165
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	166 <section name="graphics" title="Graphics Options">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	167 <param argument="--ymax" type="float" min="0" max="1" value="0.3" label="Graphical y-axis limit for nucleotide misincorporation frequency" help="(Bottom plot in the Fragmisincorporation_plot.pdf file)">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	168 <validator type="in_range" min="0" exclude_min="true" max="1" exclude_max="false" message="--ymax must be > 0 and <= 1"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	169 </param>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	170 <param argument="--readplot" type="integer" min="0" value="25" label="Number of bases to plot from 5p and 3p ends (x-axis)" help="(Bottom plot in the Fragmisincorporation_plot.pdf file) // Must be inferior or equal to --length !">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	171 <validator type="in_range" min="0" exclude_min="true" message="--readplot must be > 0"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	172 </param>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	173 <param argument="--refplot" type="integer" min="0" value="10" label="Number of upstream and downstream nucleotides to plot for the composition plots" help="(Top four plots in the Fragmisincorporation_plot.pdf file) // Must be inferior or equal to --around !"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	174 <param argument="--title" type="text" optional="true" label="Plot title" help="Title to give to the plots in the pdf files"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	175 <param argument="--theme-bw" type="select" label="Graphical theme to use for the posterior prediction plot">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	176 <option value="" selected="true">gray (default)</option>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	177 <option value="--theme-bw">bw (--theme-bw)</option>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	178 </param>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	179 </section>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	180
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	181 <!--STATISTICS OPTIONS-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	182
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	183 <section name="statistics" title="Statistical Estimation Options">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	184 <conditional name="stats">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	185 <param argument="--no-stats" type="select" label="Enable statistical estimations?">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	186 <option value="" selected="true">Yes</option>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	187 <option value="--no-stats">No</option>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	188 </param>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	189 <when value="">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	190 <param argument="--rand" type="integer" min="0" value="30" label="Number of random starting points for the likelihood optimization"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	191 <param argument="--burn" type="integer" min="0" value="10000" label="Number of burn-in iterations"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	192 <param argument="--adjust" type="integer" min="0" value="10" label="Number of adjust proposal variance parameter iterations"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	193 <param argument="--iter" type="integer" min="0" value="50000" label="Number of final MCMC iterations"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	194 <conditional name="ends">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	195 <param name="ends_to_process" type="select" label="Read ends to analyze for statistical estimation" help="(relates to --forward and --reverse options, default is to use both ends)">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	196 <option value="" selected="true">5p and 3p ends</option>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	197 <option value="--forward">5p ends only</option>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	198 <option value="--reverse">3p ends only</option>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	199 </param>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	200 <when value="">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	201 <param argument="--diff-hangs" type="boolean" checked="false" truevalue="--diff-hangs" falsevalue="" label="Overhangs are different in 5p and 3p?"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	202 </when>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	203 <when value="--forward"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	204 <when value="--reverse"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	205 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	206 <param argument="--seq-length" type="integer" min="1" value="12" label="Number of nucleotides (on both ends if both are used) to use for statistical estimations." help="Must be inferior or equal to the --length option !"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	207 <param argument="--var-disp" type="boolean" checked="false" truevalue="--var-disp" falsevalue="" label="Variable dispersion in the overhangs?"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	208 <param name="mutation_model" type="select" label="Substitution model to use in statistical estimation">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	209 <option value="" selected="true">HKY85 model (Hasegawa, Kishino and Yano, default option)</option>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	210 <option value="--jukes-cantor">Jukes-Cantor model (--jukes-cantor)</option>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	211 </param>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	212 <param name="nick_vector" type="select" label="Calculation of the nick vector" help="Default option is to estimate nick frequencies along the sequence using a GAM (Generalized Additive Model), followed by smoothing. GAM estimation will only be done if there are enough substitutions.">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	213 <option value="" selected="true">Estimate using a GAM + smoothing</option>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	214 <option value="--use-raw-nick-freq">Estimate using a GAM, no smoothing (--use-raw-nick-freq)</option>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	215 <option value="--fix-nicks">Make it constant (--fix-nicks)</option>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	216 <option value="--single-stranded">Single-stranded library protocol (makes the vector constant by filling with ones) (--single-stranded)</option>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	217 </param>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	218 </when>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	219 <when value="--no-stats"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	220 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	221 </section>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	222
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	223 <!--RESCALING OPTIONS-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	224
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	225 <section name="rescale" title="Rescaling options">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	226 <conditional name="rescaling">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	227 <param argument="--rescale" type="select" label="Perform rescaling of base quality according to DNA damage level?" help="This is helpful for downstream analyses, as damaged bases create less noise.">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	228 <option value="" selected="true">No</option>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	229 <option value="--rescale">Yes</option>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	230 </param>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	231 <when value="--rescale">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	232 <param argument="--rescale-length-5p" type="integer" min="0" optional="true" label="Number of bases to rescale at the 5p end" help="defaults to --seq-length if left empty. // Must be inferior or equal to --seq-length !"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	233 <param argument="--rescale-length-3p" type="integer" min="0" optional="true" label="Number of bases to rescale at the 3p end" help="defaults to --seq-length if left empty. // Must be inferior or equal to --seq-length !"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	234 </when>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	235 <when value=""/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	236 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	237 </section>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	238
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	239 </inputs>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	240
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	241 <outputs>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	242
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	243 <!--RUNTIME LOG FILE-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	244
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	245 <data name="runtime_log" format="txt" from_work_dir="mapDamage_results/Runtime_log.txt" label="${tool.name} on ${on_string}: Runtime_log.txt"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	246
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	247 <!--RESULT FILES THAT DESCRIBE DNA DAMAGE OBSERVED ON READS-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	248
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	249 <collection name="damage_visualisation" type="list" label="${tool.name} on ${on_string}: Data description files and plots">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	250 <data name="dnacomp" format="txt" from_work_dir="mapDamage_results/dnacomp.txt" label="${tool.name} on ${on_string}: dnacomp.txt"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	251 <data name="misincorporation" format="txt" from_work_dir="mapDamage_results/misincorporation.txt" label="${tool.name} on ${on_string}: misincorporation.txt"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	252 <data name="5pCtoT_freq" format="txt" from_work_dir="mapDamage_results/5pCtoT_freq.txt" label="${tool.name} on ${on_string}: 5pCtoT_freq.txt"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	253 <data name="3pGtoA_freq" format="txt" from_work_dir="mapDamage_results/3pGtoA_freq.txt" label="${tool.name} on ${on_string}: 3pGtoA_freq.txt"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	254 <data name="Fragmisincorporation_plot" format="pdf" from_work_dir="mapDamage_results/Fragmisincorporation_plot.pdf" label="${tool.name} on ${on_string}: Fragmisincorporation_plot.pdf"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	255 <data name="lgdistribution" format="txt" from_work_dir="mapDamage_results/lgdistribution.txt" label="${tool.name} on ${on_string}: lgdistribution.txt"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	256 <data name="Length_plot" format="pdf" from_work_dir="mapDamage_results/Length_plot.pdf" label="${tool.name} on ${on_string}: Length_plot.pdf"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	257 </collection>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	258
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	259 <!--RESULT FILES THAT DESCRIBE STATISTICAL ESTIMATIONS OF DAMAGE PARAMETERS-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	260
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	261 <collection name="statistical_estimation" type="list" label="${tool.name} on ${on_string}: Statistical estimation files and plots">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	262 <data name="dnacomp_genome" format="csv" from_work_dir="mapDamage_results/dnacomp_genome.csv" label="${tool.name} on ${on_string}: dnacomp_genome.csv"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	263 <data name="Stats_out_MCMC_iter_summ_stat" format="csv" from_work_dir="mapDamage_results/Stats_out_MCMC_iter_summ_stat.csv" label="${tool.name} on ${on_string}: Stats_out_MCMC_iter_summ_stat.csv"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	264 <data name="Stats_out_MCMC_hist" format="pdf" from_work_dir="mapDamage_results/Stats_out_MCMC_hist.pdf" label="${tool.name} on ${on_string}: Stats_out_MCMC_hist.pdf"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	265 <data name="Stats_out_MCMC_iter" format="csv" from_work_dir="mapDamage_results/Stats_out_MCMC_iter.csv" label="${tool.name} on ${on_string}: Stats_out_MCMC_iter.csv"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	266 <data name="Stats_out_MCMC_trace" format="pdf" from_work_dir="mapDamage_results/Stats_out_MCMC_trace.pdf" label="${tool.name} on ${on_string}: Stats_out_MCMC_trace.pdf"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	267 <data name="Stats_out_MCMC_correct_prob" format="csv" from_work_dir="mapDamage_results/Stats_out_MCMC_correct_prob.csv" label="${tool.name} on ${on_string}: Stats_out_MCMC_correct_prob.csv"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	268 <data name="Stats_out_MCMC_post_pred" format="pdf" from_work_dir="mapDamage_results/Stats_out_MCMC_post_pred.pdf" label="${tool.name} on ${on_string}: Stats_out_MCMC_post_pred.pdf"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	269 <filter>statistics['stats']['no_stats'] == ''</filter>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	270 </collection>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	271
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	272 <!--OPTIONAL ALIGNMENT OUTPUT FILES-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	273
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	274 <data name="rescaled_bam" format="bam" from_work_dir="mapDamage_results/alignment.rescaled.bam" label="${tool.name} on ${on_string}: Rescaled .bam file">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	275 <filter>rescale['rescaling']['rescale'] == '--rescale'</filter>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	276 </data>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	277
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	278 <data name="fasta_alignment" format="fasta" from_work_dir="mapDamage_results/alignment.fasta" label="${tool.name} on ${on_string}: FASTA file of alignments">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	279 <filter>fasta</filter>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	280 </data>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	281
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	282 </outputs>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	283
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	284 <tests>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	285
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	286 <!--GENERAL TESTS-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	287 <!--NB: only data_visualisation files are tested, as the statistical estimation process is stochastic and files will always be different-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	288
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	289 <!--SAM input-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	290 <test expect_num_outputs="17" expect_exit_code="0">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	291
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	292 <param name="sbam_file" value="test_align.sam" ftype="sam"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	293 <conditional name="reference">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	294 <param name="ref_source" value="history"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	295 <param name="history_reference" value="ref.fa" ftype="fasta"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	296 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	297
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	298 <output_collection name="damage_visualisation" type="list">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	299 <element name="misincorporation" file="reference_misincorporation.txt" compare="diff" lines_diff="2"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	300 <element name="lgdistribution" file="reference_lgdistribution.txt" compare="diff" lines_diff="2"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	301 </output_collection>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	302
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	303 </test>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	304
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	305 <!--BAM input-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	306 <test expect_num_outputs="17" expect_exit_code="0">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	307
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	308 <param name="sbam_file" value="test_align.bam" ftype="bam"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	309 <conditional name="reference">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	310 <param name="ref_source" value="history"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	311 <param name="history_reference" value="ref.fa" ftype="fasta"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	312 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	313
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	314 <output_collection name="damage_visualisation" type="list">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	315 <element name="misincorporation" file="reference_misincorporation.txt" compare="diff" lines_diff="2"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	316 <element name="lgdistribution" file="reference_lgdistribution.txt" compare="diff" lines_diff="2"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	317 </output_collection>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	318
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	319
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	320 </test>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	321
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	322 <!--TEST TO VERIFY BUILT-IN REFERENCE GENOMES WORK AS INTENDED-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	323 <test expect_num_outputs="9" expect_exit_code="0">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	324
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	325 <param name="sbam_file" value="test_align.bam" ftype="bam"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	326 <conditional name="reference">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	327 <param name="ref_source" value="builtin"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	328 <param name="builtin_reference" value="test"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	329 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	330 <section name="statistics">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	331 <conditional name="stats">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	332 <param name="no_stats" value="--no-stats"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	333 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	334 </section>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	335
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	336 <output_collection name="damage_visualisation" type="list">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	337 <element name="misincorporation" file="reference_misincorporation.txt" compare="diff" lines_diff="2"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	338 <element name="lgdistribution" file="reference_lgdistribution.txt" compare="diff" lines_diff="2"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	339 </output_collection>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	340
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	341 </test>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	342
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	343 <!--TEST TO VERIFY no_stats OPTION WORKS AS INTENDED-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	344 <test expect_num_outputs="9" expect_exit_code="0">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	345
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	346 <param name="sbam_file" value="test_align.sam" ftype="sam"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	347 <conditional name="reference">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	348 <param name="ref_source" value="history"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	349 <param name="history_reference" value="ref.fa" ftype="fasta"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	350 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	351 <section name="statistics">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	352 <conditional name="stats">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	353 <param name="no_stats" value="--no-stats"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	354 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	355 </section>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	356
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	357 <output_collection name="damage_visualisation" type="list">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	358 <element name="misincorporation" file="reference_misincorporation.txt" compare="diff" lines_diff="2"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	359 <element name="lgdistribution" file="reference_lgdistribution.txt" compare="diff" lines_diff="2"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	360 </output_collection>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	361
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	362 </test>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	363
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	364 <!--TEST TO VERIFY fasta OPTION WORKS AS INTENDED-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	365
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	366 <test expect_num_outputs="10" expect_exit_code="0">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	367
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	368 <param name="sbam_file" value="test_align.sam" ftype="sam"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	369 <conditional name="reference">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	370 <param name="ref_source" value="history"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	371 <param name="history_reference" value="ref.fa" ftype="fasta"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	372 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	373 <section name="statistics">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	374 <conditional name="stats">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	375 <param name="no_stats" value="--no-stats"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	376 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	377 </section>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	378 <param name="fasta" value="true"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	379
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	380 <output_collection name="damage_visualisation" type="list">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	381 <element name="misincorporation" file="reference_misincorporation.txt" compare="diff" lines_diff="2"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	382 <element name="lgdistribution" file="reference_lgdistribution.txt" compare="diff" lines_diff="2"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	383 </output_collection>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	384
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	385 <output name="fasta_alignment" file="alignment.fa" compare="diff" count="1"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	386
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	387 </test>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	388
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	389 <!--TEST TO VERIFY rescale OPTION WORKS AS INTENDED-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	390 <!--BAM file is not compared, as it depends on the stochastic statistical estimations, and may therefore differ (though perhaps not with this dataset)-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	391 <test expect_num_outputs="18" expect_exit_code="0">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	392
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	393 <param name="sbam_file" value="test_align.sam" ftype="sam"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	394 <conditional name="reference">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	395 <param name="ref_source" value="history"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	396 <param name="history_reference" value="ref.fa" ftype="fasta"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	397 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	398 <section name="rescale">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	399 <conditional name="rescaling">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	400 <param name="rescale" value="--rescale"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	401 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	402 </section>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	403
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	404 <output_collection name="damage_visualisation" type="list">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	405 <element name="misincorporation" file="reference_misincorporation.txt" compare="diff" lines_diff="2"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	406 <element name="lgdistribution" file="reference_lgdistribution.txt" compare="diff" lines_diff="2"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	407 </output_collection>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	408
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	409 </test>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	410
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	411 </tests>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	412
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	413 <help><![CDATA[
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	414 Overview:
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	415
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	416 mapDamage is a computational framework which allows for authentication of ancient DNA NGS reads by tracking and quantifying damage patterns which are specific to ancient DNA molecules.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	417
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	418 The following damage patterns can be studied thanks to mapDamage's plots and Bayesian statistical estimations:
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	419
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	420 * Fragment length
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	421 * Purine enrichment before strand breaks
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	422 * Cytosine deaminations and resulting misincorporations (C → T and G → A) (in single-stranded and double-stranded context)
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	423 * Nicking
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	424 * Overhang lengths
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	425
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	426 This help is divided into subsections: Inputs, Outputs, Parameters, and General Usage. For a quick read, jump down to the 'General Usage' section!
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	427
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	428 -----
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	429
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	430 Inputs:
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	431
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	432 mapDamage only needs two input files:
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	433
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	434 * An alignment map file, either in BAM or SAM format.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	435
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	436 * A reference sequence, in FASTA format. Can either be uploaded to Galaxy or chosen from a list of built-in references (no uploading required).
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	437
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	438 -----
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	439
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	440 Outputs:
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	441
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	442 The most commonly used outputs are listed in the 'General Usage' section below.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	443
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	444 mapDamage has plenty of output files, which have been grouped into Data Collections in order to improve clarity.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	445
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	446 * Runtime_log.txt: Contains general information about the command line which was executed by Galaxy, as well as the time taken by each task.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	447
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	448 * Outputs in the 'Damage Visualisation' collection: These outputs (text files and associated PDF plots) describe the damage patterns observed in your input BAM / SAM. No statistical estimations were involved in their generation.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	449
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	450 - dnacomp.txt: Contains the counts of each base (ATGC) across all reads, for the first X bases from the end in question (X is given by --length option) as well as the Y bases surrounding the end in question (Y is given by the --around option). This is broken down by end (3p/5p) and by strand (+/-), and by chromosome/contig.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	451
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	452 - misincorporation.txt: Contains the counts of each type of mutation (substitutions, deletions, insertions, soft-clipping) across all reads, for the first X bases from the end in question (X is given by the --length option). This is broken down by end (3p/5p), by strand (+/-), and by chromosome/contig.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	453
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	454 - 3pGtoA_freq.txt: Contains the frequencies of G → A substitutions across all reads, for the first N bases from the 3p end (N is given by --readplot).
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	455
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	456 - 5pCtoT_freq.txt: Contains the frequencies of C → T substitutions across all reads, for the first N bases from the 5p end (N is given by --readplot).
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	457
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	458 - Fragmisincorporation_plot.pdf: Contains plots of the above data: One frequency plot per nucleotide, as well as a plot describing the distribution of C → T and G → A substitutions
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	459
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	460 - lgdistribution.txt: Contains the distribution of reads according to strand on which they map (+/-) and length.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	461
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	462 - Length_plot.pdf: Contains plots of the above data.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	463
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	464 * Outputs in the 'Statistical Estimations' collection: These outputs describe the Bayesian statistical estimation process as well as its results.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	465
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	466 - dnacomp_genome.csv: Contains whole-genome base frequencies, as calculated by seqtk.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	467
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	468 - Stats_out_MCMC_iter_summ_stat.csv: Contains mean value, standard deviation, acceptance ratio and posterior distribution for the following parameters:
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	469
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	470 * θ : difference rate between reference and sample that is not due to DNA damage.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	471 * ρ : transversion / transition bias.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	472 * δd : rate of Cytosine deamination in a double-stranded context.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	473 * δs : rate of Cytosine deamination in a single-stranded context.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	474 * λ : probability of terminating an overhang.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	475 * The model's log-likelihood.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	476
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	477 - Stats_out_MCMC_hist.pdf: Contains plots of the posterior distribution of the 6 parameters described above.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	478
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	479 - Stats_out_MCMC_iter.csv: Contains the mean values for each of the 6 parameters described above at every MCMC iteration.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	480
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	481 - Stats_out_MCMC_trace.pdf: Contains trace plots derived from the previous file.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	482
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	483 - Stats_out_MCMC_correct_prob.csv: Contains posterior probabilities that C → T and G → A substitutions are due to DNA damage, for the first N bases from both 3p and 5p ends (N is given by --seq-length)
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	484
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	485 - Stats_out_MCMC_post_pred.pdf: Contains plots derived from the previous file, as well as predictive intervals for these probabilities.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	486
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	487
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	488
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	489 * alignment.fasta (if --fasta option was set): FASTA file containing alignments as specified by the BAM / SAM file. FASTA file also contains the nucleotides surrounding the reads as defined by the --around parameter.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	490
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	491 * alignment.rescaled.bam (if --rescale option was set): BAM file containing a rescaled version of the alignment: the --rescale parameter leads to a re-evaluation of base quality based on misincorporation probability, which can decrease the noise created by these misincorporations in downstream analyses.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	492
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	493 -----
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	494
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	495 Options:
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	496
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	497 mapDamage has many parameters, which have been grouped into sections for convenience.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	498
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	499 Here, the objective is to provide a guide on the most important tool features, and only a few key parameters are therefore detailed.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	500
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	501 More details concerning each option can be found:
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	502
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	503 - on the mapDamage GitHub.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	504 - in the descriptions given below the options.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	505
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	506 Some options may lack a detailed explanation (statistics related options in particular). In this case, please refer to the citations below and / or to the source code, available on the mapDamage GitHub.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	507
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	508 * --no-stats: Do not perform statistical estimation of damage parameters. This can be very useful if you only plan on looking at the Fragmisincorporation.pdf plot in order to see if the damage patterns are present, as it tends to vastly improve the run-time.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	509 * --rescale: Produces a new BAM alignment file where base qualities have been re-evaluated according to damage probability. Please note that this can only be done if statistical estimations are performed. Useful for reducing noise in downstream analyses: aDNA related misincorporations (C → T, G → A) are no longer falsely flagged as SNPs.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	510 * --merge-reference-sequence: Merges results for the different sequences (chromosomes or contigs) in your reference FASTA file. Instead of one table per reference sequence in the dnacomp.txt and misincorporation.txt files, there is one table describing every sequence. This greatly reduces the size of these files (size is more or less divided by the number of reference sequences)
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	511
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	512 * Options regarding specific library preparation protocols: By default, mapDamage assumes that you are working with merged paired-end reads, from a double-stranded library protocol. If that is not the case, the tool authors have made recommendations, which you can check out in the supplementary data of Jónsson et al. (2013).
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	513
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	514 - For single-stranded libraries:
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	515
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	516 * Calculation of the nick vector: single-stranded library protocol (--single-stranded). The authors recommend this option for treating single-stranded library data, and remark that the user should see elevated C → T substitution frequencies at both ends in the Stats_out_MCMC_post_pred.pdf plot.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	517
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	518 - For single-end libraries:
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	519
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	520 * Read ends to analyze for statistical estimation: 5p ends only (--forward). This forces mapDamage to only analyze the 5p ends of reads.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	521 * Overhangs are different in 5p and 3p?: Yes (--diff-hangs). This option allows different mean lengths for the two overhangs, which can be another way to account for single-end data.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	522
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	523 -----
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	524
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	525 General usage:
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	526
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	527 (This description is also based on the supplementary data of Jónsson et al. (2013))
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	528
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	529 Launching mapDamage
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	530
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	531 For a simple usage of mapDamage, the user only needs to provide the two input files (alignment file and reference file), and press the 'Run tool' button.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	532
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	533 If downstream SNP analyses are in order, then one may want to use the rescaling feature, which will reduce the noise induced by cytosine deamination in these analyses.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	534
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	535 Statistical estimation may be disabled to improve run-time, if the user doesn't intend to make use of it.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	536
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	537 Analyzing the outputs
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	538
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	539 The first outputs one should have a look at are the Fragmisincorporation_plot.pdf and the Length_plot.pdf files. One can check if the expected damage is present, and if there are any problems with the dataset.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	540
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	541 If statistical estimations were run, the user should check if the proposed model is a good fit: do the empirical substitution frequencies (Fragmisincorporation.pdf plot) fall within the prediction intervals (Stats_out_MCMC_post_pred.pdf plot) ?
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	542
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	543 The fit can also be assessed by looking at the Stats_out_MCMC_trace.pdf plot, to check if an equilibrium was reached over the course of the iterations. Finally, one can have a look at the acceptance ratio values in the Stats_out_MCMC_iter_summ_stat.csv file (3rd row), which should be between 0.1 and 0.3.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	544
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	545 If the fit is not correct, it may be improved by increasing the values of the --rand, --burn, --adjust and --iter options.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	546
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	547 If the fit looks correct, the rescaled BAM file can be confidently used, and the values of the damage parameters described in the Stats_out_MCMC_iter_summ_stat.csv may be used for comparison across samples.
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	548 ]]></help>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	549
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	550 <citations>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	551 <citation type="doi">10.1093/bioinformatics/btt193</citation>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	552 <citation type="doi">10.1093/bioinformatics/btr347</citation>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	553 </citations>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	554
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	555 </tool>

Mercurial > repos > iuc > map_damage

annotate map_damage.xml @ 1:761b6fdcac6e draft