map_damage: map_damage.xml annotate

annotate map_damage.xml @ 2:0287e2f82b64 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa

author	iuc
date	Tue, 22 Jul 2025 09:02:06 +0000
parents	761b6fdcac6e
children

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 <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	3 <macros>
2 0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	4 <token name="@TOOL_VERSION@">2.2.3</token>
0 3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	5 <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	6 </macros>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	7 <xrefs>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	8 <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	9 </xrefs>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	10 <requirements>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	11 <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	12 </requirements>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	13 <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	14 <command detect_errors="aggressive"><![CDATA[
2 0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	15
0 3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	16 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	17 #if $reference.ref_source == 'history':
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	18 ln -s '$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	19 #end if
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	20 ## 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	21
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	22 mapDamage
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 ## 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	25
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	26 --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	27
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	28 #if $reference.ref_source == 'builtin':
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	29 --reference '$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	30 #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	31 --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	32 #end if
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 --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	35
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	36 ## GENERAL OPTIONS
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	37
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	38 $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	39
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	40 #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	41 --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	42 #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	43 --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	44 #end if
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	45 #end if
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	46
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	47 --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	48 --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	49 --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	50 $fasta
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	51
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	52 ## GRAPHICS OPTIONS
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	53
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	54 --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	55 --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	56 --refplot $graphics.refplot
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	57
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	58 #if str($graphics.title):
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	59 --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	60 #end if
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 $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	63
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	64 ## STATISTICS OPTIONS
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 $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	67 $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	68 #else:
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	69 --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	70 --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	71 --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	72 --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	73 $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	74
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	75 #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	76 $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	77 #end if
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	78
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	79 --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	80 $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	81 $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	82 $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	83 #end if
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	84
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	85 ## RESCALING OPTIONS
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 #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	88 --rescale
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	89 #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	90 --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	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 #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	93 --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	94 #end if
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	95 #end if
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	96
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	97 ]]></command>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	98
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	99 <inputs>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	100
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	101 <!--INPUT FILES-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	102 <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	103
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	104 <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	105 <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	106 <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	107 <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	108 </param>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	109 <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	110 <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	111 <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	112 <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	113 </param>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	114 </when>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	115 <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	116 <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	117 </when>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	118 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	119
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	120 <!--GENERAL OPTIONS-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	121
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	122 <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	123 <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	124 <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	125 <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	126 <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	127 <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	128 <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	129 <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	130 <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	131 </param>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	132 <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	133 <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	134 <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	135 <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	136 </param>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	137 <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	138 </when>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	139 <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	140 <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	141 <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	142 </when>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	143 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	144 </section>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	145 <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	146 <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	147 <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	148 </section>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	149
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	150 <!--GRAPHICS OPTIONS-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	151
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	152 <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	153 <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	154 <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	155 </param>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	156 <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	157 <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	158 </param>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	159 <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	160 <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	161 <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	162 <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	163 <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	164 </param>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	165 </section>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	166
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	167 <!--STATISTICS OPTIONS-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	168
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	169 <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	170 <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	171 <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	172 <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	173 <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	174 </param>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	175 <when value="">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	176 <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	177 <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	178 <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	179 <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	180 <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	181 <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	182 <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	183 <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	184 <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	185 </param>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	186 <when value="">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	187 <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	188 </when>
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="--forward"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	190 <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	191 </conditional>
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="--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	193 <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	194 <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	195 <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	196 <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	197 </param>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	198 <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	199 <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	200 <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	201 <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	202 <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	203 </param>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	204 </when>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	205 <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	206 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	207 </section>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	208
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	209 <!--RESCALING OPTIONS-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	210
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	211 <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	212 <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	213 <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	214 <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	215 <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	216 </param>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	217 <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	218 <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	219 <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	220 </when>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	221 <when value=""/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	222 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	223 </section>
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 </inputs>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	226
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	227 <outputs>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	228 <!--RUNTIME LOG FILE-->
2 0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	229 <data name="runtime_log" format="txt" from_work_dir="mapDamage_results/Runtime_log.txt" label="${tool.name} on ${on_string}: Runtime_log.txt"/>
0 3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	230
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	231 <!--RESULT FILES THAT DESCRIBE DNA DAMAGE OBSERVED ON READS-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	232
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	233 <collection name="damage_visualisation" type="list" label="${tool.name} on ${on_string}: Data description files and plots">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	234 <data name="dnacomp" format="txt" from_work_dir="mapDamage_results/dnacomp.txt" label="${tool.name} on ${on_string}: dnacomp.txt"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	235 <data name="misincorporation" format="txt" from_work_dir="mapDamage_results/misincorporation.txt" label="${tool.name} on ${on_string}: misincorporation.txt"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	236 <data name="5pCtoT_freq" format="txt" from_work_dir="mapDamage_results/5pCtoT_freq.txt" label="${tool.name} on ${on_string}: 5pCtoT_freq.txt"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	237 <data name="3pGtoA_freq" format="txt" from_work_dir="mapDamage_results/3pGtoA_freq.txt" label="${tool.name} on ${on_string}: 3pGtoA_freq.txt"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	238 <data name="Fragmisincorporation_plot" format="pdf" from_work_dir="mapDamage_results/Fragmisincorporation_plot.pdf" label="${tool.name} on ${on_string}: Fragmisincorporation_plot.pdf"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	239 <data name="lgdistribution" format="txt" from_work_dir="mapDamage_results/lgdistribution.txt" label="${tool.name} on ${on_string}: lgdistribution.txt"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	240 <data name="Length_plot" format="pdf" from_work_dir="mapDamage_results/Length_plot.pdf" label="${tool.name} on ${on_string}: Length_plot.pdf"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	241 </collection>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	242
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	243 <!--RESULT FILES THAT DESCRIBE STATISTICAL ESTIMATIONS OF DAMAGE PARAMETERS-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	244
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	245 <collection name="statistical_estimation" type="list" label="${tool.name} on ${on_string}: Statistical estimation files and plots">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	246 <data name="dnacomp_genome" format="csv" from_work_dir="mapDamage_results/dnacomp_genome.csv" label="${tool.name} on ${on_string}: dnacomp_genome.csv"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	247 <data name="Stats_out_MCMC_iter_summ_stat" format="csv" from_work_dir="mapDamage_results/Stats_out_MCMC_iter_summ_stat.csv" label="${tool.name} on ${on_string}: Stats_out_MCMC_iter_summ_stat.csv"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	248 <data name="Stats_out_MCMC_hist" format="pdf" from_work_dir="mapDamage_results/Stats_out_MCMC_hist.pdf" label="${tool.name} on ${on_string}: Stats_out_MCMC_hist.pdf"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	249 <data name="Stats_out_MCMC_iter" format="csv" from_work_dir="mapDamage_results/Stats_out_MCMC_iter.csv" label="${tool.name} on ${on_string}: Stats_out_MCMC_iter.csv"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	250 <data name="Stats_out_MCMC_trace" format="pdf" from_work_dir="mapDamage_results/Stats_out_MCMC_trace.pdf" label="${tool.name} on ${on_string}: Stats_out_MCMC_trace.pdf"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	251 <data name="Stats_out_MCMC_correct_prob" format="csv" from_work_dir="mapDamage_results/Stats_out_MCMC_correct_prob.csv" label="${tool.name} on ${on_string}: Stats_out_MCMC_correct_prob.csv"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	252 <data name="Stats_out_MCMC_post_pred" format="pdf" from_work_dir="mapDamage_results/Stats_out_MCMC_post_pred.pdf" label="${tool.name} on ${on_string}: Stats_out_MCMC_post_pred.pdf"/>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	253 <filter>statistics['stats']['no_stats'] == ''</filter>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	254 </collection>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	255
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	256 <!--OPTIONAL ALIGNMENT OUTPUT FILES-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	257
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	258 <data name="rescaled_bam" format="bam" from_work_dir="mapDamage_results/alignment.rescaled.bam" label="${tool.name} on ${on_string}: Rescaled .bam file">
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	259 <filter>rescale['rescaling']['rescale'] == '--rescale'</filter>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	260 </data>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	261 <data name="fasta_alignment" format="fasta" from_work_dir="mapDamage_results/alignment.fasta" label="${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	262 <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	263 </data>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	264 </outputs>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	265
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	266 <tests>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	267
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	268 <!--GENERAL TESTS-->
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	269 <!--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	270 <!--SAM input-->
2 0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	271 <test expect_num_outputs="17" expect_exit_code="0">
0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	272 <param name="sbam_file" value="test_align.sam" ftype="sam"/>
0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	273 <conditional name="reference">
0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	274 <param name="ref_source" value="history"/>
0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	275 <param name="history_reference" value="ref.fa" ftype="fasta"/>
0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	276 </conditional>
0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	277 <output_collection name="damage_visualisation" type="list">
0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	278 <element name="misincorporation" file="reference_misincorporation.txt" compare="diff" lines_diff="2"/>
0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	279 <element name="lgdistribution" file="reference_lgdistribution.txt" compare="diff" lines_diff="2"/>
0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	280 </output_collection>
0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	281 </test>
0 3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	282
2 0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	283 <!--BAM input-->
0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	284 <test expect_num_outputs="17" expect_exit_code="0">
0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	285 <param name="sbam_file" value="test_align.bam" ftype="bam"/>
0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	286 <conditional name="reference">
0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	287 <param name="ref_source" value="history"/>
0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	288 <param name="history_reference" value="ref.fa" ftype="fasta"/>
0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	289 </conditional>
0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	290 <output_collection name="damage_visualisation" type="list">
0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	291 <element name="misincorporation" file="reference_misincorporation.txt" compare="diff" lines_diff="2"/>
0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	292 <element name="lgdistribution" file="reference_lgdistribution.txt" compare="diff" lines_diff="2"/>
0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	293 </output_collection>
0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	294 </test>
0 3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	295
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	296 <!--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	297 <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	298 <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	299 <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	300 <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	301 <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	302 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	303 <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	304 <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	305 <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	306 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	307 </section>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	308 <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	309 <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	310 <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	311 </output_collection>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	312 </test>
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 <!--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	315 <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	316 <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	317 <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	318 <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	319 <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	320 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	321 <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	322 <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	323 <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	324 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	325 </section>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	326 <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	327 <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	328 <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	329 </output_collection>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	330 </test>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	331
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	332 <!--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	333 <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	334 <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	335 <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	336 <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	337 <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	338 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	339 <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	340 <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	341 <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	342 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	343 </section>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	344 <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	345 <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	346 <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	347 <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	348 </output_collection>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	349 <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	350 </test>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	351
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	352 <!--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	353 <!--BAM file is not compared, as it depends on the stochastic statistical estimations, and may therefore differ (though perhaps not with this dataset)-->
2 0287e2f82b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 54378f7937205ec8ddf87440a5d78c3d0d3c8efa iuc parents: 1 diff changeset	354 <test expect_num_outputs="18" expect_exit_code="0">
0 3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	355 <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	356 <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	357 <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	358 <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	359 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	360 <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	361 <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	362 <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	363 </conditional>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	364 </section>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	365 <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	366 <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	367 <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	368 </output_collection>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	369 </test>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	370 </tests>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	371
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	372 <help><![CDATA[
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	373 Overview:
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	374
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	375 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	376
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	377 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	378
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	379 * Fragment length
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	380 * 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	381 * 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	382 * Nicking
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	383 * Overhang lengths
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 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	386
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	387 -----
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 Inputs:
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	390
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	391 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	392
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	393 * 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	394
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	395 * 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	396
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	397 -----
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	398
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	399 Outputs:
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	400
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	401 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	402
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	403 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	404
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	405 * 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	406
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	407 * 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	408
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	409 - 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	410
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	411 - 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	412
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	413 - 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	414
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	415 - 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	416
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	417 - 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	418
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	419 - 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	420
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	421 - 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	422
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	423 * 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	424
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	425 - 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	426
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	427 - 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	428
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	429 * 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	430 * 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	431 * 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	432 * 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	433 * 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	434 * 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	435
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	436 - 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	437
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	438 - 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	439
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	440 - 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	441
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	442 - 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	443
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	444 - 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	445
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	446
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 * 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	449
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	450 * 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	451
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	452 -----
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 Options:
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 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	457
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	458 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	459
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	460 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	461
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	462 - 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	463 - 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	464
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	465 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	466
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	467 * --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	468 * --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	469 * --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	470
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	471 * 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	472
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	473 - 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	474
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	475 * 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	476
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	477 - 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	478
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	479 * 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	480 * 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	481
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
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	484 General usage:
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	485
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	486 (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	487
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	488 Launching mapDamage
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	489
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	490 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	491
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	492 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	493
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	494 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	495
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	496 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	497
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	498 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	499
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	500 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	501
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	502 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	503
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	504 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	505
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	506 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	507 ]]></help>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	508
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	509 <citations>
3db999d4e0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage commit 3b5fcf457cea50698cc333239669bf25f6031ab5 iuc parents: diff changeset	510 <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	511 <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	512 </citations>
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 </tool>

Mercurial > repos > iuc > map_damage

annotate map_damage.xml @ 2:0287e2f82b64 draft default tip