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comparison macros.xml @ 0:a04e64efa43a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
author iuc
date Wed, 10 Nov 2021 23:33:13 +0000
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children d110a4141898
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-1:000000000000 0:a04e64efa43a
1 <macros>
2 <token name="@TOOL_VERSION@">2.1.0</token>
3 <token name="@VERSION_SUFFIX@">0</token>
4 <xml name="xrefs">
5 <xrefs>
6 <xref type="bio.tools">ragtag</xref>
7 </xrefs>
8 </xml>
9 <xml name="requirements">
10 <requirements>
11 <requirement type="package" version="@TOOL_VERSION@">ragtag</requirement>
12 </requirements>
13 </xml>
14 <xml name="citations">
15 <citations>
16 <citation type="doi">10.1186/s13059-019-1829-6</citation>
17 </citations>
18 </xml>
19 <xml name="input_options">
20 <param name="reference" type="data" format="fasta" label="Reference FASTA file"/>
21 <param name="query" type="data" format="fasta" label="Query FASTA file" />
22 </xml>
23 <xml name="common_parameters">
24 <param argument="-e" type="data" format="txt" optional="true" label="List of reference headers to ignore"
25 help="Use this parameter to provide a single column file listing any reference.fa headers that should
26 be ignored (e.g. chr0/chrUn or alt contigs)"/>
27 <param argument="-j" type="data" format="txt" optional="true" label="List of query headers to leave uncorrected"
28 help="use this parameter to provide a single column file listing any query.fa headers that shall not be broken"/>
29 <param argument="-f" type="integer" min="0" value="1000" label="Minimum unique single length"
30 help="If an alignment is not entirely unique, at least -f bp of the alignment must be unique to be considered
31 for scaffolding. By default, entirely unique alignments are considered regardless of their length, but
32 this can be disabled with --remove-small. Doing so ensures that only alignments at least -f bp in length
33 are considered for correction"/>
34 <param argument="--remove-small" type="boolean" truevalue="--remove-small"
35 falsevalue="" checked="false" label="Remove unique alignments"
36 help="Remove unique alignments shorter than the minimum unique alignment length" />
37 <param argument="-q" type="integer" min="0" value="10" label="Minimum mappping quality"
38 help="Mapping quality scores quantify the probability that a read is misplaced" />
39 <param argument="-d" type="integer" min="0" value="100000" label="Maximum alignment merge distance"
40 help="For each query sequence, syntenic alignments within -d bp of each other are merged into longer alignments"/>
41 <conditional name="mapping_conditional">
42 <param name="mapping_option" type="select" label="Aligner tool">
43 <option value="nucmer">Nucmer</option>
44 <!--Unimap is not included because according the minimap2 developers, minimap2 backports unimap features https://github.com/lh3/minimap2/releases/tag/v2.19
45 <option value="unimap">Unimap</option>
46 -->
47 <option value="minimap2" selected="true">Minimap2</option>
48 </param>
49 <when value="nucmer">
50 <param name="anchor_mode" type="select" label="Anchoring mode">
51 <option value="--mum">Use anchor matches that are unique in both the reference and query (--mum)</option>
52 <option value="--mumreference">Use anchor matches that are unique in in the reference but not necessarily unique in the query (--mumreference)</option>
53 <option value="--maxmatch" selected="true">Use all anchor matches regardless of their uniqueness (--maxmatch)</option>
54 </param>
55 <param argument="-l" type="integer" min="0" value="100" label="Minimun length of a single match"/>
56 <param argument="-c" type="integer" min="0" value="500" label="Minimum length of a cluster of matches"/>
57 </when>
58 <when value="minimap2">
59 <param argument="--mm2-params" type="select"
60 label="Select a profile of preset options"
61 help="Each profile comes with the preconfigured settings mentioned in parentheses" >
62 <option value="asm5">Asm5: the alignment will not extend to regions with 5% or higher sequence divergence (-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 --min-occ-floor=100)</option>
63 <option value="asm10">Asm10: up to 10% sequence divergence (-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 --min-occ-floor=100)</option>
64 <option value="asm20">Asm20: up to 20% sequence divergence (-k19 -w10 -A1 -B6 -O6,26 -E2,1 -s200 -z200 --min-occ-floor=100)</option>
65 </param>
66 </when>
67 </conditional>
68 </xml>
69 <token name="@INPUTS@"><![CDATA[
70 $mode_conditional.reference
71 $mode_conditional.query
72 ]]></token>
73 <token name="@COMMON_PARAMETERS@"><![CDATA[
74 --aligner $mode_conditional.advanced_options.mapping_conditional.mapping_option
75 #if $mode_conditional.advanced_options.mapping_conditional.mapping_option == 'nucmer'
76 --nucmer-params '$nucmer_params'
77 #else
78 #if $mode_conditional.advanced_options.mapping_conditional.mm2_params == 'asm5'
79 --mm2-params '-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 --min-occ-floor=100'
80 #else if $mode_conditional.advanced_options.mapping_conditional.mm2_params == 'asm10'
81 --mm2-params '-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 --min-occ-floor=100'
82 #else
83 --mm2-params '-k19 -w10 -A1 -B6 -O6,26 -E2,1 -s200 -z200 --min-occ-floor=100'
84 #end if
85 #end if
86 #if $mode_conditional.advanced_options.e
87 -e '${mode_conditional.advanced_options.e}'
88 #end if
89 #if $mode_conditional.advanced_options.j
90 -j '${mode_conditional.advanced_options.j}'
91 #end if
92 -f $mode_conditional.advanced_options.f
93 --remove-small $mode_conditional.advanced_options.remove_small
94 -q $mode_conditional.advanced_options.q
95 -d $mode_conditional.advanced_options.d
96 ]]></token>
97 </macros>