Mercurial > repos > iuc > ragtag
comparison macros.xml @ 0:a04e64efa43a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
author | iuc |
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date | Wed, 10 Nov 2021 23:33:13 +0000 |
parents | |
children | d110a4141898 |
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-1:000000000000 | 0:a04e64efa43a |
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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> |