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comparison mummer.xml @ 0:26f2cc1cc1e9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
author iuc
date Wed, 05 Dec 2018 02:38:48 -0500
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children 48badcd29c5d
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-1:000000000000 0:26f2cc1cc1e9
1 <tool id="mummer_mummer" name="Mummer" version="@MUMMER_VERSION@">
2 <description>Align two or more sequences</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements">
7 <requirement type="package" version="5.2.3">gnuplot</requirement>
8 </expand>
9 <command detect_errors="exit_code">
10 <![CDATA[
11 mummer
12 $anchoring
13 -l '$min'
14 $direction
15 $force
16 $chars
17 $print_length
18 $substring
19 $position
20 #if $options.advanced == 'enable'
21 -k '$options.suffix'
22 -threads '$options.threads'
23 -qthreads '$options.qthreads'
24 -suflink '$'options.suflink'
25 -child '$options.child'
26 -skip '$options.skip'
27 -kmer '$options.kmer'
28 #end if
29 '$reference_sequence' '$query_sequence' > '$output'
30 #if $mumplot.plot == 'yes':
31 && mummerplot
32 -b '$mumplot.breaklen'
33 $mumplot.color
34 $mumplot.coverage
35 $mumplot.filter
36 $mumplot.fat
37 #if $mumplot.labels.IDs == 'yes':
38 -IdR '$mumplot.labels.ref_id'
39 -IdQ '$mumplot.labels.query_id'
40 #end if
41 -s '$mumplot.size'
42 -terminal png
43 -title '$mumplot.title'
44 $mumplot.snp
45 #if $mumplot.range.custom == 'yes':
46 -x [$mumplot.range.min_x:$mumplot.range.max_x]
47 -y [$mumplot.range.min_y:$mumplot.range.max_y]
48 #end if
49 '$output'
50 #end if
51 ]]>
52 </command>
53 <inputs>
54 <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" help="FastA or multi-FastA" />
55 <param name="query_sequence" type="data" format="fasta" label="Query Sequence" help="FastA or multi-FastA" />
56 <param name="anchoring" type="select" label="Anchoring" help="Choose a match anchoring strategy">
57 <option value="">Maximal matches unique in only reference sequence (-mumreference) (Default)</option>
58 <option value="-mum">Maximal matches unique in both sequences (-mum)</option>
59 <option value="-maxmatch">All matches reguardless of uniqueness (-maxmatch)</option>
60 </param>
61 <param name="min" type="integer" argument="-l" value="20" label="Minimum Match Length" help="Minimum length of a match. (-l)" />
62 <param name="direction" type="select" label="Direction" help="Direction of complement sequence to use">
63 <option value="-b">Compute forward and reverse complement matches (-b)</option>
64 <option value="-r">Compute only reverse complement matches (-r)</option>
65 </param>
66 <param name="force" type="boolean" argument="-F" truevalue="-F" falsevalue="" label="Force 4 column output"
67 help="force 4 column output format regardless of the number of reference sequence inputs. (-F)" />
68 <param name="chars" type="boolean" argument="-n" truevalue="-n" falsevalue="" label="Match only the characters a, c, g, or t" help="(-n)" />
69 <param name="print_length" type="boolean" argument="-L" truevalue="-L" falsevalue="" label="Print length of query sequence in header of matches" help="(-L)" />
70 <param name="substring" type="boolean" argument="-s" truevalue="-s" falsevalue="" label= "Print first 53 characters of the matching substring" help="(-s)" />
71 <param name="position" type="boolean" argument="-c" truevalue="-c" falsevalue="" label="Position"
72 help="Report the query position of a reverse complement match relative to the forward strand of the query sequence. (-c)" />
73 <conditional name="options">
74 <param name="advanced" type="select" label="Additional options">
75 <option value="defaults">Use defaults</option>
76 <option value="enable">Select additional options</option>
77 </param>
78 <when value="enable" >
79 <param name="suffix" type="integer" argument="-k" value="1" label="Suffix" help="Sampled suffix positions. (-k)" />
80 <param name="threads" type="integer" argument="-threads" value="3" label="Threads"
81 help="Number of threads to use for -maxmatch; only valid if above parameter is greater than one. (-threads)" />
82 <param name="qthreads" type="integer" argument="-qthreads" value="3" label="Qthreads" help="Number of threads to use for queries. (-qthreads)" />
83 <param name="suflink" type="select" label="Suflink" help="Use suffix links in the index and during search? (-suflink)" >
84 <option value="0">No</option>
85 <option value="1">Yes</option>
86 </param>
87 <param name="child" type="select" label="Child" help="Use child table in the index and during search? (-child)" >
88 <option value="0">No</option>
89 <option value="1">Yes</option>
90 </param>
91 <param name="skip" type="integer" argument="-skip" value="10" label="Sparsify"
92 help="Sparsify the MEM-finding algorithm even more, performing jumps of skip*k [auto (l-10)/k]. (-skip)" />
93 <param name="kmer" type="integer" argument="-kmer" value="1" label="kmer Table"
94 help="Use kmer table containing sa-intervals (speeds up searching first k characters) in the index and during search. (-kmer)" />
95 </when>
96 <when value="defaults" />
97 </conditional>
98 <conditional name="mumplot" >
99 <param name="plot" type="select" label="Do you want to output a 2-D dotplot of the input sequences?" >
100 <option value="yes">YES</option>
101 <option value="no">NO</option>
102 </param>
103 <when value="yes" >
104 <expand macro="mumplot_input" />
105 </when>
106 <when value="no" />
107 </conditional>
108 </inputs>
109 <outputs>
110 <data name="output" format="tabular" from_work_dir="mummer.txt" label="${tool.name} on ${on_string}: alignment" />
111 <data name="png_output" format="png" from_work_dir="out.png" label="${tool.name} on ${on_string}: plot" >
112 <filter>mumplot['plot'] == 'yes'</filter>
113 </data>
114 </outputs>
115 <tests>
116 <test>
117 <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" />
118 <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
119 <param name="options" value="defaults" />
120 <param name="plot" value="yes" />
121 <output name="output" ftype="tabular" compare="diff" value="mummer.txt" />
122 <output name="png_output" ftype="png" compare="sim_size" value="plot.png" />
123 </test>
124 </tests>
125 <help><![CDATA[
126 This is the core program of the MUMmer package. It is the suffix-tree based match finding routine, and the main part of every MUMmer script. By default, mummer now finds maximal matches regardless of their uniqueness. Limiting the output to only unique matches can be specified by choosing alternative Anchoring strategies.
127
128 **Options:**::
129
130 mummer
131
132 -mumreference Compute maximal matches that are unique in the reference- sequence but not
133 necessarily in the query-sequence (default)
134
135 -maxmatch Compute all maximal matches regardless of their uniqueness
136
137 -l Set the minimum length of a match
138
139 -b Compute forward and reverse complement matches
140
141 -r Compute only reverse complement matches
142
143 -mum Compute maximal matches that are unique in both sequences
144
145 -F Force 4 column output format regardless of the number of reference sequence inputs
146
147 -n Match only the characters a, c, g, or t
148
149 -L Print length of query sequence in header of matches
150
151 -s Print first 53 characters of the matching substring
152
153 -c Report the query position of a reverse complement match
154 relative to the forward strand of the query sequence
155
156 mummerplot
157
158 -b Highlight alignments with breakpoints further than breaklen nucleotides from the nearest
159 sequence end
160
161 -color Color plot lines with a percent similarity gradient or turn off all plot color (default
162 color by match dir) If the plot is very sparse, edit the .gp script to plot with
163 'linespoints' instead of 'lines'
164
165 -c Generate a reference coverage plot (default for .tiling)
166
167 --filter Only display .delta alignments which represent the "best" hit to any particular spot on
168 either sequence, i.e. a one-to-one mapping of reference and query subsequences
169
170 --fat Layout sequences using fattest alignment only
171
172 -IdR Plot a particular reference sequence ID on the X-axis
173
174 -IdQ Plot a particular query sequence ID on the Y-axis
175
176 -s Set the output size to small, medium or large (--small) (--medium) (--large) (default 'small')
177
178 --SNP Highlight SNP locations in each alignment
179
180 -title Specify the gnuplot plot title (default none)
181
182 -x Set the xrange for the plot '[min:max]'
183
184 -y Set the yrange for the plot '[min:max]'
185
186 -R Plot an ordered set of reference sequences from Rfile
187
188 -Q Plot an ordered set of query sequences from Qfile
189
190 --layout Layout a .delta multiplot in an intelligible fashion, this option requires the -R -Q options
191
192 ]]></help>
193 <expand macro="citation" />
194 </tool>