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comparison mummer.xml @ 5:57f042937ba7 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 026db7297e987c1b7ce7f5dd4f8746d1bd435538
author iuc
date Mon, 18 Mar 2024 12:41:39 +0000
parents bcd65de9725b
children
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4:bcd65de9725b 5:57f042937ba7
7 <expand macro="requirements"> 7 <expand macro="requirements">
8 <expand macro="gnuplot_requirement"/> 8 <expand macro="gnuplot_requirement"/>
9 </expand> 9 </expand>
10 <command detect_errors="exit_code"> 10 <command detect_errors="exit_code">
11 <![CDATA[ 11 <![CDATA[
12 mummer 12 mummer
13 $anchoring 13 $anchoring
14 -l '$min' 14 -l '$min'
15 $direction 15 $direction
16 $force 16 $force
17 $chars 17 $chars
85 </param> 85 </param>
86 <param name="child" type="select" label="Child" help="Use child table in the index and during search? (-child)" > 86 <param name="child" type="select" label="Child" help="Use child table in the index and during search? (-child)" >
87 <option value="0">No</option> 87 <option value="0">No</option>
88 <option value="1">Yes</option> 88 <option value="1">Yes</option>
89 </param> 89 </param>
90 <param name="skip" type="integer" argument="-skip" value="10" label="Sparsify" 90 <param type="integer" argument="-skip" value="10" label="Sparsify"
91 help="Sparsify the MEM-finding algorithm even more, performing jumps of skip*k [auto (l-10)/k]. (-skip)" /> 91 help="Sparsify the MEM-finding algorithm even more, performing jumps of skip*k [auto (l-10)/k]. (-skip)" />
92 <param name="kmer" type="integer" argument="-kmer" value="1" label="kmer Table" 92 <param type="integer" argument="-kmer" value="1" label="kmer Table"
93 help="Use kmer table containing sa-intervals (speeds up searching first k characters) in the index and during search. (-kmer)" /> 93 help="Use kmer table containing sa-intervals (speeds up searching first k characters) in the index and during search. (-kmer)" />
94 </when> 94 </when>
95 <when value="defaults" /> 95 <when value="defaults" />
96 </conditional> 96 </conditional>
97 <conditional name="mumplot" > 97 <conditional name="mumplot" >
110 <data name="png_output" format="png" from_work_dir="out.png" label="${tool.name} on ${on_string}: plot" > 110 <data name="png_output" format="png" from_work_dir="out.png" label="${tool.name} on ${on_string}: plot" >
111 <filter>mumplot['plot'] == 'yes'</filter> 111 <filter>mumplot['plot'] == 'yes'</filter>
112 </data> 112 </data>
113 </outputs> 113 </outputs>
114 <tests> 114 <tests>
115 <test> 115 <test expect_num_outputs="2">
116 <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" /> 116 <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" />
117 <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" /> 117 <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
118 <param name="options|advanced" value="defaults" /> 118 <param name="options|advanced" value="defaults" />
119 <param name="plot" value="yes" /> 119 <param name="plot" value="yes" />
120 <output name="output" ftype="tabular" compare="diff" value="mummer.txt" /> 120 <output name="output" ftype="tabular" compare="diff" value="mummer.txt" />
126 126
127 **Options:**:: 127 **Options:**::
128 128
129 mummer 129 mummer
130 130
131 -mumreference Compute maximal matches that are unique in the reference- sequence but not 131 -mumreference Compute maximal matches that are unique in the reference- sequence but not
132 necessarily in the query-sequence (default) 132 necessarily in the query-sequence (default)
133 133
134 -maxmatch Compute all maximal matches regardless of their uniqueness 134 -maxmatch Compute all maximal matches regardless of their uniqueness
135 135
136 -l Set the minimum length of a match 136 -l Set the minimum length of a match
152 -c Report the query position of a reverse complement match 152 -c Report the query position of a reverse complement match
153 relative to the forward strand of the query sequence 153 relative to the forward strand of the query sequence
154 154
155 mummerplot 155 mummerplot
156 156
157 -b Highlight alignments with breakpoints further than breaklen nucleotides from the nearest 157 -b Highlight alignments with breakpoints further than breaklen nucleotides from the nearest
158 sequence end 158 sequence end
159 159
160 -color Color plot lines with a percent similarity gradient or turn off all plot color (default 160 -color Color plot lines with a percent similarity gradient or turn off all plot color (default
161 color by match dir) If the plot is very sparse, edit the .gp script to plot with 161 color by match dir) If the plot is very sparse, edit the .gp script to plot with
162 'linespoints' instead of 'lines' 162 'linespoints' instead of 'lines'
163 163
164 -c Generate a reference coverage plot (default for .tiling) 164 -c Generate a reference coverage plot (default for .tiling)
165 165
166 --filter Only display .delta alignments which represent the "best" hit to any particular spot on 166 --filter Only display .delta alignments which represent the "best" hit to any particular spot on
167 either sequence, i.e. a one-to-one mapping of reference and query subsequences 167 either sequence, i.e. a one-to-one mapping of reference and query subsequences
168 168
169 --fat Layout sequences using fattest alignment only 169 --fat Layout sequences using fattest alignment only
170 170
171 -IdR Plot a particular reference sequence ID on the X-axis 171 -IdR Plot a particular reference sequence ID on the X-axis