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comparison exonerate.xml @ 3:a03dead1bede draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
author iuc
date Sun, 01 Mar 2020 04:48:34 -0500
parents b03ae2ba8688
children
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2:b03ae2ba8688 3:a03dead1bede
1 <tool id="exonerate" name="Exonerate" profile="16.04" version="@VERSION@+galaxy1"> 1 <tool id="exonerate" name="Exonerate" profile="16.04" version="@VERSION@+galaxy2">
2 <description>pairwise sequence comparison</description> 2 <description>pairwise sequence comparison</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
30 --querytype protein --targettype dna 30 --querytype protein --targettype dna
31 #elif str($model) == "coding2coding" 31 #elif str($model) == "coding2coding"
32 --querytype dna --targettype dna 32 --querytype dna --targettype dna
33 #end if 33 #end if
34 34
35 #if $minintron
36 --minintron ${minintron}
37 #end if
38
39 #if $maxintron
40 --maxintron ${maxintron}
41 #end if
42
43 --cores \${GALAXY_SLOTS:-1}
44
35 #if str($outformat) == "alignment" 45 #if str($outformat) == "alignment"
36 --showalignment yes --showvulgar no > '${output_ali}' 46 --showalignment yes --showvulgar no > '${output_ali}'
37 #elif str($outformat) == "targetgff" 47 #elif str($outformat) == "targetgff"
38 --showalignment no --showvulgar no --showtargetgff yes --showquerygff no > '${output_gff}' 48 --showalignment no --showvulgar no --showtargetgff yes --showquerygff no > '${output_gff}'
39 #elif str($outformat) == "querygff" 49 #elif str($outformat) == "querygff"
40 --showalignment no --showvulgar no --showtargetgff no --showquerygff yes > '${output_gff}' 50 --showalignment no --showvulgar no --showtargetgff no --showquerygff yes > '${output_gff}'
41 #end if 51 #end if
42 52
43 --cores \${GALAXY_SLOTS:-1} 53 ## Produce a more standard GFF3
54 #if str($outformat) in ["targetgff", "querygff"]
55 && python '$__tool_directory__/exonerategff_to_gff3.py' '${output_gff}' > '${output_gff3}'
56 #end if
44 ]]></command> 57 ]]></command>
45 58
46 <inputs> 59 <inputs>
47 <param argument="--query" type="data" format="fasta" label="Select the query sequence(s) in fasta" /> 60 <param argument="--query" type="data" format="fasta" label="Select the query sequence(s) in fasta" />
48 61
81 <option value="alignment">Human readable alignment</option> 94 <option value="alignment">Human readable alignment</option>
82 </param> 95 </param>
83 <param name='score' type='integer' min="0" max="10000" value="100" label="Score threshold for gapped alignment"/> 96 <param name='score' type='integer' min="0" max="10000" value="100" label="Score threshold for gapped alignment"/>
84 <param name='percent' type='float' min="0" max="100" value="0.0" label="Report alignment over a percentage of the maximum score attainable by each query"/> 97 <param name='percent' type='float' min="0" max="100" value="0.0" label="Report alignment over a percentage of the maximum score attainable by each query"/>
85 <param name='bestn' type='integer' min="0" max="10000" value="0" label="Report best N results per query (0 to report all)"/> 98 <param name='bestn' type='integer' min="0" max="10000" value="0" label="Report best N results per query (0 to report all)"/>
99 <param argument='--minintron' type='integer' optional="true" label="Minimum intron length limit" help="This is not a hard limit - it only affects size of introns which are sought during heuristic alignment."/>
100 <param argument='--maxintron' type='integer' optional="true" label="Maximum intron length limit" help="This is not a hard limit - it only affects size of introns which are sought during heuristic alignment."/>
86 </inputs> 101 </inputs>
87 <outputs> 102 <outputs>
88 <data name="output_gff" format="gff" label="${tool.name} on $on_string"> 103 <data name="output_gff" format="gff" label="${tool.name} on $on_string - Raw GFF">
104 <filter>outformat != 'alignment'</filter>
105 </data>
106 <data name="output_gff3" format="gff3" label="${tool.name} on $on_string - GFF3">
89 <filter>outformat != 'alignment'</filter> 107 <filter>outformat != 'alignment'</filter>
90 </data> 108 </data>
91 <data name="output_ali" format="txt" label="${tool.name} on $on_string"> 109 <data name="output_ali" format="txt" label="${tool.name} on $on_string">
92 <filter>outformat == 'alignment'</filter> 110 <filter>outformat == 'alignment'</filter>
93 </data> 111 </data>
99 <param name="ref_seq_selector" value="personal"/> 117 <param name="ref_seq_selector" value="personal"/>
100 <param name="input_fasta" value="genome.fa"/> 118 <param name="input_fasta" value="genome.fa"/>
101 </conditional> 119 </conditional>
102 <param name="outformat" value="targetgff"/> 120 <param name="outformat" value="targetgff"/>
103 <output name="output_gff" file="out_target.gff" lines_diff="8"/> 121 <output name="output_gff" file="out_target.gff" lines_diff="8"/>
122 <output name="output_gff3" file="out_target.gff3" lines_diff="8"/>
104 </test> 123 </test>
105 <test> 124 <test>
106 <param name="query" value="genome.fa"/> 125 <param name="query" value="genome.fa"/>
107 <conditional name="ref_seq"> 126 <conditional name="ref_seq">
108 <param name="ref_seq_selector" value="database"/> 127 <param name="ref_seq_selector" value="database"/>
109 <param name="input_fasta" value="merlin"/> 128 <param name="input_fasta" value="merlin"/>
110 </conditional> 129 </conditional>
111 <param name="outformat" value="targetgff"/> 130 <param name="outformat" value="targetgff"/>
112 <output name="output_gff" file="out_target.gff" lines_diff="8"/> 131 <output name="output_gff" file="out_target.gff" lines_diff="8"/>
132 <output name="output_gff3" file="out_target.gff3" lines_diff="8"/>
113 </test> 133 </test>
114 <test> 134 <test>
115 <param name="query" value="genome.fa"/> 135 <param name="query" value="genome.fa"/>
116 <conditional name="ref_seq"> 136 <conditional name="ref_seq">
117 <param name="ref_seq_selector" value="personal"/> 137 <param name="ref_seq_selector" value="personal"/>
118 <param name="input_fasta" value="genome.fa"/> 138 <param name="input_fasta" value="genome.fa"/>
119 </conditional> 139 </conditional>
120 <param name="outformat" value="querygff"/> 140 <param name="outformat" value="querygff"/>
121 <output name="output_gff" file="out_query.gff" lines_diff="8"/> 141 <output name="output_gff" file="out_query.gff" lines_diff="8"/>
142 <output name="output_gff3" file="out_query.gff3" lines_diff="8"/>
122 </test> 143 </test>
123 <test> 144 <test>
124 <param name="query" value="genome.fa"/> 145 <param name="query" value="genome.fa"/>
125 <conditional name="ref_seq"> 146 <conditional name="ref_seq">
126 <param name="ref_seq_selector" value="personal"/> 147 <param name="ref_seq_selector" value="personal"/>
136 <param name="input_fasta" value="genome.fa"/> 157 <param name="input_fasta" value="genome.fa"/>
137 </conditional> 158 </conditional>
138 <param name="model" value="est2genome"/> 159 <param name="model" value="est2genome"/>
139 <param name="outformat" value="targetgff"/> 160 <param name="outformat" value="targetgff"/>
140 <output name="output_gff" file="est2genome.gff" lines_diff="4"/> 161 <output name="output_gff" file="est2genome.gff" lines_diff="4"/>
162 <output name="output_gff3" file="est2genome.gff3" lines_diff="4"/>
141 </test> 163 </test>
142 <test> 164 <test>
143 <param name="query" value="proteome.fa"/> 165 <param name="query" value="proteome.fa"/>
144 <conditional name="ref_seq"> 166 <conditional name="ref_seq">
145 <param name="ref_seq_selector" value="personal"/> 167 <param name="ref_seq_selector" value="personal"/>
146 <param name="input_fasta" value="genome.fa"/> 168 <param name="input_fasta" value="genome.fa"/>
147 </conditional> 169 </conditional>
148 <param name="model" value="protein2genome"/> 170 <param name="model" value="protein2genome"/>
149 <param name="outformat" value="targetgff"/> 171 <param name="outformat" value="targetgff"/>
150 <output name="output_gff" file="protein2genome.gff" lines_diff="2"/> 172 <output name="output_gff" file="protein2genome.gff" lines_diff="2"/>
173 <output name="output_gff3" file="protein2genome.gff3" lines_diff="2"/>
151 </test> 174 </test>
152 <test> 175 <test>
153 <param name="query" value="genome.fa"/> 176 <param name="query" value="genome.fa"/>
154 <conditional name="ref_seq"> 177 <conditional name="ref_seq">
155 <param name="ref_seq_selector" value="personal"/> 178 <param name="ref_seq_selector" value="personal"/>
156 <param name="input_fasta" value="genome.fa"/> 179 <param name="input_fasta" value="genome.fa"/>
157 </conditional> 180 </conditional>
158 <param name="model" value="coding2coding"/> 181 <param name="model" value="coding2coding"/>
159 <param name="outformat" value="targetgff"/> 182 <param name="outformat" value="targetgff"/>
160 <output name="output_gff" file="coding2coding.gff" lines_diff="4"/> 183 <output name="output_gff" file="coding2coding.gff" lines_diff="4"/>
184 <output name="output_gff3" file="coding2coding.gff3" lines_diff="4"/>
185 </test>
186 <test>
187 <param name="query" value="transcriptome.fa"/>
188 <conditional name="ref_seq">
189 <param name="ref_seq_selector" value="personal"/>
190 <param name="input_fasta" value="genome.fa"/>
191 </conditional>
192 <param name="model" value="est2genome"/>
193 <param name="outformat" value="targetgff"/>
194 <param name="minintron" value="100"/>
195 <param name="maxintron" value="200"/>
196 <output name="output_gff" file="est2genome_introns.gff" lines_diff="6"/>
197 <output name="output_gff3" file="est2genome_introns.gff3" lines_diff="4"/>
161 </test> 198 </test>
162 </tests> 199 </tests>
163 <help><![CDATA[ 200 <help><![CDATA[
164 Exonerate is a generic tool for pairwise sequence comparison. 201 Exonerate is a generic tool for pairwise sequence comparison.
165 It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. 202 It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics.