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comparison exonerate.xml @ 1:3222a35ab2ae draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit 9655295f3e3f9831fe1e04c1bc7f9b5db1046ec5
author iuc
date Wed, 17 Oct 2018 09:49:21 -0400
parents b1fd74cb7cb9
children 29d1f9b7200b
comparison
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0:b1fd74cb7cb9 1:3222a35ab2ae
81 <param name='score' type='integer' min="0" max="10000" value="100" label="Score threshold for gapped alignment"/> 81 <param name='score' type='integer' min="0" max="10000" value="100" label="Score threshold for gapped alignment"/>
82 <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"/> 82 <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"/>
83 <param name='bestn' type='integer' min="0" max="10000" value="0" label="Report best N results per query (0 to report all)"/> 83 <param name='bestn' type='integer' min="0" max="10000" value="0" label="Report best N results per query (0 to report all)"/>
84 </inputs> 84 </inputs>
85 <outputs> 85 <outputs>
86 <data name="output_gff" format="txt" label="${tool.name} on $on_string"> 86 <data name="output_gff" format="gff" label="${tool.name} on $on_string">
87 <filter>outformat != 'alignment'</filter> 87 <filter>outformat != 'alignment'</filter>
88 </data> 88 </data>
89 <data name="output_ali" format="gff" label="${tool.name} on $on_string"> 89 <data name="output_ali" format="txt" label="${tool.name} on $on_string">
90 <filter>outformat == 'alignment'</filter> 90 <filter>outformat == 'alignment'</filter>
91 </data> 91 </data>
92 </outputs> 92 </outputs>
93 <tests> 93 <tests>
94 <test> 94 <test>
96 <conditional name="ref_seq"> 96 <conditional name="ref_seq">
97 <param name="ref_seq_selector" value="personal"/> 97 <param name="ref_seq_selector" value="personal"/>
98 <param name="input_fasta" value="genome.fa"/> 98 <param name="input_fasta" value="genome.fa"/>
99 </conditional> 99 </conditional>
100 <param name="outformat" value="targetgff"/> 100 <param name="outformat" value="targetgff"/>
101 <output name="output_gff" file="out_target.gff"/> 101 <output name="output_gff" file="out_target.gff" lines_diff="8"/>
102 </test> 102 </test>
103 <test> 103 <test>
104 <param name="query" value="genome.fa"/> 104 <param name="query" value="genome.fa"/>
105 <conditional name="ref_seq"> 105 <conditional name="ref_seq">
106 <param name="ref_seq_selector" value="database"/> 106 <param name="ref_seq_selector" value="database"/>
107 <param name="input_fasta" value="merlin"/> 107 <param name="input_fasta" value="merlin"/>
108 </conditional> 108 </conditional>
109 <param name="outformat" value="targetgff"/> 109 <param name="outformat" value="targetgff"/>
110 <output name="output_gff" file="out_target.gff"/> 110 <output name="output_gff" file="out_target.gff" lines_diff="8"/>
111 </test> 111 </test>
112 <test> 112 <test>
113 <param name="query" value="genome.fa"/> 113 <param name="query" value="genome.fa"/>
114 <conditional name="ref_seq"> 114 <conditional name="ref_seq">
115 <param name="ref_seq_selector" value="personal"/> 115 <param name="ref_seq_selector" value="personal"/>
116 <param name="input_fasta" value="genome.fa"/> 116 <param name="input_fasta" value="genome.fa"/>
117 </conditional> 117 </conditional>
118 <param name="outformat" value="querygff"/> 118 <param name="outformat" value="querygff"/>
119 <output name="output_gff" file="out_query.gff"/> 119 <output name="output_gff" file="out_query.gff" lines_diff="8"/>
120 </test> 120 </test>
121 <test> 121 <test>
122 <param name="query" value="genome.fa"/> 122 <param name="query" value="genome.fa"/>
123 <conditional name="ref_seq"> 123 <conditional name="ref_seq">
124 <param name="ref_seq_selector" value="personal"/> 124 <param name="ref_seq_selector" value="personal"/>
133 <param name="ref_seq_selector" value="personal"/> 133 <param name="ref_seq_selector" value="personal"/>
134 <param name="input_fasta" value="genome.fa"/> 134 <param name="input_fasta" value="genome.fa"/>
135 </conditional> 135 </conditional>
136 <param name="model" value="est2genome"/> 136 <param name="model" value="est2genome"/>
137 <param name="outformat" value="targetgff"/> 137 <param name="outformat" value="targetgff"/>
138 <output name="output_gff" file="est2genome.gff"/> 138 <output name="output_gff" file="est2genome.gff" lines_diff="4"/>
139 </test> 139 </test>
140 <test> 140 <test>
141 <param name="query" value="proteome.fa"/> 141 <param name="query" value="proteome.fa"/>
142 <conditional name="ref_seq"> 142 <conditional name="ref_seq">
143 <param name="ref_seq_selector" value="personal"/> 143 <param name="ref_seq_selector" value="personal"/>
144 <param name="input_fasta" value="genome.fa"/> 144 <param name="input_fasta" value="genome.fa"/>
145 </conditional> 145 </conditional>
146 <param name="model" value="protein2genome"/> 146 <param name="model" value="protein2genome"/>
147 <param name="outformat" value="targetgff"/> 147 <param name="outformat" value="targetgff"/>
148 <output name="output_gff" file="protein2genome.gff"/> 148 <output name="output_gff" file="protein2genome.gff" lines_diff="2"/>
149 </test> 149 </test>
150 <test> 150 <test>
151 <param name="query" value="genome.fa"/> 151 <param name="query" value="genome.fa"/>
152 <conditional name="ref_seq"> 152 <conditional name="ref_seq">
153 <param name="ref_seq_selector" value="personal"/> 153 <param name="ref_seq_selector" value="personal"/>
154 <param name="input_fasta" value="genome.fa"/> 154 <param name="input_fasta" value="genome.fa"/>
155 </conditional> 155 </conditional>
156 <param name="model" value="coding2coding"/> 156 <param name="model" value="coding2coding"/>
157 <param name="outformat" value="targetgff"/> 157 <param name="outformat" value="targetgff"/>
158 <output name="output_gff" file="coding2coding.gff"/> 158 <output name="output_gff" file="coding2coding.gff" lines_diff="4"/>
159 </test> 159 </test>
160 </tests> 160 </tests>
161 <help><![CDATA[ 161 <help><![CDATA[
162 Exonerate is a generic tool for pairwise sequence comparison. 162 Exonerate is a generic tool for pairwise sequence comparison.
163 It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. 163 It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics.