Mercurial > repos > rnateam > locarna_pairwise

comparison locarna_pairwise.xml @ 3:f3f08a777c10 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 10ccc47885ce71e602d66e157bd475f1facbd042
author bgruening
date Mon, 05 Dec 2022 14:29:12 +0000
parents 433601e9f132
children 4839df2b2f6b
comparison
equal deleted inserted replaced
2:433601e9f132 3:f3f08a777c10
1 <tool id="locarna_pairwise" name="LocARNA Pairwise Aligner" version="@VERSION@.1"> 1 <tool id="locarna_pairwise" name="LocARNA Pairwise Aligner" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description> 2 <description>
3 Pairwise Simultaneous Alignment and Folding of RNAs (locarna, sparse) 3 Pairwise Simultaneous Alignment and Folding of RNAs (locarna, sparse)
4 </description> 4 </description>
5 5
6 <macros> 6 <macros>
21 #end if 21 #end if
22 22
23 '$inputA' 23 '$inputA'
24 '$inputB' 24 '$inputB'
25 25
26 --width 60 26 ## --width 60
27 27
28 ## -------------------- alignment mode and specific options 28 ## -------------------- alignment mode and specific options
29 29
30 #if str($alignment_mode.alignment_mode_selector) == "global_locarna" 30 #if str($alignment_mode.alignment_mode_selector) == "global_locarna"
31 #if str($alignment_mode.free_endgaps) != "----" 31 #if str($alignment_mode.free_endgaps) != "----"
132 132
133 <when value="structure_sequence_local_locarna" /> 133 <when value="structure_sequence_local_locarna" />
134 <when value="structure_local_locarna" /> 134 <when value="structure_local_locarna" />
135 </conditional> 135 </conditional>
136 136
137 <param name="outputs" type="select" display="checkboxes" multiple="True" 137 <param name="outputs" type="select" display="checkboxes" multiple="true"
138 label="Output options"> 138 label="Output options">
139 <option value="clustal_strict" selected="True">Output alignment 139 <option value="clustal_strict" selected="true">Output alignment
140 in ClustalW format</option> 140 in ClustalW format</option>
141 <option value="clustal" selected="False">Output alignment 141 <option value="clustal" selected="false">Output alignment
142 in constraint-annotated ClustalW format</option> 142 in constraint-annotated ClustalW format</option>
143 <option value="stockholm" selected="False">Output 143 <option value="stockholm" selected="false">Output
144 alignment in Stockholm format</option> 144 alignment in Stockholm format</option>
145 <option value="pp" selected="False">Output 145 <option value="pp" selected="false">Output
146 alignment in LocARNA's PP 2.0 format</option> 146 alignment in LocARNA's PP 2.0 format</option>
147 </param> 147 </param>
148 148
149 <param name="stdout_verbosity" type="select" label="Standard output verbosity"> 149 <param name="stdout_verbosity" type="select" label="Standard output verbosity">
150 <option value="--quiet">Don't report standard 150 <option value="--quiet">Don't report standard
180 </inputs> 180 </inputs>
181 181
182 <outputs> 182 <outputs>
183 <expand macro="standard_outupt" /> 183 <expand macro="standard_outupt" />
184 <data format="clustal" name="clustal" 184 <data format="clustal" name="clustal"
185 label="${tool.name} alignment (annotated clustal) on ${on_string}"> 185 label="${tool.name} on ${on_string}: alignment (annotated clustal)">
186 <filter>'clustal' in outputs</filter> 186 <filter>'clustal' in outputs</filter>
187 </data> 187 </data>
188 <data format="clustal" name="clustal_strict" 188 <data format="clustal" name="clustal_strict"
189 label="${tool.name} alignment (clustal) on ${on_string}"> 189 label="${tool.name}on ${on_string}: alignment (clustal)">
190 <filter>'clustal_strict' in outputs</filter> 190 <filter>'clustal_strict' in outputs</filter>
191 </data> 191 </data>
192 <data format="stockholm" name="stockholm" 192 <data format="stockholm" name="stockholm"
193 label="${tool.name} alignment (stockholm) on ${on_string}"> 193 label="${tool.name} on ${on_string}: alignment (stockholm)">
194 <filter>'stockholm' in outputs</filter> 194 <filter>'stockholm' in outputs</filter>
195 </data> 195 </data>
196 <data format="txt" name="pp" 196 <data format="txt" name="pp"
197 label="${tool.name} alignment (PP 2.0) on ${on_string}"> 197 label="${tool.name} on ${on_string}: alignment (PP 2.0)">
198 <filter>'pp' in outputs</filter> 198 <filter>'pp' in outputs</filter>
199 </data> 199 </data>
200 </outputs> 200 </outputs>
201 201
202 <tests> 202 <tests>
203 <test> 203 <test expect_num_outputs="1">
204 <param name="inputA" value="tRNA_2-1.fa" /> 204 <param name="inputA" value="tRNA_2-1.fa" />
205 <param name="inputB" value="tRNA_2-2.fa" /> 205 <param name="inputB" value="tRNA_2-2.fa" />
206 <param name="outputs" value="clustal" /> 206 <param name="outputs" value="clustal" />
207 <output name="clustal" file="tRNA_2.aln" lines_diff="2" /> 207 <output name="clustal" file="tRNA_2.aln" lines_diff="2" />
208 </test> 208 </test>
209 <test> 209 <test expect_num_outputs="2">
210 <param name="inputA" value="haca.snoRNA-1.aln" /> 210 <param name="inputA" value="haca.snoRNA-1.aln" />
211 <param name="inputB" value="haca.snoRNA-2.aln" /> 211 <param name="inputB" value="haca.snoRNA-2.aln" />
212 <param name="outputs" value="clustal_strict,clustal" /> 212 <param name="outputs" value="clustal_strict,clustal" />
213 <output name="clustal" file="haca.snoRNA-c.aln" lines_diff="2" /> 213 <output name="clustal" file="haca.snoRNA-c.aln" lines_diff="2" />
214 <output name="clustal_strict" file="haca.snoRNA.aln" lines_diff="1" /> 214 <output name="clustal_strict" file="haca.snoRNA.aln" lines_diff="2" />
215 </test> 215 </test>
216 </tests> 216 </tests>
217 217
218 <help><![CDATA[ **LocARNA -- Pairwise alignment of RNAs** 218 <help><![CDATA[ **LocARNA -- Pairwise alignment of RNAs**
219 219