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comparison lastdb.xml @ 8:bd3a1cc88f0a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 4568799de240022f4058ec1602e08f536916e2af"
author iuc
date Thu, 25 Mar 2021 20:52:41 +0000
parents 657fb614ee81
children 18ff8319181f
comparison
equal deleted inserted replaced
7:657fb614ee81 8:bd3a1cc88f0a
32 $lastdb.sequences_type.protein 32 $lastdb.sequences_type.protein
33 -a $lastdb.sequences_type.a 33 -a $lastdb.sequences_type.a
34 -R $lastdb.repeats.uppercase$lastdb.repeats.simple_repeat 34 -R $lastdb.repeats.uppercase$lastdb.repeats.simple_repeat
35 $lastdb.repeats.sm_lower 35 $lastdb.repeats.sm_lower
36 -S $lastdb.lastdb_advanced.S 36 -S $lastdb.lastdb_advanced.S
37 -u $lastdb.lastdb_advanced.seeds.u 37 #if $lastdb.lastdb_advanced.seeds.u != ''
38 -u $lastdb.lastdb_advanced.seeds.u
39 #end if
38 -w $lastdb.lastdb_advanced.seeds.w 40 -w $lastdb.lastdb_advanced.seeds.w
39 #if $lastdb.lastdb_advanced.seeds.W 41 #if $lastdb.lastdb_advanced.seeds.W
40 -W $lastdb.lastdb_advanced.seeds.W 42 -W $lastdb.lastdb_advanced.seeds.W
41 #end if 43 #end if
42 -m $lastdb.lastdb_advanced.seeds.m 44 -m $lastdb.lastdb_advanced.seeds.m
88 <option value="1" selected="true">Forward</option> 90 <option value="1" selected="true">Forward</option>
89 <option value="2">Both</option> 91 <option value="2">Both</option>
90 </param> 92 </param>
91 93
92 <conditional name="seeds"> 94 <conditional name="seeds">
93 <param argument="-u" type="select" multiple="false" optional="true" label="Specify a seeding scheme."> 95 <param argument="-u" type="select" multiple="false" label="Specify a seeding scheme.">
96 <option value="">Do not apply seeding scheme</option>
94 <option value="BISF">BISF</option> 97 <option value="BISF">BISF</option>
95 <option value="BISR">BISR</option> 98 <option value="BISR">BISR</option>
96 <option value="MAM4">MAM4</option> 99 <option value="MAM4">MAM4</option>
97 <option value="MAM8">MAM8</option> 100 <option value="MAM8">MAM8</option>
98 <option value="MURPHY10">MURPHY10</option> 101 <option value="MURPHY10">MURPHY10</option>
99 <option value="NEAR">NEAR</option> 102 <option value="NEAR">NEAR</option>
100 <option value="YASS" selected="true">YASS</option> 103 <option value="YASS" selected="true">YASS</option>
101 <!-- Add filename option --> 104 <!-- Add filename option -->
102 </param> 105 </param>
106 <when value=""/>
103 <when value="BISF"> 107 <when value="BISF">
104 <expand macro="step_macro" step="2"/> 108 <expand macro="step_macro" step="2"/>
105 </when> 109 </when>
106 <when value="BISR"> 110 <when value="BISR">
107 <expand macro="step_macro" step="2"/> 111 <expand macro="step_macro" step="2"/>
169 </conditional> 173 </conditional>
170 </section> 174 </section>
171 <section name="lastdb_advanced"> 175 <section name="lastdb_advanced">
172 <conditional name="seeds"> 176 <conditional name="seeds">
173 <param name="u" value="MURPHY10"/> 177 <param name="u" value="MURPHY10"/>
178 </conditional>
174 </section> 179 </section>
175 <output name="outfile" compare="contains" file="hedgdb.lastdb" ftype="lastdb"> 180 <output name="outfile" compare="contains" file="hedgdb.lastdb" ftype="lastdb">
176 <extra_files type="file" value="hedgdb.bck" name="lastdb.bck" compare="sim_size" delta="1"/> 181 <extra_files type="file" value="hedgdb.bck" name="lastdb.bck" compare="sim_size" delta="1"/>
177 <extra_files type="file" value="hedgdb.des" name="lastdb.des"/> 182 <extra_files type="file" value="hedgdb.des" name="lastdb.des"/>
178 <extra_files type="file" value="hedgdb.prj" name="lastdb.prj"/> 183 <extra_files type="file" value="hedgdb.prj" name="lastdb.prj"/>
190 <param name="uppercase" value="0"/> 195 <param name="uppercase" value="0"/>
191 <param name="simple_repeat" value="1"/> 196 <param name="simple_repeat" value="1"/>
192 <param name="sm_lower" value="true"/> 197 <param name="sm_lower" value="true"/>
193 </section> 198 </section>
194 </section> 199 </section>
195 <output name="outfile" compare="contains" file="hedgdb.lastdb" ftype="lastdb"> 200 <output name="outfile" compare="contains" file="humdb-sanger.lastdb" ftype="lastdb">
196 <extra_files type="file" value="humdb-sanger.bck" name="lastdb.bck" compare="sim_size" delta="1"/> 201 <extra_files type="file" value="humdb-sanger.bck" name="lastdb.bck" compare="sim_size" delta="1"/>
197 <extra_files type="file" value="humdb-sanger.des" name="lastdb.des"/> 202 <extra_files type="file" value="humdb-sanger.des" name="lastdb.des"/>
198 <extra_files type="file" value="humdb-sanger.prj" name="lastdb.prj" lines_diff="2"/> 203 <extra_files type="file" value="humdb-sanger.prj" name="lastdb.prj" lines_diff="2"/>
199 <extra_files type="file" value="humdb-sanger.sds" name="lastdb.sds"/> 204 <extra_files type="file" value="humdb-sanger.sds" name="lastdb.sds"/>
200 <extra_files type="file" value="humdb-sanger.ssp" name="lastdb.ssp" compare="sim_size" delta="1"/> 205 <extra_files type="file" value="humdb-sanger.ssp" name="lastdb.ssp" compare="sim_size" delta="1"/>