Mercurial > repos > iuc > last
comparison lastdb.xml @ 5:f5a5a2b39ff2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 4568799de240022f4058ec1602e08f536916e2af"
| author | iuc |
|---|---|
| date | Thu, 25 Mar 2021 20:53:27 +0000 |
| parents | 8705e0d74a0f |
| children | 19c265784f35 |
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| 4:8705e0d74a0f | 5:f5a5a2b39ff2 |
|---|---|
| 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"/> |