Mercurial > repos > iuc > deepmicro
comparison deepmicro.xml @ 1:c58c1a99578b draft
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 19cd7fd52900e23704975869cd66d5f7b219ae3e
| author | iuc |
|---|---|
| date | Sat, 10 Jun 2023 21:59:04 +0000 |
| parents | 77cbfe3e1b0d |
| children | 2d20b3a1babd |
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| 0:77cbfe3e1b0d | 1:c58c1a99578b |
|---|---|
| 28 | 28 |
| 29 ln -s '$mode.class_labels' data/labels.csv && | 29 ln -s '$mode.class_labels' data/labels.csv && |
| 30 | 30 |
| 31 #for $params in $mode.parameter_set: | 31 #for $params in $mode.parameter_set: |
| 32 | 32 |
| 33 #if $params.rl_type.rl_type_choice == "--pca" or $params.rl_type.rl_type_choice == "--rp": | 33 ## only train classifier without encoding |
| 34 #if $params.rl_type.rl_type_choice == "no_rl": | |
| 35 DM.py -r 1 -cd features.csv -cl labels.csv --save_rep -m '$params.rl_type.classifier' -t \${GALAXY_SLOTS:-8} && | |
| 36 #elif $params.rl_type.rl_type_choice == "--pca" or $params.rl_type.rl_type_choice == "--rp": | |
| 34 DM.py -r 1 -cd features.csv -cl labels.csv '$params.rl_type.rl_type_choice' --save_rep -m '$params.rl_type.classifier' -t \${GALAXY_SLOTS:-8} && | 37 DM.py -r 1 -cd features.csv -cl labels.csv '$params.rl_type.rl_type_choice' --save_rep -m '$params.rl_type.classifier' -t \${GALAXY_SLOTS:-8} && |
| 35 #else: | 38 #else: |
| 36 DM.py -r 1 -cd features.csv -cl labels.csv '$params.rl_type.rl_type_choice' -dm '$params.rl_type.dm' --save_rep -m '$params.rl_type.classifier' -t \${GALAXY_SLOTS:-8} && | 39 DM.py -r 1 -cd features.csv -cl labels.csv '$params.rl_type.rl_type_choice' -dm '$params.rl_type.dm' --save_rep -m '$params.rl_type.classifier' -t \${GALAXY_SLOTS:-8} && |
| 37 #end if | 40 #end if |
| 38 #end for | 41 #end for |
| 213 </assert_contents> | 216 </assert_contents> |
| 214 </output> | 217 </output> |
| 215 | 218 |
| 216 </test> | 219 </test> |
| 217 | 220 |
| 221 <test expect_num_outputs="1"> | |
| 222 <param name="features" value="UserDataExample.csv" /> | |
| 223 <param name="mode_type" value="e_and_c" /> | |
| 224 <param name="class_labels" value="UserLabelExample.csv" /> | |
| 225 <param name="rl_type_choice" value="no_rl" /> | |
| 226 <param name="classifier" value="rf" /> | |
| 227 <output ftype="tabular" name="results" > | |
| 228 <assert_contents> | |
| 229 <has_text text="rf" /> | |
| 230 </assert_contents> | |
| 231 </output> | |
| 232 | |
| 233 </test> | |
| 234 | |
| 218 <!-- test multiple parameter sets --> | 235 <!-- test multiple parameter sets --> |
| 219 <test expect_num_outputs="1"> | 236 <test expect_num_outputs="1"> |
| 220 <param name="features" value="UserDataExample.csv" /> | 237 <param name="features" value="UserDataExample.csv" /> |
| 221 <conditional name="mode"> | 238 <conditional name="mode"> |
| 222 <param name="mode_type" value="e_and_c" /> | 239 <param name="mode_type" value="e_and_c" /> |