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comparison deepmicro.xml @ 1:c58c1a99578b draft

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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
comparison
equal deleted inserted replaced
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" />