Mercurial > repos > iuc > deepmicro
annotate deepmicro.xml @ 2:2d20b3a1babd draft default tip
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
author | iuc |
---|---|
date | Tue, 23 Jul 2024 15:56:32 +0000 |
parents | c58c1a99578b |
children |
rev | line source |
---|---|
0
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
1 <tool id="deepmicro" name="DeepMicro" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
2 <description> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
3 Representation learning and classification framework |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
4 </description> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
5 <macros> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
6 <import>macros.xml</import> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
7 </macros> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
8 <expand macro="biotools" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
9 <expand macro="requirements" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
10 <expand macro="version" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
11 <command detect_errors="exit_code"><![CDATA[ |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
12 mkdir data && |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
13 mkdir results && |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
14 ln -s '$features' data/features.csv && |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
15 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
16 #if $mode.mode_type == "only_encoding": |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
17 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
18 #for $params in $mode.parameter_set: |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
19 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
20 #if $params.rl_type.rl_type_choice == "--pca" or $params.rl_type.rl_type_choice == "--rp": |
2
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
21 DM.py -r 1 |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
22 -cd features.csv |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
23 '$params.rl_type.rl_type_choice' |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
24 --save_rep |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
25 --no_clf |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
26 -t \${GALAXY_SLOTS:-8} && |
0
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
27 #else: |
2
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
28 DM.py -r 1 |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
29 -cd features.csv |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
30 '$params.rl_type.rl_type_choice' |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
31 -dm '$params.rl_type.dm' |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
32 --save_rep |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
33 --no_clf |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
34 -t \${GALAXY_SLOTS:-8} && |
0
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
35 #end if |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
36 #end for |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
37 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
38 #else: |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
39 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
40 ln -s '$mode.class_labels' data/labels.csv && |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
41 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
42 #for $params in $mode.parameter_set: |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
43 |
2
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
44 ## general args |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
45 DM.py |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
46 -r '$mode.repeat' |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
47 -cd features.csv |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
48 -cl labels.csv |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
49 --save_rep |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
50 -m '$params.rl_type.classifier' |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
51 --scoring '$mode.scoring' |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
52 -f '$mode.folds' |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
53 -t \${GALAXY_SLOTS:-8} |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
54 |
1
c58c1a99578b
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 19cd7fd52900e23704975869cd66d5f7b219ae3e
iuc
parents:
0
diff
changeset
|
55 ## only train classifier without encoding |
c58c1a99578b
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 19cd7fd52900e23704975869cd66d5f7b219ae3e
iuc
parents:
0
diff
changeset
|
56 #if $params.rl_type.rl_type_choice == "no_rl": |
2
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
57 && echo "Only train Clf - no encoding!" |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
58 ## add rl type |
1
c58c1a99578b
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 19cd7fd52900e23704975869cd66d5f7b219ae3e
iuc
parents:
0
diff
changeset
|
59 #elif $params.rl_type.rl_type_choice == "--pca" or $params.rl_type.rl_type_choice == "--rp": |
2
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
60 '$params.rl_type.rl_type_choice' |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
61 ## add rl type and dm options |
0
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
62 #else: |
2
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
63 '$params.rl_type.rl_type_choice' |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
64 -dm '$params.rl_type.dm' |
0
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
65 #end if |
2
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
66 && |
0
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
67 #end for |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
68 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
69 #end if |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
70 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
71 echo Done ! |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
72 ]]> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
73 </command> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
74 <inputs> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
75 <param argument="--features" type="data" format="tabular" label="Feature table" help="Dataset containing the features of samples"/> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
76 <conditional name="mode"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
77 <param name="mode_type" type="select" label="Mode" help="The tool can either only create a latent |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
78 representation of the data or create a latent representation of the data and cross validate a classifier using that encoding."> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
79 <option value="only_encoding">Create only encoding</option> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
80 <option value="e_and_c">Create encoding and cross validate a classifier</option> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
81 </param> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
82 <when value="only_encoding"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
83 <repeat name="parameter_set" title="Parameter Set"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
84 <conditional name="rl_type"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
85 <param name="rl_type_choice" type="select" label="Representation learning type" help="The type of representation learning" > |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
86 <option value="--pca">PCA</option> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
87 <option value="--rp">Random Projection</option> |
2
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
88 <option value="--ae">Shallow Autoencoder or Deep Autoencoder (SAE, DAE)</option> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
89 <option value="--vae">Variational Autoencoder (VAE)</option> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
90 <option value="--cae">Convolutional Autoencoder (CAE)</option> |
0
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
91 </param> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
92 <when value="--pca"/> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
93 <when value="--rp"/> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
94 <when value="--ae"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
95 <expand macro="dm" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
96 </when> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
97 <when value="--vae"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
98 <expand macro="dm" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
99 </when> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
100 <when value="--cae"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
101 <expand macro="dm" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
102 </when> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
103 </conditional> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
104 </repeat> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
105 </when> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
106 <when value="e_and_c"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
107 <param argument="--class_labels" type="data" format="tabular" label="Class labels" help="Dataset containing the class labels corresponding to the features"/> |
2
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
108 <param name="scoring" type="select" label="Scoring function for the classifiere" help="The classifiere will be optimized for this scoring function." > |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
109 <option value="roc_auc">ROC AUC</option> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
110 <option value="accuracy">Accuracy</option> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
111 <option value="f1">F1 Score</option> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
112 <option value="recall">Recall</option> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
113 <option value="precision">Precision</option> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
114 </param> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
115 <param name="folds" type="integer" value="5" label="Cross-validation folds" min="2" max="10" help="The number of folds for cross-validation in the tranining set"/> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
116 <param name="repeat" type="integer" value="1" label="Repeat the experiment with different seed" min="1" max="5" help="Repeat the experiment with different seeds. Leads to a different train / test split each time."/> |
0
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
117 <repeat name="parameter_set" title="Parameter Set"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
118 <conditional name="rl_type"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
119 <param name="rl_type_choice" type="select" label="Representation learning type" help="The type of representation learning. `Train on input` trains the classifier on the input features without representation learning" > |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
120 <option value="--pca">PCA</option> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
121 <option value="--rp">Random Projection</option> |
2
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
122 <option value="--ae">Shallow Autoencoder or Deep Autoencoder (SAE, DAE)</option> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
123 <option value="--vae">Variational Autoencoder (VAE)</option> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
124 <option value="--cae">Convolutional Autoencoder (CAE)</option> |
0
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
125 <option value="no_rl">Train on input</option> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
126 </param> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
127 <when value="no_rl"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
128 <expand macro="clfs" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
129 </when> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
130 <when value="--pca"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
131 <expand macro="clfs" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
132 </when> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
133 <when value="--rp"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
134 <expand macro="clfs" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
135 </when> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
136 <when value="--ae"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
137 <expand macro="dm" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
138 <expand macro="clfs" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
139 </when> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
140 <when value="--vae"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
141 <expand macro="dm" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
142 <expand macro="clfs" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
143 </when> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
144 <when value="--cae"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
145 <expand macro="dm" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
146 <expand macro="clfs" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
147 </when> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
148 </conditional> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
149 </repeat> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
150 </when> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
151 </conditional> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
152 </inputs> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
153 <outputs> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
154 <data name="results" format="tabular" from_work_dir="./results/*_result.txt" label="${tool.name} on ${on_string}: Results"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
155 <!-- results are only for classifiers --> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
156 <filter>mode["mode_type"] == "e_and_c"</filter> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
157 </data> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
158 <collection name="encoded_features" type="list" label="Encoded Features"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
159 <!-- the encoded features generated by the tool are only for the training set, this is not very useful, therefore omitting |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
160 todo change tool do export features complete dataset also when classification is performed --> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
161 <filter>mode["mode_type"] == "only_encoding"</filter> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
162 <discover_datasets directory="results" pattern="(?P<designation>.*)_rep\.csv" format="tabular" visible="false" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
163 </collection> |
2
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
164 <collection name="model" type="list" label="Keras Models"> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
165 <!-- the encoded features generated by the tool are only for the training set, this is not very useful, therefore omitting |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
166 todo change tool do export features complete dataset also when classification is performed --> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
167 <filter>mode["mode_type"] == "only_encoding"</filter> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
168 <discover_datasets directory="." pattern="(?P<designation>.*).h5" format="data" visible="false" /> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
169 </collection> |
0
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
170 </outputs> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
171 <tests> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
172 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
173 <!-- only encoding --> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
174 <!-- test one parameter sets --> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
175 |
2
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
176 <test expect_num_outputs="2"> |
0
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
177 <param name="mode_type" value="only_encoding" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
178 <param name="features" value="UserDataExample.csv" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
179 <param name="rl_type_choice" value="--ae" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
180 <param name="dm" value="40" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
181 <output_collection name="encoded_features" type="list"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
182 <!-- output is non determinisitc --> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
183 <element name="AE[40]_features" ftype="tabular" > |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
184 <assert_contents> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
185 <has_n_lines n="20"/> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
186 <!-- <has_n_columns n="40" sep="," /> --> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
187 </assert_contents> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
188 </element> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
189 </output_collection> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
190 </test> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
191 |
2
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
192 <test expect_num_outputs="2"> |
0
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
193 <param name="mode_type" value="only_encoding" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
194 <param name="features" value="UserDataExample.csv" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
195 <param name="rl_type_choice" value="--pca" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
196 <output_collection name="encoded_features" type="list"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
197 <element name="PCA_features" ftype="tabular" > |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
198 <assert_contents> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
199 <has_n_lines n="20"/> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
200 <!-- <has_n_columns n="40" sep="," /> --> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
201 </assert_contents> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
202 </element> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
203 </output_collection> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
204 </test> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
205 |
2
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
206 <!-- only encoding --> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
207 |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
208 <test expect_num_outputs="2"> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
209 <param name="mode_type" value="only_encoding" /> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
210 <param name="features" value="UserDataExample.csv" /> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
211 <param name="rl_type_choice" value="--ae" /> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
212 <param name="dm" value="40" /> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
213 |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
214 <output_collection name="encoded_features" type="list"> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
215 <!-- output is non determinisitc --> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
216 <element name="AE[40]_features" ftype="tabular" > |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
217 <assert_contents> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
218 <has_n_lines n="20"/> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
219 <!-- <has_n_columns n="40" sep="," /> --> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
220 </assert_contents> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
221 </element> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
222 </output_collection> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
223 </test> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
224 |
0
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
225 <!-- test multiple parameter sets --> |
2
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
226 <test expect_num_outputs="2"> |
0
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
227 <param name="features" value="UserDataExample.csv" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
228 <conditional name="mode"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
229 <param name="mode_type" value="only_encoding" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
230 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
231 <repeat name="parameter_set"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
232 <conditional name="rl_type"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
233 <param name="rl_type_choice" value="--pca" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
234 </conditional> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
235 </repeat> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
236 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
237 <repeat name="parameter_set"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
238 <conditional name="rl_type"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
239 <param name="rl_type_choice" value="--ae" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
240 <param name="dm" value="40" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
241 </conditional> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
242 </repeat> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
243 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
244 </conditional> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
245 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
246 <output_collection name="encoded_features" type="list"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
247 <element name="AE[40]_features" ftype="tabular" > |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
248 <assert_contents> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
249 <has_n_lines n="20"/> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
250 <!-- <has_n_columns n="40" sep="," /> --> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
251 </assert_contents> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
252 </element> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
253 <element name="PCA_features" ftype="tabular" > |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
254 <assert_contents> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
255 <has_n_lines n="20"/> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
256 <!-- <has_n_columns n="40" sep="," /> --> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
257 </assert_contents> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
258 </element> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
259 </output_collection> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
260 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
261 </test> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
262 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
263 <!-- encoding and clf --> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
264 <!-- test one parameter set --> |
2
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
265 <!-- test additional parameters scoring / folds and repeat --> |
0
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
266 <test expect_num_outputs="1"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
267 <param name="features" value="UserDataExample.csv" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
268 <param name="mode_type" value="e_and_c" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
269 <param name="class_labels" value="UserLabelExample.csv" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
270 <param name="rl_type_choice" value="--vae" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
271 <param name="dm" value="40" /> |
2
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
272 <param name="scoring" value="roc_auc" /> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
273 <param name="folds" value="2" /> |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
274 <param name="repeat" value="2" /> |
0
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
275 <param name="classifier" value="rf" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
276 <output ftype="tabular" name="results" > |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
277 <assert_contents> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
278 <has_text text="VAE[40]_rf" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
279 </assert_contents> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
280 </output> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
281 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
282 </test> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
283 |
2
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
284 |
2d20b3a1babd
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 574cb8c241e18a15f006bf307235c7dd23f07c69
iuc
parents:
1
diff
changeset
|
285 <!-- no rl --> |
1
c58c1a99578b
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 19cd7fd52900e23704975869cd66d5f7b219ae3e
iuc
parents:
0
diff
changeset
|
286 <test expect_num_outputs="1"> |
c58c1a99578b
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 19cd7fd52900e23704975869cd66d5f7b219ae3e
iuc
parents:
0
diff
changeset
|
287 <param name="features" value="UserDataExample.csv" /> |
c58c1a99578b
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 19cd7fd52900e23704975869cd66d5f7b219ae3e
iuc
parents:
0
diff
changeset
|
288 <param name="mode_type" value="e_and_c" /> |
c58c1a99578b
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 19cd7fd52900e23704975869cd66d5f7b219ae3e
iuc
parents:
0
diff
changeset
|
289 <param name="class_labels" value="UserLabelExample.csv" /> |
c58c1a99578b
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 19cd7fd52900e23704975869cd66d5f7b219ae3e
iuc
parents:
0
diff
changeset
|
290 <param name="rl_type_choice" value="no_rl" /> |
c58c1a99578b
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 19cd7fd52900e23704975869cd66d5f7b219ae3e
iuc
parents:
0
diff
changeset
|
291 <param name="classifier" value="rf" /> |
c58c1a99578b
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 19cd7fd52900e23704975869cd66d5f7b219ae3e
iuc
parents:
0
diff
changeset
|
292 <output ftype="tabular" name="results" > |
c58c1a99578b
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 19cd7fd52900e23704975869cd66d5f7b219ae3e
iuc
parents:
0
diff
changeset
|
293 <assert_contents> |
c58c1a99578b
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 19cd7fd52900e23704975869cd66d5f7b219ae3e
iuc
parents:
0
diff
changeset
|
294 <has_text text="rf" /> |
c58c1a99578b
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 19cd7fd52900e23704975869cd66d5f7b219ae3e
iuc
parents:
0
diff
changeset
|
295 </assert_contents> |
c58c1a99578b
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 19cd7fd52900e23704975869cd66d5f7b219ae3e
iuc
parents:
0
diff
changeset
|
296 </output> |
c58c1a99578b
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 19cd7fd52900e23704975869cd66d5f7b219ae3e
iuc
parents:
0
diff
changeset
|
297 |
c58c1a99578b
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 19cd7fd52900e23704975869cd66d5f7b219ae3e
iuc
parents:
0
diff
changeset
|
298 </test> |
c58c1a99578b
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 19cd7fd52900e23704975869cd66d5f7b219ae3e
iuc
parents:
0
diff
changeset
|
299 |
0
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
300 <!-- test multiple parameter sets --> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
301 <test expect_num_outputs="1"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
302 <param name="features" value="UserDataExample.csv" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
303 <conditional name="mode"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
304 <param name="mode_type" value="e_and_c" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
305 <param name="class_labels" value="UserLabelExample.csv" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
306 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
307 <repeat name="parameter_set"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
308 <conditional name="rl_type"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
309 <param name="rl_type_choice" value="--cae" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
310 <param name="dm" value="20" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
311 <param name="classifier" value="rf" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
312 </conditional> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
313 </repeat> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
314 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
315 <repeat name="parameter_set"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
316 <conditional name="rl_type"> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
317 <param name="rl_type_choice" value="--vae" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
318 <param name="dm" value="40" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
319 <param name="classifier" value="mlp" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
320 </conditional> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
321 </repeat> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
322 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
323 </conditional> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
324 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
325 <output ftype="tabular" name="results" > |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
326 <assert_contents> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
327 <has_text text="CAE[20]_rf" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
328 <has_text text="VAE[40]_mlp" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
329 </assert_contents> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
330 </output> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
331 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
332 </test> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
333 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
334 </tests> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
335 <help> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
336 <![CDATA[ |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
337 DeepMicro is a deep representation learning framework exploiting various autoencoders |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
338 to learn robust low-dimensional representations from high-dimensional data and training |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
339 classification models based on the learned representation. |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
340 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
341 ====================================== |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
342 Option 1) Only representation learning |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
343 ====================================== |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
344 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
345 The representation learning does not require class labels and can be learned from the features alone. |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
346 The wrapper allows to explore multiple paramertes (i.e. different modes to |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
347 generate the features, please refer to the publication for details), for each |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
348 added parameter the encoded features are generated. Those features can then be passed to subsequent ML tools, |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
349 such as `Ensemble methods for classification and regression` or `Split Dataset into training and test subsets` |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
350 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
351 ===================================================== |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
352 Option 2) Representation learning and classification |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
353 ===================================================== |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
354 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
355 The tool itself can also evaluate the performance of the generated representation learning for different |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
356 classifiers internally using 5 fold CV. The wrapper allows to explore multiple paramertes and clfs. |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
357 Each parameter run will be stored as a line to the result file. If this option is chosen the latent representation is not |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
358 exported as output. To create the latent representation of the complete feature set, run the tool again |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
359 with the same parameters using the `Only representation learning` option. |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
360 The header of the result file is: |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
361 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
362 '{Encoding}_{classifier}, AUC, ACC, Recall, Precision, F1_score, time-end, runtime(sec), classfication time(sec), best hyper-parameter' |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
363 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
364 The overall schema of the tool is shown in: |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
365 |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
366 .. image:: ML_Workflow.png |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
367 ]]> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
368 </help> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
369 <expand macro="citations" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
370 <expand macro="creator" /> |
77cbfe3e1b0d
planemo upload for repository https://github.com/paulzierep/DeepMicro commit 1bbea291a9d77beafaeba83ab775d870ec24719e
iuc
parents:
diff
changeset
|
371 </tool> |