Mercurial > repos > tduigou > icfree_instructor

annotate instructor.xml @ 4:fba5810f3946 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/brsynth/icfree-ml commit 79b4751f34792a1a346ada38f7b6f64571dd51e9
author tduigou
date Thu, 09 Mar 2023 16:47:34 +0000
parents 444a90deafa9
children 190889521a9e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
1 <tool id="icfree_instructor" name="iCFree instructor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@">
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
2 <description>Generates a list of Echo-compatible instructions to prepare samples</description>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
3 <macros>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
4 <import>macros.xml</import>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
5 </macros>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
6 <expand macro="requirements"/>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
7 <expand macro="stdio"/>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
9 #if str($conditional_source_json.type) == "collection":
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
10 #for $input in $conditional_source_json.collection.keys():
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
11 ln -sfn $conditional_source_json.collection[$input] '.' &&
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
12 #end for
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
13 #set input_source_json = '" "'.join([str($file) for $file in $conditional_source_json.collection[$input]])
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
14 #elif str($conditional_source_json.type) == "files":
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
15 #set input_source_json = '" "'.join([str($file) for $file in $conditional_source_json.files])
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
16 #end if
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
17
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
18 #if str($conditional_source_tsv.type) == "collection":
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
19 #for $input in $conditional_source_tsv.collection.keys():
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
20 ln -sfn $conditional_source_tsv.collection[$input] '.' &&
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
21 #end for
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
22 #set input_source_tsv = '" "'.join([str($file) for $file in $conditional_source_tsv.collection[$input]])
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
23 #elif str($conditional_source_tsv.type) == "files":
4
fba5810f3946 planemo upload for repository https://github.com/brsynth/icfree-ml commit 79b4751f34792a1a346ada38f7b6f64571dd51e9
tduigou
parents: 1
diff changeset
24 #set inputs_source_tsv = []
0
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
25 #for $f in $conditional_source_tsv.files
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
26 ln -sfn '$f' '$f.element_identifier' &&
4
fba5810f3946 planemo upload for repository https://github.com/brsynth/icfree-ml commit 79b4751f34792a1a346ada38f7b6f64571dd51e9
tduigou
parents: 1
diff changeset
27 #silent inputs_source_tsv.append(str($f.element_identifier))
0
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
28 #end for
4
fba5810f3946 planemo upload for repository https://github.com/brsynth/icfree-ml commit 79b4751f34792a1a346ada38f7b6f64571dd51e9
tduigou
parents: 1
diff changeset
29 #set input_source_tsv = '" "'.join(inputs_source_tsv)
0
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
30 #end if
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
31
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
32 #if str($conditional_destination_json.type) == "collection":
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
33 #for $input in $conditional_destination_json.collection.keys():
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
34 ln -sfn $conditional_destination_json.collection[$input] '.' &&
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
35 #end for
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
36 #set input_destination_json = '" "'.join([str($file) for $file in $conditional_destination_json.collection[$input]])
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
37 #elif str($conditional_destination_json.type) == "files":
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
38 #set input_destination_json = '" "'.join([str($file) for $file in $conditional_destination_json.files])
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
39 #end if
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
40
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
41 #if str($conditional_destination_tsv.type) == "collection":
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
42 #for $input in $conditional_destination_tsv.collection.keys():
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
43 ln -sfn $conditional_destination_tsv.collection[$input] '.' &&
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
44 #end for
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
45 #set input_destination_tsv = '" "'.join([str($file) for $file in $conditional_destination_tsv.collection[$input]])
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
46 #elif str($conditional_destination_tsv.type) == "files":
4
fba5810f3946 planemo upload for repository https://github.com/brsynth/icfree-ml commit 79b4751f34792a1a346ada38f7b6f64571dd51e9
tduigou
parents: 1
diff changeset
47 #set inputs_destination_tsv = []
0
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
48 #for $f in $conditional_destination_tsv.files
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
49 ln -sfn '$f' '$f.element_identifier' &&
4
fba5810f3946 planemo upload for repository https://github.com/brsynth/icfree-ml commit 79b4751f34792a1a346ada38f7b6f64571dd51e9
tduigou
parents: 1
diff changeset
50 #silent inputs_destination_tsv.append(str($f.element_identifier))
0
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
51 #end for
4
fba5810f3946 planemo upload for repository https://github.com/brsynth/icfree-ml commit 79b4751f34792a1a346ada38f7b6f64571dd51e9
tduigou
parents: 1
diff changeset
52 #set input_destination_tsv = '" "'.join(inputs_destination_tsv)
0
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
53 #end if
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
54
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
55 python -m icfree.instructor
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
56 --source_plates "${input_source_json}"
4
fba5810f3946 planemo upload for repository https://github.com/brsynth/icfree-ml commit 79b4751f34792a1a346ada38f7b6f64571dd51e9
tduigou
parents: 1
diff changeset
57 --source_wells "${input_source_tsv}"
0
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
58 --dest_plates "${input_destination_json}"
4
fba5810f3946 planemo upload for repository https://github.com/brsynth/icfree-ml commit 79b4751f34792a1a346ada38f7b6f64571dd51e9
tduigou
parents: 1
diff changeset
59 --dest_wells "${input_destination_tsv}"
0
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
60 --robot '$adv.robot'
4
fba5810f3946 planemo upload for repository https://github.com/brsynth/icfree-ml commit 79b4751f34792a1a346ada38f7b6f64571dd51e9
tduigou
parents: 1
diff changeset
61 --output-folder '.' &&
fba5810f3946 planemo upload for repository https://github.com/brsynth/icfree-ml commit 79b4751f34792a1a346ada38f7b6f64571dd51e9
tduigou
parents: 1
diff changeset
62 mv volumes_warnings.tsv '$output_warning' &&
fba5810f3946 planemo upload for repository https://github.com/brsynth/icfree-ml commit 79b4751f34792a1a346ada38f7b6f64571dd51e9
tduigou
parents: 1
diff changeset
63 mv instructions.csv '$output_instruction'
0
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
64 ]]></command>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
65 <inputs>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
66 <conditional name="conditional_source_json">
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
67 <param name="type" type="select" label="Source plate (json)">
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
68 <option value="files" selected="True">File(s)</option>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
69 <option value="collection">Collection</option>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
70 </param>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
71 <when value="files">
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
72 <param name="files" type="data" format="json" multiple="true" label="Source plates information (json)" />
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
73 </when>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
74 <when value="collection">
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
75 <param name="collection" type="data_collection" collection_type="list" format="json" label="Source plates information (json)" />
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
76 </when>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
77 </conditional>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
78 <conditional name="conditional_source_tsv">
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
79 <param name="type" type="select" label="Source plate (tsv)">
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
80 <option value="files" selected="True">File(s)</option>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
81 <option value="collection">Collection</option>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
82 </param>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
83 <when value="files">
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
84 <param name="files" type="data" format="tabular" multiple="true" label="Source plates information (tsv)" />
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
85 </when>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
86 <when value="collection">
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
87 <param name="collection" type="data_collection" collection_type="list" format="tabular" label="Source plates information (tsv)" />
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
88 </when>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
89 </conditional>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
90 <conditional name="conditional_destination_json">
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
91 <param name="type" type="select" label="Source plate (json)">
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
92 <option value="files" selected="True">File(s)</option>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
93 <option value="collection">Collection</option>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
94 </param>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
95 <when value="files">
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
96 <param name="files" type="data" format="json" multiple="true" label="Destination plates information (json)" />
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
97 </when>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
98 <when value="collection">
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
99 <param name="collection" type="data_collection" collection_type="list" format="json" label="Destination plates information (json)" />
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
100 </when>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
101 </conditional>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
102 <conditional name="conditional_destination_tsv">
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
103 <param name="type" type="select" label="Source plate (tsv)">
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
104 <option value="files" selected="True">File(s)</option>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
105 <option value="collection">Collection</option>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
106 </param>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
107 <when value="files">
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
108 <param name="files" type="data" format="tabular" multiple="true" label="Destination plates information (tsv)" />
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
109 </when>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
110 <when value="collection">
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
111 <param name="collection" type="data_collection" collection_type="list" format="tabular" label="Destination plates information (tsv)" />
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
112 </when>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
113 </conditional>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
114 <section name="adv" title="Advanced Options" expanded="false">
1
444a90deafa9 planemo upload for repository https://github.com/brsynth/icfree-ml commit 13e7cacbe8d65c6e798625de6bba986e89def461
tduigou
parents: 0
diff changeset
115 <param name="robot" type="text" value="echo" label="Robot name">
444a90deafa9 planemo upload for repository https://github.com/brsynth/icfree-ml commit 13e7cacbe8d65c6e798625de6bba986e89def461
tduigou
parents: 0
diff changeset
116 <validator type="empty_field" message="Not empty"/>
444a90deafa9 planemo upload for repository https://github.com/brsynth/icfree-ml commit 13e7cacbe8d65c6e798625de6bba986e89def461
tduigou
parents: 0
diff changeset
117 </param>
0
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
118 </section>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
119 </inputs>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
120 <outputs>
4
fba5810f3946 planemo upload for repository https://github.com/brsynth/icfree-ml commit 79b4751f34792a1a346ada38f7b6f64571dd51e9
tduigou
parents: 1
diff changeset
121 <data name="output_warning" format="tabular" label="${tool.name} - Warning" />
fba5810f3946 planemo upload for repository https://github.com/brsynth/icfree-ml commit 79b4751f34792a1a346ada38f7b6f64571dd51e9
tduigou
parents: 1
diff changeset
122 <data name="output_instruction" format="csv" label="${tool.name} - Instruction" />
0
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
123 </outputs>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
124 <tests>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
125 <test>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
126 <!-- test 1: check if identical outputs are produced with default parameters -->
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
127 <conditional name="conditional_source_json">
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
128 <param name="type" value="files"/>
4
fba5810f3946 planemo upload for repository https://github.com/brsynth/icfree-ml commit 79b4751f34792a1a346ada38f7b6f64571dd51e9
tduigou
parents: 1
diff changeset
129 <param name="files" value="plates_generator_source_plate_1.test-1.json" />
0
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
130 </conditional>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
131 <conditional name="conditional_source_tsv">
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
132 <param name="type" value="files"/>
4
fba5810f3946 planemo upload for repository https://github.com/brsynth/icfree-ml commit 79b4751f34792a1a346ada38f7b6f64571dd51e9
tduigou
parents: 1
diff changeset
133 <param name="files" value="plates_generator_source_plate_1.test-1.tsv" />
0
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
134 </conditional>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
135 <conditional name="conditional_destination_json">
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
136 <param name="type" value="files"/>
4
fba5810f3946 planemo upload for repository https://github.com/brsynth/icfree-ml commit 79b4751f34792a1a346ada38f7b6f64571dd51e9
tduigou
parents: 1
diff changeset
137 <param name="files" value="plates_generator_destination_plate_1.test-1.json" />
0
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
138 </conditional>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
139 <conditional name="conditional_destination_tsv">
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
140 <param name="type" value="files"/>
4
fba5810f3946 planemo upload for repository https://github.com/brsynth/icfree-ml commit 79b4751f34792a1a346ada38f7b6f64571dd51e9
tduigou
parents: 1
diff changeset
141 <param name="files" value="plates_generator_destination_plate_1.test-1.tsv" />
0
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
142 </conditional>
4
fba5810f3946 planemo upload for repository https://github.com/brsynth/icfree-ml commit 79b4751f34792a1a346ada38f7b6f64571dd51e9
tduigou
parents: 1
diff changeset
143 <output name="output_warning" ftype="tabular">
fba5810f3946 planemo upload for repository https://github.com/brsynth/icfree-ml commit 79b4751f34792a1a346ada38f7b6f64571dd51e9
tduigou
parents: 1
diff changeset
144 <assert_contents>
fba5810f3946 planemo upload for repository https://github.com/brsynth/icfree-ml commit 79b4751f34792a1a346ada38f7b6f64571dd51e9
tduigou
parents: 1
diff changeset
145 <has_n_lines n="12"/>
fba5810f3946 planemo upload for repository https://github.com/brsynth/icfree-ml commit 79b4751f34792a1a346ada38f7b6f64571dd51e9
tduigou
parents: 1
diff changeset
146 <has_line_matching expression="^Parameter\tMin\tMax\tPlate$"/>
fba5810f3946 planemo upload for repository https://github.com/brsynth/icfree-ml commit 79b4751f34792a1a346ada38f7b6f64571dd51e9
tduigou
parents: 1
diff changeset
147 </assert_contents>
0
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
148 </output>
4
fba5810f3946 planemo upload for repository https://github.com/brsynth/icfree-ml commit 79b4751f34792a1a346ada38f7b6f64571dd51e9
tduigou
parents: 1
diff changeset
149 <output name="output_instruction" file="instructor_instructions.csv" ftype="csv" compare="diff" />
0
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
150 </test>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
151 </tests>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
152 <help><![CDATA[
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
153 Instructor
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
154 ==========
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
155
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
156 The module generates a list of instructions to perform the experiment.
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
157
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
158 Input
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
159 -----
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
160 Required:
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
161 * **Source plates file**: description of the source plates (source well name, source well volume...) (JSON format)
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
162 * **Destination plates file**: description of the destination plates (destination well name, destination well volume...) (JSON format)
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
163
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
164 Advanced options:
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
165 -----------------
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
166 * **Robot name**: name of the robot to generate instructions for (default: "echo")
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
167
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
168 Output
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
169 ------
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
170 * **instructions**: contains the instructions to perform the experiment
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
171 * **volumes_warning**: contains the volumes that may cause issues with the chosen robot
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
172 ]]></help>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
173 <expand macro="creator"/>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
174 <expand macro="citation"/>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
diff changeset
175 </tool>