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comparison instructor.xml @ 0:f60f2f6ec0cc draft

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planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
author tduigou
date Mon, 06 Mar 2023 12:52:35 +0000
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children 444a90deafa9
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-1:000000000000 0:f60f2f6ec0cc
1 <tool id="icfree_instructor" name="iCFree instructor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@">
2 <description>Generates a list of Echo-compatible instructions to prepare samples</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <command detect_errors="exit_code"><![CDATA[
9 #if str($conditional_source_json.type) == "collection":
10 #for $input in $conditional_source_json.collection.keys():
11 ln -sfn $conditional_source_json.collection[$input] '.' &&
12 #end for
13 #set input_source_json = '" "'.join([str($file) for $file in $conditional_source_json.collection[$input]])
14 #elif str($conditional_source_json.type) == "files":
15 #set input_source_json = '" "'.join([str($file) for $file in $conditional_source_json.files])
16 #end if
17
18 #if str($conditional_source_tsv.type) == "collection":
19 #for $input in $conditional_source_tsv.collection.keys():
20 ln -sfn $conditional_source_tsv.collection[$input] '.' &&
21 #end for
22 #set input_source_tsv = '" "'.join([str($file) for $file in $conditional_source_tsv.collection[$input]])
23 #elif str($conditional_source_tsv.type) == "files":
24 #set input_source_tsv = []
25 #for $f in $conditional_source_tsv.files
26 ln -sfn '$f' '$f.element_identifier' &&
27 #silent input_source_tsv.append(str($f.element_identifier))
28 #end for
29 #set inputs_source_tsv = '" "'.join(input_source_tsv)
30 #end if
31
32
33 #if str($conditional_destination_json.type) == "collection":
34 #for $input in $conditional_destination_json.collection.keys():
35 ln -sfn $conditional_destination_json.collection[$input] '.' &&
36 #end for
37 #set input_destination_json = '" "'.join([str($file) for $file in $conditional_destination_json.collection[$input]])
38 #elif str($conditional_destination_json.type) == "files":
39 #set input_destination_json = '" "'.join([str($file) for $file in $conditional_destination_json.files])
40 #end if
41
42 #if str($conditional_destination_tsv.type) == "collection":
43 #for $input in $conditional_destination_tsv.collection.keys():
44 ln -sfn $conditional_destination_tsv.collection[$input] '.' &&
45 #end for
46 #set input_destination_tsv = '" "'.join([str($file) for $file in $conditional_destination_tsv.collection[$input]])
47 #elif str($conditional_destination_tsv.type) == "files":
48 #set input_destination_tsv = []
49 #for $f in $conditional_destination_tsv.files
50 ln -sfn '$f' '$f.element_identifier' &&
51 #silent input_destination_tsv.append(str($f.element_identifier))
52 #end for
53 #set inputs_destination_tsv = '" "'.join(input_destination_tsv)
54 #end if
55
56
57 python -m icfree.instructor
58 --source_plates "${input_source_json}"
59 --source_wells "${inputs_source_tsv}"
60 --dest_plates "${input_destination_json}"
61 --dest_wells "${inputs_destination_tsv}"
62 --robot '$adv.robot'
63 --output-folder out
64 ]]></command>
65 <inputs>
66 <conditional name="conditional_source_json">
67 <param name="type" type="select" label="Source plate (json)">
68 <option value="files" selected="True">File(s)</option>
69 <option value="collection">Collection</option>
70 </param>
71 <when value="files">
72 <param name="files" type="data" format="json" multiple="true" label="Source plates information (json)" />
73 </when>
74 <when value="collection">
75 <param name="collection" type="data_collection" collection_type="list" format="json" label="Source plates information (json)" />
76 </when>
77 </conditional>
78 <conditional name="conditional_source_tsv">
79 <param name="type" type="select" label="Source plate (tsv)">
80 <option value="files" selected="True">File(s)</option>
81 <option value="collection">Collection</option>
82 </param>
83 <when value="files">
84 <param name="files" type="data" format="tabular" multiple="true" label="Source plates information (tsv)" />
85 </when>
86 <when value="collection">
87 <param name="collection" type="data_collection" collection_type="list" format="tabular" label="Source plates information (tsv)" />
88 </when>
89 </conditional>
90 <conditional name="conditional_destination_json">
91 <param name="type" type="select" label="Source plate (json)">
92 <option value="files" selected="True">File(s)</option>
93 <option value="collection">Collection</option>
94 </param>
95 <when value="files">
96 <param name="files" type="data" format="json" multiple="true" label="Destination plates information (json)" />
97 </when>
98 <when value="collection">
99 <param name="collection" type="data_collection" collection_type="list" format="json" label="Destination plates information (json)" />
100 </when>
101 </conditional>
102 <conditional name="conditional_destination_tsv">
103 <param name="type" type="select" label="Source plate (tsv)">
104 <option value="files" selected="True">File(s)</option>
105 <option value="collection">Collection</option>
106 </param>
107 <when value="files">
108 <param name="files" type="data" format="tabular" multiple="true" label="Destination plates information (tsv)" />
109 </when>
110 <when value="collection">
111 <param name="collection" type="data_collection" collection_type="list" format="tabular" label="Destination plates information (tsv)" />
112 </when>
113 </conditional>
114 <section name="adv" title="Advanced Options" expanded="false">
115 <param argument="robot" type="text" value="echo" label="Robot name" />
116 </section>
117 </inputs>
118 <outputs>
119 <data name="tabulars" format="tabular">
120 <discover_datasets pattern="__designation__" ext="tabular" directory="out" />
121 </data>
122 </outputs>
123 <tests>
124 <test>
125 <!-- test 1: check if identical outputs are produced with default parameters -->
126 <conditional name="conditional_source_json">
127 <param name="type" value="files"/>
128 <param name="files" value="plates_generator_source_plate_1.json" />
129 </conditional>
130 <conditional name="conditional_source_tsv">
131 <param name="type" value="files"/>
132 <param name="files" value="plates_generator_source_plate_1.tsv" />
133 </conditional>
134 <conditional name="conditional_destination_json">
135 <param name="type" value="files"/>
136 <param name="files" value="plates_generator_destination_plate_1.json" />
137 </conditional>
138 <conditional name="conditional_destination_tsv">
139 <param name="type" value="files"/>
140 <param name="files" value="plates_generator_destination_plate_1.tsv" />
141 </conditional>
142 <output name="tabulars" ftype="tabular">
143 <discovered_dataset designation="volumes_warnings.tsv" ftype="tabular">
144 <assert_contents>
145 <has_n_lines n="12"/>
146 <has_line_matching expression="^Parameter\tMin\tMax\tPlate$"/>
147 </assert_contents>
148 </discovered_dataset>
149 <discovered_dataset designation="instructions.csv" ftype="tabular">
150 <assert_contents>
151 <has_line_matching expression="^Source Plate Name,Source Plate Type,Source Well,Destination Plate Name,Destination Well,Transfer Volume,Sample ID$"/>
152 <has_n_lines n="1701"/>
153 </assert_contents>
154
155 </discovered_dataset>
156 </output>
157 </test>
158 </tests>
159 <help><![CDATA[
160 Instructor
161 ==========
162
163 The module generates a list of instructions to perform the experiment.
164
165 Input
166 -----
167 Required:
168 * **Source plates file**: description of the source plates (source well name, source well volume...) (JSON format)
169 * **Destination plates file**: description of the destination plates (destination well name, destination well volume...) (JSON format)
170
171 Advanced options:
172 -----------------
173 * **Robot name**: name of the robot to generate instructions for (default: "echo")
174
175 Output
176 ------
177 * **instructions**: contains the instructions to perform the experiment
178 * **volumes_warning**: contains the volumes that may cause issues with the chosen robot
179 ]]></help>
180 <expand macro="creator"/>
181 <expand macro="citation"/>
182 </tool>