Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Updating icfree from version 2.1.2 to 2.4.0 #170

Closed
wants to merge 9 commits into from
Closed

Updating icfree from version 2.1.2 to 2.4.0 #170

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
fbc56d9
Updating icfree from version 2.1.2 to 2.1.3
guillaume-gricourt Dec 18, 2023
c6781dd
Updating icfree from version 2.1.3 to 2.2.0
guillaume-gricourt Dec 25, 2023
be333db
fix(tools): icfree, test file
guillaume-gricourt Feb 14, 2024
0a6f746
fix(tools): icfree, update tests
guillaume-gricourt Feb 14, 2024
3f38e8d
fix(tools): icfree, update test
guillaume-gricourt Feb 14, 2024
215422f
fix(tools): icfree, instructor test files
guillaume-gricourt Feb 14, 2024
994d236
fix(tools): icfree, update test
guillaume-gricourt Feb 14, 2024
28b1e0b
Updating icfree from version 2.2.0 to 2.3.3
guillaume-gricourt Jul 15, 2024
6c27bd6
Updating icfree from version 2.3.3 to 2.4.0
guillaume-gricourt Jul 22, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
13 changes: 3 additions & 10 deletions tools/icfree/converter.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -26,16 +26,9 @@
<tests>
<!-- test 1: check if identical outputs are produced with default parameters -->
<test>
<param name="cfps_file" value="converter_proCFPS_parameters.tsv" />
<param name="concentrations_file" value="converter_sampling_concentrations.tsv" />
<output name="output_sampling" file="converter_sampling_volumes.test-1.tsv" ftype="tabular" compare="diff" />
</test>
<!-- test 2: advanced options -->
<test>
<param name="cfps_file" value="converter_proCFPS_parameters.tsv" />
<param name="concentrations_file" value="converter_sampling_concentrations.tsv" />
<param name="sample_volume" value="100" />
<output name="output_sampling" file="converter_sampling_volumes.test-2.tsv" ftype="tabular" compare="diff" />
<param name="cfps_file" value="converter/input/parameters.tsv" />
<param name="concentrations_file" value="converter/input/sampling_concentrations.tsv" />
<output name="output_sampling" file="converter/output/sampling_volumes.tsv" ftype="tabular" compare="diff" />
</test>
</tests>
<help><![CDATA[
Expand Down
9 changes: 4 additions & 5 deletions tools/icfree/instructor.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -61,15 +61,14 @@
<!-- test 1: check if identical outputs are produced with default parameters -->
<param name="plates_generator">
<collection type="list">
<element name="source_plate_1.json" value="plates_generator_source_plate_1.test-1.json" />
<element name="source_plate_1.tsv" value="plates_generator_source_plate_1.test-1.tsv" />
<element name="destination_plate_1.json" value="plates_generator_destination_plate_1.test-1.json" />
<element name="destination_plate_1.tsv" value="plates_generator_destination_plate_1.test-1.tsv" />
<element name="source_plate_1.json" value="plates_generator/output/source_plate_1.json" />
<element name="source_plate_1.tsv" value="plates_generator/output/source_plate_1.tsv" />
<element name="destination_plate_1.json" value="plates_generator/output/destination_plate_1.json" />
<element name="destination_plate_1.tsv" value="plates_generator/output/destination_plate_1.tsv" />
</collection>
</param>
<output name="output_warning" ftype="tabular">
<assert_contents>
<has_n_lines n="12"/>
<has_line_matching expression="^Parameter\tMin\tMax\tPlate$"/>
</assert_contents>
</output>
Expand Down
2 changes: 1 addition & 1 deletion tools/icfree/macros.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<macros>
<token name="@TOOL_VERSION@">2.1.2</token>
<token name="@TOOL_VERSION@">2.4.0</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@LICENSE@">MIT</token>
<xml name="requirements">
Expand Down
37 changes: 8 additions & 29 deletions tools/icfree/plates_generator.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@
<validator type="regex" message="Some letters followed by a number">^(?:[A-K]{1}([1-9]|1[0-2]))$</validator>
</param>

<param name="nplicate" type="integer" value="3" min="1" max="12" label="Numbers of copies of volume sets"/>
<param name="nplicate" type="integer" value="1" min="1" max="12" label="Numbers of copies of volume sets"/>
<param name="keep_nil_vol" type="boolean" truevalue="True" falsevalue="False" checked="true" display="checkboxes" label="Keep nil volumes in instructions or not"/>

<param name="source_plate_well_capacity" type="integer" value="60000" label="Maximum volume capacity of the source plate in nL" />
Expand Down Expand Up @@ -79,43 +79,22 @@
<tests>
<!-- test 1: check if identical outputs are produced with default parameters -->
<test>
<param name="cfps_file" value="converter_proCFPS_parameters.tsv" />
<param name="volume_file" value="converter_sampling_concentrations.tsv" />
<output name="volumes_summary" file="plates_generator_volumes_summary.test-1.tsv" ftype="tabular" compare="diff" />
<param name="cfps_file" value="plates_generator/input/parameters.tsv" />
<param name="volume_file" value="plates_generator/input/sampling.tsv" />
<output name="volumes_summary" file="plates_generator/output/volumes_summary.tsv" ftype="tabular" compare="diff" />
<output_collection name="output_source_dest" type="list" count="4">
<element name="source_plate_1.json" ftype="json">
<assert_contents>
<has_n_lines n="26"/>
<has_n_lines n="18"/>
</assert_contents>
</element>
<element name="source_plate_1.tsv" file="plates_generator_source_plate_1.test-1.tsv" ftype="tabular" compare="diff" />
<element name="source_plate_1.tsv" file="plates_generator/output/source_plate_1.tsv" ftype="tabular" compare="diff" />
<element name="destination_plate_1.json" ftype="json">
<assert_contents>
<has_n_lines n="26"/>
<has_n_lines n="18"/>
</assert_contents>
</element>
<element name="destination_plate_1.tsv" file="plates_generator_destination_plate_1.test-1.tsv" ftype="tabular" compare="diff" />
</output_collection>
</test>
<!-- test 2: advance arguments -->
<test>
<param name="cfps_file" value="converter_proCFPS_parameters.tsv" />
<param name="volume_file" value="converter_sampling_concentrations.tsv" />
<param name="source_plate_dead_volume" value="1500" />
<param name="dest_plate_dead_volume" value="1000" />
<param name="dest_starting_well" value="C3" />
<param name="src_starting_well" value="A2" />
<param name="nplicate" value="2" />
<param name="keep_nil_vol" value="False" />
<param name="plate_dimensions" value="32x32" />
<repeat name="rep">
<param name="optimize_well_volumes" value="RBS" />
</repeat>
<repeat name="rep">
<param name="optimize_well_volumes" value="Promoter" />
</repeat>
<output_collection name="output_source_dest" type="list" count="4">
<element name="destination_plate_1.tsv" file="plates_generator_destination_plate_1.test-2.tsv" ftype="tabular" compare="diff" />
<element name="destination_plate_1.tsv" file="plates_generator/output/destination_plate_1.tsv" ftype="tabular" compare="diff" />
</output_collection>
</test>
</tests>
Expand Down
8 changes: 8 additions & 0 deletions tools/icfree/test-data/converter/input/parameters.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
Component maxValue stockConcentration deadVolume Ratios
Component_1 4 168 0 0.0 0.1 0.3 0.5 1.0
Component_2 80 3360 0
Component_3 0.26 210 0 1
Component_4 30 1400 0
Component_5 1.5 630 0
Component_6 0.33 138.6 0
Component_7 0.068 28.56 0
101 changes: 101 additions & 0 deletions tools/icfree/test-data/converter/input/sampling_concentrations.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,101 @@
Component_1 Component_2 Component_3 Component_4 Component_5 Component_6 Component_7
2.0 0.0 0.26 0.0 1.125 0.2475 0.017
2.0 0.0 0.26 15.0 0.0 0.33 0.017
0.0 0.0 0.26 0.0 0.0 0.165 0.034
4.0 20.0 0.26 22.5 0.375 0.0825 0.017
1.2 20.0 0.26 15.0 1.125 0.165 0.068
0.0 40.0 0.26 15.0 0.375 0.33 0.034
0.0 20.0 0.26 15.0 1.5 0.0825 0.0
1.2 40.0 0.26 7.5 0.375 0.0 0.0
0.0 40.0 0.26 30.0 0.375 0.0825 0.0
1.2 80.0 0.26 15.0 0.375 0.0 0.051000000000000004
0.4 40.0 0.26 0.0 0.75 0.0 0.034
4.0 80.0 0.26 0.0 1.5 0.165 0.051000000000000004
0.0 60.0 0.26 30.0 1.125 0.2475 0.051000000000000004
0.4 40.0 0.26 0.0 0.75 0.2475 0.068
2.0 0.0 0.26 30.0 0.0 0.2475 0.068
0.4 60.0 0.26 7.5 1.125 0.0825 0.068
2.0 60.0 0.26 30.0 1.125 0.165 0.068
0.0 60.0 0.26 22.5 1.5 0.0825 0.051000000000000004
0.4 40.0 0.26 22.5 1.5 0.165 0.0
0.0 80.0 0.26 22.5 0.375 0.0 0.068
4.0 60.0 0.26 15.0 1.125 0.33 0.0
1.2 60.0 0.26 30.0 1.5 0.0 0.017
2.0 60.0 0.26 7.5 0.0 0.2475 0.034
4.0 80.0 0.26 7.5 1.125 0.2475 0.051000000000000004
0.0 60.0 0.26 30.0 0.75 0.165 0.051000000000000004
4.0 0.0 0.26 7.5 0.375 0.165 0.017
2.0 20.0 0.26 22.5 0.375 0.0825 0.068
0.4 60.0 0.26 0.0 1.5 0.2475 0.068
2.0 80.0 0.26 30.0 1.5 0.0825 0.034
4.0 40.0 0.26 7.5 1.125 0.165 0.017
1.2 60.0 0.26 22.5 1.125 0.0 0.051000000000000004
4.0 20.0 0.26 15.0 1.5 0.0 0.0
2.0 20.0 0.26 0.0 0.0 0.33 0.034
0.4 60.0 0.26 30.0 0.0 0.165 0.051000000000000004
0.0 40.0 0.26 0.0 0.375 0.165 0.051000000000000004
4.0 0.0 0.26 15.0 1.125 0.0 0.051000000000000004
2.0 80.0 0.26 22.5 1.125 0.165 0.068
2.0 20.0 0.26 30.0 0.75 0.2475 0.051000000000000004
4.0 20.0 0.26 0.0 1.5 0.2475 0.034
1.2 0.0 0.26 30.0 1.5 0.2475 0.051000000000000004
0.4 20.0 0.26 30.0 0.375 0.33 0.0
0.0 60.0 0.26 22.5 0.0 0.0 0.034
0.4 80.0 0.26 7.5 1.5 0.165 0.034
4.0 0.0 0.26 22.5 1.125 0.33 0.034
4.0 0.0 0.26 22.5 0.75 0.33 0.034
1.2 60.0 0.26 22.5 0.0 0.33 0.051000000000000004
1.2 80.0 0.26 7.5 0.75 0.0825 0.017
0.0 40.0 0.26 7.5 0.0 0.2475 0.017
1.2 60.0 0.26 7.5 1.125 0.0825 0.068
4.0 60.0 0.26 30.0 0.375 0.165 0.0
0.4 0.0 0.26 15.0 1.125 0.0825 0.017
4.0 20.0 0.26 15.0 0.75 0.165 0.0
4.0 40.0 0.26 30.0 0.375 0.0 0.051000000000000004
1.2 0.0 0.26 0.0 1.125 0.33 0.017
2.0 0.0 0.26 22.5 1.5 0.0825 0.017
0.0 0.0 0.26 7.5 0.0 0.165 0.068
0.0 0.0 0.26 7.5 0.75 0.0825 0.068
1.2 40.0 0.26 15.0 0.75 0.0825 0.051000000000000004
1.2 80.0 0.26 0.0 1.125 0.2475 0.034
2.0 0.0 0.26 0.0 1.5 0.0825 0.051000000000000004
0.4 80.0 0.26 22.5 0.375 0.0825 0.017
0.0 80.0 0.26 7.5 0.0 0.33 0.017
2.0 80.0 0.26 15.0 0.375 0.165 0.068
2.0 20.0 0.26 22.5 0.75 0.0 0.051000000000000004
4.0 40.0 0.26 7.5 0.0 0.165 0.068
0.0 40.0 0.26 22.5 1.125 0.2475 0.017
1.2 80.0 0.26 15.0 0.75 0.0 0.051000000000000004
4.0 40.0 0.26 22.5 1.5 0.0825 0.034
0.4 80.0 0.26 0.0 0.75 0.0 0.017
4.0 60.0 0.26 15.0 0.0 0.165 0.068
0.4 80.0 0.26 30.0 1.125 0.165 0.0
1.2 60.0 0.26 30.0 0.0 0.2475 0.034
0.4 0.0 0.26 15.0 0.375 0.2475 0.0
1.2 20.0 0.26 22.5 0.0 0.0 0.017
0.4 60.0 0.26 0.0 0.0 0.33 0.034
0.4 60.0 0.26 7.5 0.375 0.33 0.017
2.0 40.0 0.26 30.0 0.375 0.0 0.017
1.2 40.0 0.26 7.5 1.5 0.0825 0.0
0.0 40.0 0.26 0.0 1.5 0.2475 0.0
4.0 0.0 0.26 15.0 1.5 0.2475 0.0
0.4 20.0 0.26 15.0 1.5 0.33 0.051000000000000004
2.0 80.0 0.26 7.5 0.75 0.0825 0.0
2.0 80.0 0.26 0.0 0.0 0.0 0.0
2.0 20.0 0.26 30.0 1.5 0.0 0.034
0.0 40.0 0.26 15.0 0.75 0.33 0.034
0.0 0.0 0.26 22.5 0.75 0.0 0.068
0.4 20.0 0.26 30.0 0.75 0.0825 0.0
2.0 20.0 0.26 22.5 0.375 0.165 0.034
4.0 40.0 0.26 0.0 1.125 0.2475 0.017
0.4 80.0 0.26 15.0 0.375 0.33 0.068
2.0 20.0 0.26 22.5 1.5 0.0 0.051000000000000004
1.2 40.0 0.26 0.0 0.75 0.0825 0.068
0.0 80.0 0.26 7.5 0.75 0.33 0.0
4.0 80.0 0.26 15.0 1.125 0.33 0.068
1.2 20.0 0.26 0.0 0.75 0.2475 0.034
1.2 0.0 0.26 7.5 0.0 0.33 0.017
0.0 0.0 0.26 7.5 0.75 0.33 0.034
0.4 20.0 0.26 0.0 0.0 0.33 0.0
1.2 60.0 0.26 30.0 0.375 0.0 0.068
0.4 20.0 0.26 30.0 0.0 0.2475 0.0
101 changes: 101 additions & 0 deletions tools/icfree/test-data/converter/output/sampling_volumes.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,101 @@
Component_1 Component_2 Component_3 Component_4 Component_5 Component_6 Component_7
12.5 0.0 2.5 0.0 2.5 2.5 0.0
12.5 0.0 2.5 10.0 0.0 2.5 0.0
0.0 0.0 2.5 0.0 0.0 0.0 0.0
25.0 5.0 2.5 15.0 0.0 0.0 0.0
7.5 5.0 2.5 10.0 2.5 0.0 2.5
0.0 12.5 2.5 10.0 0.0 2.5 0.0
0.0 5.0 2.5 10.0 2.5 0.0 0.0
7.5 12.5 2.5 5.0 0.0 0.0 0.0
0.0 12.5 2.5 22.5 0.0 0.0 0.0
7.5 25.0 2.5 10.0 0.0 0.0 2.5
2.5 12.5 2.5 0.0 0.0 0.0 0.0
25.0 25.0 2.5 0.0 2.5 0.0 2.5
0.0 17.5 2.5 22.5 2.5 2.5 2.5
2.5 12.5 2.5 0.0 0.0 2.5 2.5
12.5 0.0 2.5 22.5 0.0 2.5 2.5
2.5 17.5 2.5 5.0 2.5 0.0 2.5
12.5 17.5 2.5 22.5 2.5 0.0 2.5
0.0 17.5 2.5 15.0 2.5 0.0 2.5
2.5 12.5 2.5 15.0 2.5 0.0 0.0
0.0 25.0 2.5 15.0 0.0 0.0 2.5
25.0 17.5 2.5 10.0 2.5 2.5 0.0
7.5 17.5 2.5 22.5 2.5 0.0 0.0
12.5 17.5 2.5 5.0 0.0 2.5 0.0
25.0 25.0 2.5 5.0 2.5 2.5 2.5
0.0 17.5 2.5 22.5 0.0 0.0 2.5
25.0 0.0 2.5 5.0 0.0 0.0 0.0
12.5 5.0 2.5 15.0 0.0 0.0 2.5
2.5 17.5 2.5 0.0 2.5 2.5 2.5
12.5 25.0 2.5 22.5 2.5 0.0 0.0
25.0 12.5 2.5 5.0 2.5 0.0 0.0
7.5 17.5 2.5 15.0 2.5 0.0 2.5
25.0 5.0 2.5 10.0 2.5 0.0 0.0
12.5 5.0 2.5 0.0 0.0 2.5 0.0
2.5 17.5 2.5 22.5 0.0 0.0 2.5
0.0 12.5 2.5 0.0 0.0 0.0 2.5
25.0 0.0 2.5 10.0 2.5 0.0 2.5
12.5 25.0 2.5 15.0 2.5 0.0 2.5
12.5 5.0 2.5 22.5 0.0 2.5 2.5
25.0 5.0 2.5 0.0 2.5 2.5 0.0
7.5 0.0 2.5 22.5 2.5 2.5 2.5
2.5 5.0 2.5 22.5 0.0 2.5 0.0
0.0 17.5 2.5 15.0 0.0 0.0 0.0
2.5 25.0 2.5 5.0 2.5 0.0 0.0
25.0 0.0 2.5 15.0 2.5 2.5 0.0
25.0 0.0 2.5 15.0 0.0 2.5 0.0
7.5 17.5 2.5 15.0 0.0 2.5 2.5
7.5 25.0 2.5 5.0 0.0 0.0 0.0
0.0 12.5 2.5 5.0 0.0 2.5 0.0
7.5 17.5 2.5 5.0 2.5 0.0 2.5
25.0 17.5 2.5 22.5 0.0 0.0 0.0
2.5 0.0 2.5 10.0 2.5 0.0 0.0
25.0 5.0 2.5 10.0 0.0 0.0 0.0
25.0 12.5 2.5 22.5 0.0 0.0 2.5
7.5 0.0 2.5 0.0 2.5 2.5 0.0
12.5 0.0 2.5 15.0 2.5 0.0 0.0
0.0 0.0 2.5 5.0 0.0 0.0 2.5
0.0 0.0 2.5 5.0 0.0 0.0 2.5
7.5 12.5 2.5 10.0 0.0 0.0 2.5
7.5 25.0 2.5 0.0 2.5 2.5 0.0
12.5 0.0 2.5 0.0 2.5 0.0 2.5
2.5 25.0 2.5 15.0 0.0 0.0 0.0
0.0 25.0 2.5 5.0 0.0 2.5 0.0
12.5 25.0 2.5 10.0 0.0 0.0 2.5
12.5 5.0 2.5 15.0 0.0 0.0 2.5
25.0 12.5 2.5 5.0 0.0 0.0 2.5
0.0 12.5 2.5 15.0 2.5 2.5 0.0
7.5 25.0 2.5 10.0 0.0 0.0 2.5
25.0 12.5 2.5 15.0 2.5 0.0 0.0
2.5 25.0 2.5 0.0 0.0 0.0 0.0
25.0 17.5 2.5 10.0 0.0 0.0 2.5
2.5 25.0 2.5 22.5 2.5 0.0 0.0
7.5 17.5 2.5 22.5 0.0 2.5 0.0
2.5 0.0 2.5 10.0 0.0 2.5 0.0
7.5 5.0 2.5 15.0 0.0 0.0 0.0
2.5 17.5 2.5 0.0 0.0 2.5 0.0
2.5 17.5 2.5 5.0 0.0 2.5 0.0
12.5 12.5 2.5 22.5 0.0 0.0 0.0
7.5 12.5 2.5 5.0 2.5 0.0 0.0
0.0 12.5 2.5 0.0 2.5 2.5 0.0
25.0 0.0 2.5 10.0 2.5 2.5 0.0
2.5 5.0 2.5 10.0 2.5 2.5 2.5
12.5 25.0 2.5 5.0 0.0 0.0 0.0
12.5 25.0 2.5 0.0 0.0 0.0 0.0
12.5 5.0 2.5 22.5 2.5 0.0 0.0
0.0 12.5 2.5 10.0 0.0 2.5 0.0
0.0 0.0 2.5 15.0 0.0 0.0 2.5
2.5 5.0 2.5 22.5 0.0 0.0 0.0
12.5 5.0 2.5 15.0 0.0 0.0 0.0
25.0 12.5 2.5 0.0 2.5 2.5 0.0
2.5 25.0 2.5 10.0 0.0 2.5 2.5
12.5 5.0 2.5 15.0 2.5 0.0 2.5
7.5 12.5 2.5 0.0 0.0 0.0 2.5
0.0 25.0 2.5 5.0 0.0 2.5 0.0
25.0 25.0 2.5 10.0 2.5 2.5 2.5
7.5 5.0 2.5 0.0 0.0 2.5 0.0
7.5 0.0 2.5 5.0 0.0 2.5 0.0
0.0 0.0 2.5 5.0 0.0 2.5 0.0
2.5 5.0 2.5 0.0 0.0 2.5 0.0
7.5 17.5 2.5 22.5 0.0 0.0 2.5
2.5 5.0 2.5 22.5 0.0 2.5 0.0
17 changes: 0 additions & 17 deletions tools/icfree/test-data/converter_proCFPS_parameters.tsv
View file
Open in desktop

This file was deleted.

Loading
Loading