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Updating icfree from version 2.4.0 to 2.5.0 #196

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merged 12 commits into from
Dec 20, 2024
Merged

Updating icfree from version 2.4.0 to 2.5.0 #196

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d82c782
Updating icfree from version 2.4.0 to 2.5.0
guillaume-gricourt Sep 23, 2024
7fb98a6
feat(tools): icfree, update version
guillaume-gricourt Nov 14, 2024
89b2203
feat(tools): icfree, add `calibrator` wrapper
guillaume-gricourt Nov 14, 2024
366849f
Updating doe_synbio from version 2.5.0 to 2.5.1
guillaume-gricourt Nov 18, 2024
4995dee
feat(tools): `icfree`, update to 2.5.2
guillaume-gricourt Nov 22, 2024
87163fa
fix(tools): icfree, fix output name
guillaume-gricourt Nov 22, 2024
ba875cd
Updating doe_synbio from version 2.5.1 to 2.5.2
guillaume-gricourt Nov 25, 2024
8538ca1
feat(tools): icfree, update version and citation
guillaume-gricourt Dec 16, 2024
f4d6384
Merge branch 'brsynth-doe_synbio' of github.com:brsynth/galaxytools i…
guillaume-gricourt Dec 16, 2024
9ac6ff0
tests(tools): icfree, update
guillaume-gricourt Dec 17, 2024
8dde46b
feat(tools): icfree, update version
guillaume-gricourt Dec 20, 2024
e171d88
Merge branch 'main' into brsynth-icfree
guillaume-gricourt Dec 20, 2024
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120 changes: 120 additions & 0 deletions tools/icfree/calibrator.xml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,120 @@
<tool id="icfree_calibrator" name="iCFree calibrator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT">
<description>Calculate yield based on fluorescence data and optionally apply calibration</description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements"/>
<command detect_errors="exit_code"><![CDATA[
cp '$initial_data_file' 'initial_data.csv' &&
cp '$sampling_file' 'sampling.csv' &&
cp '$ref_file' 'reference.csv' &&
python -m icfree.learner.extractor
--initial_data_file 'initial_data.csv'
--sampling_file 'sampling.csv'
--output_file 'extractor.csv'
#if str($adv.num_samples) != ''
--num_samples '$adv.num_samples'
#end if
#if str($adv.num_replicates) != ''
--num_replicates '$adv.num_replicates'
#end if
&&
python -m icfree.learner.calibrator
--output 'calibrated.csv'
--plot '$output_graph'
--jove_plus '$jove_plus'
--jove_minus '$jove_minus'
--r2_limit '$adv.r2_limit'
#if str($adv.num_control_points) != ''
--num_control_points '$adv.num_control_points'
#end if
#if str($adv.num_samples) != ''
--num '$adv.num_samples'
#end if
'extractor.csv' 'reference.csv' &&
mv 'calibrated.csv' '$output_calibrated' &&
mv 'calibrated_control_points.csv' '$output_control_points'
]]></command>
<inputs>
<param name="initial_data_file" type="data" format="csv" label="Initial file" help="Initial file"/>
<param name="sampling_file" type="data" format="csv" label="Sampling file" help="Sampling file"/>
<param name="ref_file" type="data" format="csv" label="Reference input file" help="Reference input file"/>
<param argument="jove_plus" type="integer" value="3" label="Line number for Jove+ (1-based index)" help="Line number for Jove+ (1-based index)" />
<param argument="jove_minus" type="integer" value="2" label="Line number for Jove- (1-based index)" help="Line number for Jove- (1-based index)" />
<section name="adv" title="Advanced Options" expanded="false">
<param argument="num_samples" type="integer" optional="true" label="Number of samples" help="Number of samples" />
<!-- Extractor -->
<param argument="num_replicates" type="integer" optional="true" label="Number of replicates" help="Number of replicates." />
<!-- Calibrator -->
<param argument="r2_limit" type="float" value="0.8" label="R-squared limit for the regression" help="R-squared limit for the regression" />
<param argument="num_control_points" type="integer" optional="true" label="Number of control points to select" help="Number of control points to select" />
</section>
</inputs>
<outputs>
<data name="output_calibrated" format="csv" label="${tool.name} - Calibrated yields" />
<data name="output_control_points" format="csv" label="${tool.name} - Control points" />
<data name="output_graph" format="png" label="${tool.name} - Graph" />
</outputs>
<tests>
<test expect_num_outputs="3">
<!-- python -m icfree.learner.extractor -initial_data_file calibrator.input.initial_data.csv -sampling_file calibrator.input.sampling.csv -output_file calibrator.extractor_output.1.csv -->
<!-- python -m icfree.learner.calibrator -output calibrator.output.calibrated.1.csv -jove_plus 3 -jove_minus 2 -plot calibrator.output.1.png calibrator.output.extractor.1.csv calibrator.input.ref.csv -->
<param name="initial_data_file" value="calibrator.input.initial_data.csv" />
<param name="sampling_file" value="calibrator.input.sampling.csv" />
<param name="ref_file" value="calibrator.input.ref.csv" />
<param name="jove_plus" value="3" />
<param name="jove_minus" value="2" />
<output name="output_calibrated" ftype="csv">
<assert_contents>
<has_n_lines n="58" />
</assert_contents>
</output>
<output name="output_control_points" ftype="csv">
<assert_contents>
<has_n_lines n="6" />
</assert_contents>
</output>
<output name="output_graph" ftype="png" >
<assert_contents>
<has_size value="45000" delta="2000" />
</assert_contents>
</output>
</test>
<test expect_num_outputs="3">
<!-- python -m icfree.learner.extractor -initial_data_file calibrator.input.initial_data.csv -sampling_file calibrator.input.sampling.tsv -output_file calibrator.output.extractor.2.csv -num_samples 20 -num_replicates 3 -->
<!-- python -m icfree.learner.calibrator -plot calibrator.output.2.png -output calibrator.output.2.csv -jove_plus 4 -jove_minus 3 -r2_limit 0.9 -num 20 -num_control_points 4 calibrator.output.extractor.2.csv calibrator.input.ref.csv -->
<param name="initial_data_file" value="calibrator.input.initial_data.csv" />
<param name="sampling_file" value="calibrator.input.sampling.csv" />
<param name="ref_file" value="calibrator.input.ref.csv" />
<param name="num_samples" value="20" />
<param name="num_replicates" value="3" />
<param name="r2_limit" value="0.9" />
<param name="num_control_points" value="4" />
<param name="jove_plus" value="4" />
<param name="jove_minus" value="3" />
<output name="output_calibrated" ftype="csv">
<assert_contents>
<has_n_lines n="21" />
</assert_contents>
</output>
<output name="output_control_points" ftype="csv">
<assert_contents>
<has_n_lines n="21" />
</assert_contents>
</output>
<output name="output_graph" ftype="png" >
<assert_contents>
<has_size value="38000" delta="1000" />
</assert_contents>
</output>
</test>
</tests>
<help><![CDATA[
Calibrator
==========
Calculate yield based on fluorescence data and apply calibration.

]]></help>
<expand macro="creator"/>
<expand macro="citation"/>
</tool>
10 changes: 2 additions & 8 deletions tools/icfree/macros.xml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<macros>
<token name="@TOOL_VERSION@">2.4.0</token>
<token name="@TOOL_VERSION@">2.7.0</token>
<token name="@VERSION_SUFFIX@">0</token>
<xml name="requirements">
<requirements>
Expand All @@ -9,13 +9,7 @@
</xml>
<xml name="citation">
<citations>
<citation type="bibtex">
@unpublished{icfree
author = {Joan Hérisson, Yorgo El Moubayed},
title = {{icfree}},
url = {https://github.com/brsynth/icfree-ml/},
}
</citation>
<citation type="doi">10.1101/2024.10.28.619828</citation>
</citations>
</xml>
<xml name="creator">
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