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Icfree, update to 2.9.0 #200

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39 changes: 7 additions & 32 deletions tools/icfree/calibrator.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,20 +5,8 @@
</macros>
<expand macro="requirements"/>
<command detect_errors="exit_code"><![CDATA[
cp '$initial_data_file' 'initial_data.csv' &&
cp '$sampling_file' 'sampling.csv' &&
cp '$extractor_file' 'extractor.csv' &&
cp '$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 '$output_graph'
Expand All @@ -28,23 +16,16 @@
#if str($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="extractor_file" type="data" format="csv" label="Extractor file" help="Extractor 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" />
Expand All @@ -57,10 +38,8 @@
</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" />
<!-- python -m icfree.learner.calibrator -output calibrator.output.calibrated.1.csv -jove_plus 3 -jove_minus 2 -plot calibrator.output.1.png extractor.output.1.csv calibrator.input.ref.csv -->
<param name="extractor_file" value="extractor.output.1.csv" />
<param name="ref_file" value="calibrator.input.ref.csv" />
<param name="jove_plus" value="3" />
<param name="jove_minus" value="2" />
Expand All @@ -81,13 +60,9 @@
</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" />
<!-- python -m icfree.learner.calibrator -output calibrator.output.calibrated.2.csv -jove_plus 4 -jove_minus 3 -r2_limit 0.9 -num 20 -num_control_points 4 -plot calibrator.output.2.png extractor.output.2.csv calibrator.input.ref.csv -->
<param name="extractor_file" value="extractor.output.2.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" />
Expand All @@ -99,7 +74,7 @@
</output>
<output name="output_control_points" ftype="csv">
<assert_contents>
<has_n_lines n="21" />
<has_n_lines n="5" />
</assert_contents>
</output>
<output name="output_graph" ftype="png" >
Expand Down
66 changes: 66 additions & 0 deletions tools/icfree/extractor.xml
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@@ -0,0 +1,66 @@
<tool id="icfree_extractor" name="iCFree extractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT">
<description>Process fluorescence data</description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements"/>
<command detect_errors="exit_code"><![CDATA[
cp '$initial_data_file' 'initial_data.csv' &&
cp '$sampling_file' 'sampling.csv' &&
python -m icfree.learner.extractor
--initial_data_file 'initial_data.csv'
--sampling_file 'sampling.csv'
--output_file 'extractor.csv'
#if str($adv.num_samples) != ''
--num_samples '$adv.num_samples'
#end if
#if str($adv.num_replicates) != ''
--num_replicates '$adv.num_replicates'
#end if
&&
mv 'extractor.csv' '$output'
]]></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"/>
<section name="adv" title="Advanced Options" expanded="false">
<param argument="num_samples" type="integer" optional="true" label="Number of samples" help="Number of samples" />
<param argument="num_replicates" type="integer" optional="true" label="Number of replicates" help="Number of replicates." />
</section>
</inputs>
<outputs>
<data name="output" format="csv" label="${tool.name}" />
</outputs>
<tests>
<test expect_num_outputs="1">
<!-- python -m icfree.learner.extractor -initial_data_file extractor.input.initial_data.csv -sampling_file extractor.input.sampling.csv -output_file extractor.output.1.csv -->
<param name="initial_data_file" value="extractor.input.initial_data.csv" />
<param name="sampling_file" value="extractor.input.sampling.csv" />
<output name="output" ftype="csv">
<assert_contents>
<has_n_lines n="58" />
</assert_contents>
</output>
</test>
<test expect_num_outputs="1">
<!-- python -m icfree.learner.extractor -initial_data_file extractor.input.initial_data.csv -sampling_file extractor.input.sampling.csv -output_file extractor.output.2.csv -num_samples 20 -num_replicates 3 -->
<param name="initial_data_file" value="extractor.input.initial_data.csv" />
<param name="sampling_file" value="extractor.input.sampling.csv" />
<param name="num_samples" value="20" />
<param name="num_replicates" value="3" />
<output name="output" ftype="csv">
<assert_contents>
<has_n_lines n="21" />
</assert_contents>
</output>
</test>
</tests>
<help><![CDATA[
Extractor
==========
Process fluoresence data

]]></help>
<expand macro="creator"/>
<expand macro="citation"/>
</tool>
23 changes: 15 additions & 8 deletions tools/icfree/instructor.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,9 @@
#if str($adv.split_components) != ''
--split_components '$adv.split_components'
#end if
#if str($adv.dispense_order) != ''
--dispense_order '$adv.dispense_order'
#end if
]]></command>
<inputs>
<param name="source_plate_file" type="data" format="csv" label="Source corresponding to plate/wells" help="Output from iCFree plates designer"/>
Expand All @@ -30,8 +33,8 @@
</param>
<param argument="max_transfer_volume" type="integer" optional="true" label="Maximum transfer volume" help="Maximum volume for a single transfer. If not specified, no splitting will be performed." />
<param argument="split_threshold" type="integer" optional="true" label="Split threshold" help="Volume threshold above which transfers need to be split. If not specified, no splitting will be performed." />
<param name="split_components" type="text" optional="true" label="Split components" help="Comma-separated list of component names to create separate files for." >
</param>
<param name="split_components" type="text" optional="true" label="Split components" help="Comma-separated list of component names to create separate files for." />
<param name="dispense_order" type="text" optional="true" label="Dispense order" help="Comma-separated list of component specifying dispensing order." />
</section>
</inputs>
<outputs>
Expand All @@ -41,17 +44,21 @@
</outputs>
<tests>
<test>
<!-- python -m icfree.instructor plates_designer.source_plate.test-2.csv plates_designer.destination_plate.test-2.csv 'instructor.test-1.csv' -source_plate_type 'default:384PP_AQ_GP3' -max_transfer_volume '500' -split_threshold '500' -->
<param name="source_plate_file" value="plates_designer.source_plate.test-2.csv" />
<param name="destination_plate_file" value="plates_designer.destination_plate.test-2.csv" />
<!-- python -m icfree.instructor ../plate_designer.source_plate.test-2.csv ../plate_designer.destination_plate.test-2.csv 'instructor.test-1.csv' -source_plate_type 'default:384PP_AQ_GP3' -max_transfer_volume '500' -split_threshold '500' -->
<param name="source_plate_file" value="plate_designer.source_plate.test-2.csv" />
<param name="destination_plate_file" value="plate_designer.destination_plate.test-2.csv" />
<param name="max_transfer_volume" value="500" />
<param name="split_threshold" value="500" />
<output_collection name="output_instructor" type="list" count="1">
<element name="instructions" file="instructor.test-1.csv" ftype="csv" compare="diff" />
</output_collection>
</test>
<test>
<!-- python -m icfree.instructor plates_designer.source_plate.test-2.csv plates_designer.destination_plate.test-2.csv 'instructor.csv' -source_plate_type 'Hela lysate:384PP_AQ_CP,Access prot 50X:384PP_AQ_GP3,Reaction mix:384PP_AQ_GP3,RNA 1ug/uL:384PP_AQ_GP3' -max_transfer_volume '500' -split_threshold '500' -split_components 'Hela lysate,Access prot 50X' -->
<param name="source_plate_file" value="plates_designer.source_plate.test-2.csv" />
<param name="destination_plate_file" value="plates_designer.destination_plate.test-2.csv" />
<!-- python -m icfree.instructor plate_designer.source_plate.test-2.csv plate_designer.destination_plate.test-2.csv 'instructor.csv' -source_plate_type 'Hela lysate:384PP_AQ_CP,Access prot 50X:384PP_AQ_GP3,Reaction mix:384PP_AQ_GP3,RNA 1ug/uL:384PP_AQ_GP3' -max_transfer_volume '500' -split_threshold '500' -split_components 'Hela lysate,Access prot 50X' -dispense_order 'Access prot 50X,Hela lysate' -->
<param name="source_plate_file" value="plate_designer.source_plate.test-2.csv" />
<param name="destination_plate_file" value="plate_designer.destination_plate.test-2.csv" />
<param name="max_transfer_volume" value="500" />
<param name="split_threshold" value="500" />
<param name="source_plate_type" value="Hela lysate:384PP_AQ_CP,Access prot 50%:384PP_AQ_GP3,Reaction mix:384PP_AQ_GP3,RNA 1ug/uL:384PP_AQ_GP3" />
<param name="split_components" value="Hela lysate,Access prot 50%" />
<output_collection name="output_instructor" type="list" count="3">
Expand Down
2 changes: 1 addition & 1 deletion tools/icfree/macros.xml
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@@ -1,5 +1,5 @@
<macros>
<token name="@TOOL_VERSION@">2.7.1</token>
<token name="@TOOL_VERSION@">2.9.0</token>
<token name="@VERSION_SUFFIX@">0</token>
<xml name="requirements">
<requirements>
Expand Down
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