diff plates_designer.xml @ 0:92adc3382124 draft

planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plates_designer.xml	Tue Jul 23 13:59:11 2024 +0000
@@ -0,0 +1,118 @@
+<tool id="icfree_plates_designer" name="iCFree plates designer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@">
+    <description>Prepare source and destination well-plate mappings with advanced options.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command detect_errors="exit_code"><![CDATA[
+        #set well_capacity = []
+        #set dead_volumes = []
+        #for $x in $adv.rep
+            #silent well_capacity.append(str($x.component_name) + "=" + str($x.well_capacity))
+            #silent dead_volumes.append(str($x.component_name) + "=" + str($x.dead_volumes))
+        #end for
+        #set swell_capacity = ','.join($well_capacity)
+        #set sdead_volumes = ','.join($dead_volumes)
+
+        python -m icfree.plate_designer
+            '$sampling_file'
+            '$sample_volume'
+            --start_well_src_plt '$adv.start_well_src_plt'
+            --start_well_dst_plt '$adv.start_well_dst_plt'
+            --plate_dims '$adv.plate_dims'
+            #if len($well_capacity) > 0
+                --well_capacity '$swell_capacity'
+            #end if
+            --default_well_capacity '$adv.default_well_capacity'
+            #if len($dead_volumes) > 0
+                --dead_volumes '$sdead_volumes'
+            #end if
+            --default_dead_volume '$adv.default_dead_volume'
+            --num_replicates '$adv.num_replicates' &&
+        mv source_plate.csv '$output_source_plate' &&
+        mv destination_plate.csv '$output_destination_plate'
+           ]]></command>
+    <inputs>
+        <param name="sampling_file" type="data" format="csv" label="Sampling file" />
+        <param name="sample_volume" type="integer" optional="false" label="Wanted sample volume in the destination plate" />
+        <section name="adv" title="Advanced Options" expanded="false">
+            <param name="start_well_src_plt" type="text" value="A1" label="Starting well for the source plate">
+                <validator type="empty_field" message="Not empty"/>
+                <validator type="regex" message="Some letters followed by a number">^(?:[A-K]{1}([1-9]|1[0-2]))$</validator>
+            </param>
+            <param name="start_well_dst_plt" type="text" value="A1" label="Starting well for the destination plate">
+                <validator type="empty_field" message="Not empty"/>
+                <validator type="regex" message="Some letters followed by a number">^(?:[A-K]{1}([1-9]|1[0-2]))$</validator>
+            </param>
+            <param name="plate_dims" type="text" value="16x24" label="Plate dimensions (Format: NxM)">
+                <validator type="empty_field" message="Not empty"/>
+                <validator type="regex" message="An 'x' separator is expected">^(?:\d+x\d+)$</validator>
+            </param>
+            <param name="default_well_capacity" type="integer" value="60000" min="1" max="250000" label="Default well capacity in nL for components not specified in well_capacity" />
+            <param name="default_dead_volume" type="integer" value="15000" min="1" max="250000" label="Default dead volume in nL for the source plate"/>
+            <param name="num_replicates" type="integer" value="1" min="1" max="10" label="Number of wanted replicates"/>
+            <repeat name="rep" title="Specific components">
+                <param name="component_name" type="text" value="" label="Component Name">
+                    <validator type="empty_field" message="Not empty"/>
+                </param>
+                <param name="well_capacity" type="integer" value="60000" min="1" max="250000" label="Well capacity" />
+                <param name="dead_volumes" type="integer" value="15000" min="1" max="250000" label="Dead volumes" />
+            </repeat>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output_source_plate" format="csv" label="${tool.name} - Source" />
+        <data name="output_destination_plate" format="csv" label="${tool.name} - Destination" />
+    </outputs>
+    <tests>
+        <test>
+            <!-- python -m icfree.plate_designer sampling.test-1.csv 6000 -default_well_capacity 60000 -default_dead_volume 20000 -num_replicates 1 -->
+            <param name="sampling_file" value="sampling.test-1.csv" />
+            <param name="sample_volume" value="6000" />
+            <param name="default_well_capacity" value="60000" />
+            <param name="default_dead_volume" value="20000" />
+            <param name="num_replicates" value="1" />
+            <output name="output_source_plate" file="plates_designer.source_plate.test-1.csv" ftype="csv" compare="diff" />
+            <output name="output_destination_plate" file="plates_designer.destination_plate.test-1.csv" ftype="csv" compare="diff" />
+        </test>
+        <test>
+            <!-- python -m icfree.plate_designer sampling.test-1.csv '5000' -start_well_src_plt 'A1' -start_well_dst_plt 'A1' -plate_dims '16x24' -well_capacity 'Hela lysate=3000,Access prot 50X=4000,Reaction mix=3000,RNA 1ug/uL=2000' -default_well_capacity '60000' -dead_volumes 'Hela lysate=30,Access prot 50X=5,Reaction mix=10,RNA 1ug/uL=20' -default_dead_volume '20000' -num_replicates '2' -->
+            <param name="sampling_file" value="sampling.test-1.csv" />
+            <param name="sample_volume" value="5000" />
+            <param name="default_well_capacity" value="60000" />
+            <param name="default_dead_volume" value="20000" />
+            <param name="num_replicates" value="2" />
+            <repeat name="rep">
+                <param name="component_name" value="Hela lysate" />
+                <param name="well_capacity" value="3000" />
+                <param name="dead_volumes" value="30" />
+            </repeat>
+            <repeat name="rep">
+                <param name="component_name" value="Access prot 50%" />
+                <param name="well_capacity" value="4000" />
+                <param name="dead_volumes" value="5" />
+            </repeat>
+            <repeat name="rep">
+                <param name="component_name" value="Reaction mix" />
+                <param name="well_capacity" value="3000" />
+                <param name="dead_volumes" value="10" />
+            </repeat>
+            <repeat name="rep">
+                <param name="component_name" value="RNA 1ug/uL" />
+                <param name="well_capacity" value="2000" />
+                <param name="dead_volumes" value="20" />
+            </repeat>
+            <output name="output_source_plate" file="plates_designer.source_plate.test-2.csv" ftype="csv" compare="diff" />
+            <output name="output_destination_plate" file="plates_designer.destination_plate.test-2.csv" ftype="csv" compare="diff" />
+        </test>
+    </tests>
+    <help><![CDATA[
+Plates Generator
+================
+
+Prepare source and destination well-plate mappings with advanced options.
+    ]]></help>
+    <expand macro="creator"/>
+    <expand macro="citation"/>
+</tool>