--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/instructor.xml	Mon Mar 06 12:52:35 2023 +0000
@@ -0,0 +1,182 @@
+<tool id="icfree_instructor" name="iCFree instructor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@">
+    <description>Generates a list of Echo-compatible instructions to prepare samples</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command detect_errors="exit_code"><![CDATA[
+        #if str($conditional_source_json.type) == "collection":
+            #for $input in $conditional_source_json.collection.keys():
+                ln -sfn $conditional_source_json.collection[$input] '.' &&
+            #end for
+            #set input_source_json = '" "'.join([str($file) for $file in $conditional_source_json.collection[$input]])
+        #elif str($conditional_source_json.type) == "files":
+            #set input_source_json = '" "'.join([str($file) for $file in $conditional_source_json.files])
+        #end if
+
+        #if str($conditional_source_tsv.type) == "collection":
+            #for $input in $conditional_source_tsv.collection.keys():
+                ln -sfn $conditional_source_tsv.collection[$input] '.' &&
+            #end for
+            #set input_source_tsv = '" "'.join([str($file) for $file in $conditional_source_tsv.collection[$input]])
+        #elif str($conditional_source_tsv.type) == "files":
+            #set input_source_tsv = []
+            #for $f in $conditional_source_tsv.files
+                ln -sfn '$f' '$f.element_identifier' &&
+                #silent input_source_tsv.append(str($f.element_identifier))
+            #end for
+            #set inputs_source_tsv = '" "'.join(input_source_tsv)
+        #end if
+
+
+        #if str($conditional_destination_json.type) == "collection":
+            #for $input in $conditional_destination_json.collection.keys():
+                ln -sfn $conditional_destination_json.collection[$input] '.' &&
+            #end for
+            #set input_destination_json = '" "'.join([str($file) for $file in $conditional_destination_json.collection[$input]])
+        #elif str($conditional_destination_json.type) == "files":
+            #set input_destination_json = '" "'.join([str($file) for $file in $conditional_destination_json.files])
+        #end if
+
+        #if str($conditional_destination_tsv.type) == "collection":
+            #for $input in $conditional_destination_tsv.collection.keys():
+                ln -sfn $conditional_destination_tsv.collection[$input] '.' &&
+            #end for
+            #set input_destination_tsv = '" "'.join([str($file) for $file in $conditional_destination_tsv.collection[$input]])
+        #elif str($conditional_destination_tsv.type) == "files":
+            #set input_destination_tsv = []
+            #for $f in $conditional_destination_tsv.files
+                ln -sfn '$f' '$f.element_identifier' &&
+                #silent input_destination_tsv.append(str($f.element_identifier))
+            #end for
+            #set inputs_destination_tsv = '" "'.join(input_destination_tsv)
+        #end if
+
+
+        python -m icfree.instructor
+            --source_plates "${input_source_json}"
+            --source_wells "${inputs_source_tsv}"
+            --dest_plates "${input_destination_json}"
+            --dest_wells "${inputs_destination_tsv}"
+            --robot '$adv.robot'
+            --output-folder out
+    ]]></command>
+    <inputs>
+        <conditional name="conditional_source_json">
+            <param name="type" type="select" label="Source plate (json)">
+                <option value="files" selected="True">File(s)</option>
+                <option value="collection">Collection</option>
+            </param>
+            <when value="files">
+                <param name="files" type="data" format="json" multiple="true" label="Source plates information (json)" />
+            </when>
+            <when value="collection">
+                <param name="collection" type="data_collection" collection_type="list" format="json" label="Source plates information (json)" />
+            </when>
+        </conditional>
+        <conditional name="conditional_source_tsv">
+            <param name="type" type="select" label="Source plate (tsv)">
+                <option value="files" selected="True">File(s)</option>
+                <option value="collection">Collection</option>
+            </param>
+            <when value="files">
+                <param name="files" type="data" format="tabular" multiple="true" label="Source plates information (tsv)" />
+            </when>
+            <when value="collection">
+                <param name="collection" type="data_collection" collection_type="list" format="tabular" label="Source plates information (tsv)" />
+            </when>
+        </conditional>
+        <conditional name="conditional_destination_json">
+            <param name="type" type="select" label="Source plate (json)">
+                <option value="files" selected="True">File(s)</option>
+                <option value="collection">Collection</option>
+            </param>
+            <when value="files">
+                <param name="files" type="data" format="json" multiple="true" label="Destination plates information (json)" />
+            </when>
+            <when value="collection">
+                <param name="collection" type="data_collection" collection_type="list" format="json" label="Destination plates information (json)" />
+            </when>
+        </conditional>
+        <conditional name="conditional_destination_tsv">
+            <param name="type" type="select" label="Source plate (tsv)">
+                <option value="files" selected="True">File(s)</option>
+                <option value="collection">Collection</option>
+            </param>
+            <when value="files">
+                <param name="files" type="data" format="tabular" multiple="true" label="Destination plates information (tsv)" />
+            </when>
+            <when value="collection">
+                <param name="collection" type="data_collection" collection_type="list" format="tabular" label="Destination plates information (tsv)" />
+            </when>
+        </conditional>
+        <section name="adv" title="Advanced Options" expanded="false">
+            <param argument="robot" type="text" value="echo" label="Robot name" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="tabulars" format="tabular">
+            <discover_datasets pattern="__designation__" ext="tabular" directory="out" />
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <!-- test 1: check if identical outputs are produced with default parameters  -->
+            <conditional name="conditional_source_json">
+                <param name="type" value="files"/>
+                <param name="files" value="plates_generator_source_plate_1.json" />
+            </conditional>
+            <conditional name="conditional_source_tsv">
+                <param name="type" value="files"/>
+                <param name="files" value="plates_generator_source_plate_1.tsv" />
+            </conditional>
+            <conditional name="conditional_destination_json">
+                <param name="type" value="files"/>
+                <param name="files" value="plates_generator_destination_plate_1.json" />
+            </conditional>
+            <conditional name="conditional_destination_tsv">
+                <param name="type" value="files"/>
+                <param name="files" value="plates_generator_destination_plate_1.tsv" />
+            </conditional>
+            <output name="tabulars" ftype="tabular">
+                <discovered_dataset designation="volumes_warnings.tsv" ftype="tabular">
+                    <assert_contents>
+                        <has_n_lines n="12"/>
+                        <has_line_matching expression="^Parameter\tMin\tMax\tPlate$"/>
+                    </assert_contents>
+                </discovered_dataset>
+                <discovered_dataset designation="instructions.csv" ftype="tabular">
+                    <assert_contents>
+                        <has_line_matching expression="^Source Plate Name,Source Plate Type,Source Well,Destination Plate Name,Destination Well,Transfer Volume,Sample ID$"/>
+                        <has_n_lines n="1701"/>
+                    </assert_contents>
+
+                </discovered_dataset>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Instructor
+==========
+
+The module generates a list of instructions to perform the experiment.
+
+Input
+-----
+Required:
+* **Source plates file**: description of the source plates (source well name, source well volume...) (JSON format)
+* **Destination plates file**: description of the destination plates (destination well name, destination well volume...) (JSON format)
+
+Advanced options:
+-----------------
+* **Robot name**: name of the robot to generate instructions for (default: "echo")
+
+Output
+------
+* **instructions**: contains the instructions to perform the experiment
+* **volumes_warning**: contains the volumes that may cause issues with the chosen robot
+    ]]></help>
+    <expand macro="creator"/>
+    <expand macro="citation"/>
+</tool>