diff scpred_train_test_split.xml @ 0:8ec19f24fcf3 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scpred_train_test_split.xml	Wed Apr 08 06:37:16 2020 -0400
@@ -0,0 +1,37 @@
+<tool id="scpred_traint_test_split" name="Scpred train-test split" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+    <description>CPM normalise and partition into train/test data</description>
+    <macros>
+        <import>scpred_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        scpred_train_test_split.R --input-sce-object "${input_sce_object}" --normalised-counts-slot "${norm_counts_slot}" --training-matrix "${training_mat}" --test-matrix "${test_mat}" --cell-types-column "${cell_types_col}" --training-labels "${training_labs}" --test-labels "${test_labs}" --training-ratio "${training_ratio}" ]]></command>
+    <inputs>
+        <param type="data" name="input_sce_object" label="SCE object containing expression data" format="rdata" help="File with serialized SingleCellExperiment object that contains expression matrix" />
+        <param type="text" name="norm_counts_slot" value="normcounts" label="Normalised counts slot" help="Slot containing normalised counts in input SCE object" />
+        <param type="text" name="cell_types_col"  label="Column name for assigned cell types" />
+        <param type="float" name="training_ratio" label="Train/test split ratio" value="0.7" help="What proportion of the data set (0 to 1) should be used for training" />
+    </inputs>
+    <outputs>
+        <data name="training_mat" format="rdata" />
+        <data name="test_mat" format="rdata" />
+        <data name="training_labs" format="txt" />
+        <data name="test_labs" format="txt" /> 
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_sce_object" value="pollen_cpm.rds" />
+            <param name="cell_types_col" value="cell_type2" />
+            <output name="training_mat" file="train_matrix.mtx" compare="sim_size"/>
+            <output name="test_mat" file="test_matrix.mtx" compare="sim_size"/>
+            <output name="training_labs" file="train_metadata.txt" compare="sim_size" />
+            <output name="test_labs" file="test_metadata.txt" compare="sim_size" />
+        </test>
+    </tests>
+    <help><![CDATA[
+    @HELP@
+    
+    @VERSION_HISTORY@
+    ]]></help>
+    <expand macro="citations" />
+</tool>