diff scpred_get_feature_space.xml @ 0:db7ecc1aaf59 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_get_feature_space.xml	Wed Apr 08 06:38:03 2020 -0400
@@ -0,0 +1,31 @@
+<tool id='scpred_get_feature_space' name='ScPred feature space' version='@TOOL_VERSION@+galaxy0' profile="@PROFILE@">
+    <description>Get feature space for training matrix</description>
+    <macros>
+         <import>scpred_macros.xml</import>
+    </macros>
+    <expand macro='requirements' />
+    <command detect_errors='exit_code'><![CDATA[
+        scpred_get_feature_space.R  --input-object '${input_object}'  --prediction-column '${prediction_column}' --explained-var-limit '${explained_var_limit}' --output-path '${output_obj_path}' --eigenvalue-plot-path '${eigenvalue_plot_path}']]></command>
+    <inputs>
+        <param type='data' name='input_object' label='Input SCE object' format='rdata' help='Input SCE object in .rds format' />
+        <param type='text' name='prediction_column' label='Prediction column' help='Name of the metadata column that contains training labels' />
+        <param type='float' name='explained_var_limit' label='Limit of explained variance' value="0.01" help='Threshold to filter principal components based on variance explained' />
+    </inputs>
+    <outputs>
+        <data name='output_obj_path' format='rdata' />
+        <data name='eigenvalue_plot_path' format='png' />
+    </outputs>
+     <tests>
+        <test>
+            <param name="input_object" value="scPred_object.rds" />
+            <param name="prediction_column" value="cell_type2" />
+            <output name="output_obj_path" file="scPred_feat_space.rds" compare="sim_size" />
+        </test>
+    </tests>
+    <help><![CDATA[
+    @HELP@
+    
+    @VERSION_HISTORY@
+    ]]></help>
+    <expand macro='citations' />
+</tool>
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