diff scmap_scmap_cluster.xml @ 0:5421e01f640a draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scmap_scmap_cluster.xml	Mon Sep 16 09:58:40 2019 -0400
@@ -0,0 +1,33 @@
+<tool id="scmap_scmap_cluster" name="scmap cluster projection" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5">
+    <description>projects one dataset to another</description>
+    <macros>
+        <import>scmap_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        scmap-scmap-cluster.R --index-object-file '$index_single_cell_experiment' --projection-object-file '$project_single_cell_experiment' --threshold '$threshold' --output-object-file '$output_single_cell_experiment' --output-text-file '$output_txt'
+    ]]></command>
+    <inputs>
+        <param type="data" name="index_single_cell_experiment" label="Index SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object as produced by 'scmap select features' and 'scmap index clusters', onto which another dataset will be projected." />
+        <param type="data" name="project_single_cell_experiment" label="SingleCellExperiment object to project" format="rdata" help="File with serialized SingleCellExperiment object to project onto the index'" />
+        <param name="threshold" type="float" label="Threshold" value="0.7" help="Threshold on similarity (or probability for SVM and RF)." />
+    </inputs>
+    <outputs>
+        <data name="output_single_cell_experiment" format="rdata" />
+        <data name="output_txt" format="csv" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="index_single_cell_experiment" value="index_cluster.rds" ftype="rdata"/>
+            <param name="project_single_cell_experiment" value="test_sce.rds" ftype="rdata"/>
+            <output name="output_single_cell_experiment" file="project_cluster.rds"/>
+            <output name="output_txt" file="project_cluster.csv"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+    @HELP@
+    
+    @VERSION_HISTORY@
+    ]]></help>
+    <expand macro="citations" />
+</tool>