diff scmap_index_cell.xml @ 0:ff7d99bbd31d draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scmap_index_cell.xml	Fri Apr 03 10:32:40 2020 +0000
@@ -0,0 +1,33 @@
+<tool id="scmap_index_cell" name="scmap index cells" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+    <description>creates a cell index for a dataset to enable fast approximate nearest neighbour search</description>
+    <macros>
+        <import>scmap_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object "${input_single_cell_experiment}.preprocessed" && scmap-index-cell.R --input-object-file "${input_single_cell_experiment}.preprocessed" --number-chunks '$n_chunks' --number-clusters '$n_clusters' --output-object-file '$output_single_cell_experiment' --random-seed '$random_seed'
+    ]]></command>
+    <inputs>
+        <param type="data" name="input_single_cell_experiment" label="SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object as produced by 'scmap select features'" />
+        <param name="n_chunks" type="integer" label="Number of chunks" value='' help="Number of chunks into which the expr matrix is split" />
+        <param name="n_clusters" type="integer" label="Number of clusters" value='' help="Number of clusters per group for k-means clustering" />
+        <param name="random_seed" type="integer" label="Random seed" value='1' help="scmap-cell contains k-means step which makes it stochastic, i.e. running it multiple times will provide slightly different results. A fixed random seed ensures reproducibility." />
+    </inputs>
+    <outputs>
+        <data name="output_single_cell_experiment" format="rdata" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="n_chunks" value="50" />
+            <param name="n_clusters" value="9" />
+            <param name="input_single_cell_experiment" value="select_features.rds" ftype="rdata"/>
+            <output name="output_single_cell_experiment" file="index_cell.rds" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+    @HELP@
+    
+    @VERSION_HISTORY@
+    ]]></help>
+    <expand macro="citations" />
+</tool>