Mercurial > repos > ebi-gxa > scpred_preprocess_data

diff scpred_preprocess_data.xml @ 0:ec6d9a9fb273 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
author ebi-gxa
date Mon, 27 Apr 2020 09:43:08 -0400
parents
children 03b45c148df7
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scpred_preprocess_data.xml	Mon Apr 27 09:43:08 2020 -0400
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+<tool id="scpred_preprocess_data" name="Scpred pre-process" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+    <description>Pre-process input dataset (no train/test split)</description>
+    <macros>
+        <import>scpred_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        scpred_preprocess_data.R --input-sce-object "${input_sce_object}" --normalised-counts-slot "${norm_counts_slot}" --output-matrix-object "${output_mat_object}" --output-labels "${output_labels}" ]]></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" />
+    </inputs> 
+    <outputs>
+        <data name="output_mat_object" format="rdata" />
+        <data name="output_labels" format="txt" />
+    </outputs>
+    <help><![CDATA[
+    @HELP@
+    
+    @VERSION_HISTORY@
+    ]]></help>
+    <expand macro="citations" />
+</tool>