diff scater-create-qcmetric-ready-sce.xml @ 0:2d455a7e8a3d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scater-create-qcmetric-ready-sce.xml	Thu Jul 18 11:14:06 2019 -0400
@@ -0,0 +1,46 @@
+<tool id="scater_create_qcmetric_ready_sce" name="Scater: Calculate QC metrics" version="@TOOL_VERSION@">
+    <description>Computes QC metrics from single-cell expression matrix</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+Rscript '$__tool_directory__/scater-create-qcmetric-ready-sce.R'
+-a '$counts'
+#if $col_data:
+    -c '$col_data'
+#end if
+#if $mt_controls:
+    -f '$mt_controls'
+#end if
+#if $ercc_controls:
+    -p '$ercc_controls'
+#end if
+#if $cell_controls:
+    -l '$cell_controls'
+#end if
+-o '$output_loom'
+    ]]></command>
+    <inputs>
+        <param name="counts" type="data" format="tabular" label="Expression matrix in tabular format" help="The first column of all files is assumed to be feature names and the first row is assumed to be sample names" />
+        <param name="col_data" type="data" format="tabular" optional="true" label="Format dataset describing the features in tabular format" help="The number of rows (samples) must equal the number of columns in the expression matrix" />
+        <param name="mt_controls" type="data" format="txt" optional="true" label="Dataset containing the list of the mitochondrial control genes" />
+        <param name="ercc_controls" type="data" format="txt" optional="true" label="Dataset containing the list of the ERCC controls" />
+        <param name="cell_controls" type="data" format="txt" optional="true" label="Dataset containing the list of the cell controls" help="Cell (sample) names used to identify cell controls (for example, blank wells or bulk controls)" />
+    </inputs>
+    <outputs>
+        <data name="output_loom" format="loom" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="counts" value="counts.txt" />
+            <param name="col_data" value="annotation.txt" />
+            <param name="mt_controls" value="mt_controls.txt" />
+            <output name="output_loom" file="scater_qcready.loom" compare="sim_size" />
+        </test>
+    </tests>
+    <help><![CDATA[
+Calculate QC metrics for single-cell RNA-seq analysis using Scater.
+    ]]></help>
+    <expand macro="citations" />
+</tool>