diff scater-calculate-cpm.xml @ 0:66e18f77e161 draft default tip

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scater-calculate-cpm.xml	Wed Apr 03 11:44:15 2019 -0400
@@ -0,0 +1,40 @@
+<tool id="scater_calculate_cpm" name="Scater CalculateCPM" version="@TOOL_VERSION@+galaxy0">
+  <description>from raw counts</description>
+  <macros>
+    <import>scater_macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command detect_errors="exit_code"><![CDATA[
+scater-calculate-cpm.R -i '${R_scater_serialized}'
+    -s '$size_factors'
+    -o '$R_scater_cpm'
+    -t '$cpm_matrix'
+  ]]></command>
+
+  <inputs>
+    <param name="R_scater_serialized" type="data" format="rdata" label="Serialized SingleCellExperiment in RDS format"
+           help="File name in which a serialized R SingleCellExperiment object where object matrix found"/>
+    <param name="size_factors" argument="--size-factors" type="boolean" label="Use pre-calculated size factors in the input object if available"/>
+
+  </inputs>
+
+  <outputs>
+    <data name="R_scater_cpm" format="rdata" label="${tool.name} on ${on_string}: serialized SingeleCellExperiment object holding CPM"/>
+    <data name="cpm_matrix" format="txt" label="${tool.name} on ${on_string}: CPM matrix in text format"/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="R_scater_serialized" ftype="rdata" value="R_scater_serialized.rds"/>
+      <output name="R_scater_cpm" ftype="rdata" file="R_scater_cpm.rds"/>
+      <output name="cpm_matrix" ftype="txt" file="cpm_matrix.txt"/>
+    </test>
+  </tests>
+
+  <help><![CDATA[
+@HELP@
+
+@VERSION_HISTORY@
+  ]]></help>
+  <expand macro="citations" />
+</tool>