diff scanpy-regress-variable.xml @ 0:88b0cb06c2b1 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scanpy-regress-variable.xml	Thu Mar 12 09:12:49 2020 +0000
@@ -0,0 +1,57 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="scanpy_regress_variable" name="Scanpy RegressOut" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@">
+  <description>variables that might introduce batch effect</description>
+  <macros>
+    <import>scanpy_macros2.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[
+#if $variable_keys
+  ln -s '${input_obj_file}' input.h5 &&
+  PYTHONIOENCODING=utf-8 scanpy-regress
+      --keys '${variable_keys}'
+      @INPUT_OPTS@
+      @OUTPUT_OPTS@
+#else
+  echo "No regression variables passed, simply passing original input as output unchanged.";
+  cp '${input_obj_file}' '${output_h5}'
+#end if
+]]></command>
+
+  <inputs>
+    <expand macro="input_object_params"/>
+    <expand macro="output_object_params"/>
+    <param name="variable_keys" type="text" label="Variables to regress out" help="Use comma to separate multiple variables. Not supplying variables will simply pass the input data as output unchanged.">
+      <sanitizer>
+        <valid initial="string.printable"/>
+      </sanitizer>
+    </param>
+  </inputs>
+
+  <outputs>
+    <expand macro="output_data_obj" description="Regressed out ${variable_keys}"/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input_obj_file" value="find_variable_genes.h5"/>
+      <param name="input_format" value="anndata"/>
+      <param name="output_format" value="anndata"/>
+      <param name="variable_keys" value="n_counts"/>
+      <output name="output_h5" file="scale_data.h5" ftype="h5" compare="sim_size"/>
+    </test>
+  </tests>
+
+  <help><![CDATA[
+    .. class:: infomark
+
+    **What it does**
+
+    Regress out unwanted source of variance (`scanpy.pp.regress_out`)
+
+    @HELP@
+
+    @VERSION_HISTORY@
+]]></help>
+  <expand macro="citations"/>
+</tool>