diff scanpy-scale-data.xml @ 0:96b851e96dd0 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scanpy-scale-data.xml	Wed Apr 03 11:09:38 2019 -0400
@@ -0,0 +1,72 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="scanpy_scale_data" name="Scanpy ScaleData" version="@TOOL_VERSION@+galaxy1">
+  <description>to make expression variance the same for all genes</description>
+  <macros>
+    <import>scanpy_macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[
+ln -s '${input_obj_file}' input.h5 &&
+PYTHONIOENCODING=utf-8 scanpy-scale-data.py
+    -i input.h5
+    -f '${input_format}'
+    -o output.h5
+    -F '${output_format}'
+    #if $scale_max
+        -x '${scale_max}'
+    #end if
+    #if $var_to_regress
+        -V '${var_to_regress}'
+    #end if
+    #if $do_log
+        --do-log
+    #end if
+    #if $zero_center
+        --zero-center
+    #end if
+]]></command>
+
+  <inputs>
+    <expand macro="input_object_params"/>
+    <expand macro="output_object_params"/>
+    <param name="do_log" argument="--do-log" type="boolean" checked="true" label="Do log(x+1) transformation"/>
+    <param name="zero_center" argument="--zero-center" type="boolean" checked="true" label="Zero center data before scaling"/>
+    <param name="var_to_regress" argument="--var-to-regress" type="text" optional="true" label="Variable(s) to regress out">
+      <option value="n_counts">n_counts</option>
+    </param>
+    <param name="scale_max" argument="--scale-max" type="float" optional="true" label="Truncate to this value after scaling"/>
+  </inputs>
+
+  <outputs>
+    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Scaled data"/>
+  </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="do_log" value="true"/>
+      <param name="zero_center" value="true"/>
+      <param name="scale_max" value="10"/>
+      <output name="output_h5" file="scale_data.h5" ftype="h5" compare="sim_size"/>
+    </test>
+  </tests>
+
+  <help><![CDATA[
+    .. class:: infomark
+
+    **What it does**
+
+    Scale data to unit variance and zero mean (`pp.scale`)
+    Regress out unwanted sources of variation (`pp.regress_out`)
+
+    Regress out unwanted sources of variation, using simple linear regression. This is
+    inspired by Seurat's `regressOut` function in R.
+
+    @HELP@
+
+    @VERSION_HISTORY@
+]]></help>
+  <expand macro="citations"/>
+</tool>