diff scanpy-normalise-data.xml @ 0:1dda36e73482 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-normalise-data.xml	Wed Apr 03 11:07:51 2019 -0400
@@ -0,0 +1,61 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="scanpy_normalise_data" name="Scanpy NormaliseData" version="@TOOL_VERSION@+galaxy1">
+  <description>to make all cells having the same total expression</description>
+  <macros>
+    <import>scanpy_macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[
+ln -s '${input_obj_file}' input.h5 &&
+PYTHONIOENCODING=utf-8 scanpy-normalise-data.py
+    -i input.h5
+    -f '${input_format}'
+    -o output.h5
+    -F '${output_format}'
+    -s '${scale_factor}'
+    #if $save_raw
+        '${save_raw}'
+    #end if
+    @EXPORT_MTX_OPTS@
+]]></command>
+
+  <inputs>
+    <expand macro="input_object_params"/>
+    <expand macro="output_object_params"/>
+    <param name="scale_factor" argument="--scale-factor" type="float" value="1e4" label="Target number to normalise to" help="Aimed counts per cell after normalisation, default: 1e4"/>
+    <param name="save_raw" argument="--save-raw" type="boolean" truevalue="--save-raw" falsevalue="" checked="true" label="Save pre-normalised data" help="Save raw quantification in log scale before normalisation."/>
+    <expand macro="export_mtx_params"/>
+  </inputs>
+
+  <outputs>
+    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Normalized data" />
+    <expand macro="export_mtx_outputs"/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input_obj_file" value="filter_genes.h5"/>
+      <param name="input_format" value="anndata"/>
+      <param name="output_format" value="anndata"/>
+      <param name="scale_factor" value="1e4"/>
+      <param name="save_raw" value="false"/>
+      <output name="output_h5" file="normalise_data.h5" ftype="h5" compare="sim_size"/>
+    </test>
+  </tests>
+
+  <help><![CDATA[
+=========================================================
+Normalize total counts per cell (`pp.normalize_per_cell`)
+=========================================================
+
+Normalize each cell by total counts over all genes, so that every cell has
+the same total count after normalization.
+
+Similar functions are used, for example, by Seurat, Cell Ranger or SPRING.
+
+@HELP@
+
+@VERSION_HISTORY@
+]]></help>
+  <expand macro="citations"/>
+</tool>