diff scanpy-find-variable-genes.xml @ 0:305d0cbe0ffd 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-find-variable-genes.xml	Wed Apr 03 11:12:05 2019 -0400
@@ -0,0 +1,93 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="scanpy_find_variable_genes" name="Scanpy FindVariableGenes" version="@TOOL_VERSION@+galaxy0">
+  <description>based on normalised dispersion of expression</description>
+  <macros>
+    <import>scanpy_macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[
+ln -s '${input_obj_file}' input.h5 &&
+PYTHONIOENCODING=utf-8 scanpy-find-variable-genes.py -i input.h5
+    -f '${input_format}'
+    -o output.h5
+    -F '${output_format}'
+    --flavor '${flavor}'
+    -b '${n_bin}'
+    #if $parameters
+        #set pars = ','.join([str($p['name']) for $p in $parameters])
+        -p '${pars}'
+        #set mins = ','.join([str($p['min']) for $p in $parameters])
+        -l '${mins}'
+        #set maxs = ','.join([str($p['max']) for $p in $parameters])
+        -j '${maxs}'
+    #end if
+    #if $n_top_gene
+        -n '${n_top_gene}'
+    #end if
+]]></command>
+
+  <inputs>
+    <expand macro="input_object_params"/>
+    <expand macro="output_object_params"/>
+    <param name="flavor" argument="--flavor" type="select" value="seurat" label="Flavor of computing normalised dispersion">
+      <option value="seurat">Seurat</option>
+      <option value="cell_ranger">Cell-ranger</option>
+    </param>
+    <repeat name="parameters" min="1" title="Parameters used to find variable genes">
+      <param name="name" type="select" label="Name of parameter to filter on">
+        <option value="mean">Mean of expression</option>
+        <option value="disp">Dispersion of expression</option>
+      </param>
+      <param name="min" type="float" value="0" label="Min value"/>
+      <param name="max" type="float" value="1e9" label="Max value"/>
+    </repeat>
+    <param name="n_bin" argument="--n-bins" type="integer" value="20" label="Number of bins for binning the mean expression"/>
+    <param name="n_top_gene" argument="--n-top-genes" type="integer" optional="true" label="Number of top variable genes to keep"/>
+  </inputs>
+
+  <outputs>
+    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Variable genes"/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input_obj_file" value="normalise_data.h5"/>
+      <param name="input_format" value="anndata"/>
+      <param name="output_format" value="anndata"/>
+      <param name="flavor" value="seurat"/>
+      <param name="n_bin" value="20"/>
+      <repeat name="parameters">
+        <param name="name" value="mean"/>
+        <param name="min" value="0.0125"/>
+        <param name="max" value="3"/>
+      </repeat>
+      <repeat name="parameters">
+        <param name="name" value="disp"/>
+        <param name="min" value="0.5"/>
+        <param name="max" value="1e9"/>
+      </repeat>
+      <output name="output_h5" file="find_variable_genes.h5" ftype="h5" compare="sim_size"/>
+    </test>
+  </tests>
+
+  <help><![CDATA[
+============================================================
+Extract highly variable genes (`pp.filter_genes_dispersion`)
+============================================================
+
+Depending on `flavor`, this reproduces the R-implementations of Seurat and Cell Ranger.
+
+The normalized dispersion is obtained by scaling with the mean and standard
+deviation of the dispersions for genes falling into a given bin for mean
+expression of genes. This means that for each bin of mean expression, highly
+variable genes are selected.
+
+@HELP@
+
+@VERSION_HISTORY@
+]]></help>
+  <expand macro="citations">
+    <citation type="doi">10.1038/nbt.3192</citation>
+    <citation type="doi">10.1038/ncomms14049</citation>
+  </expand>
+</tool>