diff scanpy-filter-cells.xml @ 0:9f0ca1641ab2 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-filter-cells.xml	Wed Apr 03 11:12:31 2019 -0400
@@ -0,0 +1,79 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="scanpy_filter_cells" name="Scanpy FilterCells" version="@TOOL_VERSION@+galaxy0">
+  <description>based on counts and numbers of genes expressed</description>
+  <macros>
+    <import>scanpy_macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[
+ln -s '${input_obj_file}' input.h5 &&
+PYTHONIOENCODING=utf-8 scanpy-filter-cells.py
+    -i input.h5
+    -f '${input_format}'
+    -o output.h5
+    -F '${output_format}'
+    #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 $subset
+        -s '${subset}'
+    #end if
+    ]]></command>
+
+  <inputs>
+    <expand macro="input_object_params"/>
+    <expand macro="output_object_params"/>
+    <repeat name="parameters" title="Parameters used to filter cells" min="1">
+      <param name="name" type="text" value="n_genes" label="Name of parameter to filter on" help="for example n_genes or n_counts">
+        <option value="n_genes">n_genes</option>
+        <option value="n_counts">n_counts</option>
+      </param>
+      <param name="min" type="float" value="0" min="0" label="Min value"/>
+      <param name="max" type="float" value="1e9" label="Max value"/>
+    </repeat>
+    <param name="subset" argument="--subset-list" type="data" format="tsv" optional="true" label="List of barcodes"/>
+  </inputs>
+
+  <outputs>
+    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Filtered cells"/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input_obj_file" value="read_10x.h5"/>
+      <param name="input_format" value="anndata"/>
+      <param name="output_format" value="anndata"/>
+      <repeat name="parameters">
+        <param name="name" value="n_genes"/>
+        <param name="min" value="200"/>
+        <param name="max" value="2500"/>
+      </repeat>
+      <repeat name="parameters">
+        <param name="name" value="n_counts"/>
+        <param name="min" value="0"/>
+        <param name="max" value="1e9"/>
+      </repeat>
+      <output name="output_h5" file="filter_cells.h5" ftype="h5" compare="sim_size"/>
+    </test>
+  </tests>
+
+  <help><![CDATA[
+========================================================================================
+Filter cells outliers based on counts and numbers of genes expressed (`pp.filter_cells`)
+========================================================================================
+
+For instance, only keep cells with at least `min_counts` counts or
+`min_genes` genes expressed. This is to filter measurement outliers, i.e.,
+"unreliable" observations.
+
+@HELP@
+
+@VERSION_HISTORY@
+]]></help>
+  <expand macro="citations"/>
+</tool>