diff scanpy-find-cluster.xml @ 0:ce27ae8a36cd 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-cluster.xml	Wed Apr 03 11:09:12 2019 -0400
@@ -0,0 +1,102 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy1">
+  <description>based on community detection on KNN graph</description>
+  <macros>
+    <import>scanpy_macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[
+ln -s '${input_obj_file}' input.h5 &&
+PYTHONIOENCODING=utf-8 scanpy-find-cluster.py
+    -i input.h5
+    -f '${input_format}'
+    -o output.h5
+    -F '${output_format}'
+    #if $output_cluster
+        --output-text-file output.tsv
+    #end if
+    #if $settings.default == "false"
+        --flavor '${settings.flavor}'
+        --key-added '${settings.key_added}'
+        -s '${settings.random_seed}'
+        #if $settings.flavor == "vtraag" and $settings.resolution_file
+            --resolution \$( cat $settings.resolution_file )
+        #elif $settings.flavor == "vtraag"
+            --resolution '${settings.resolution}'
+        #end if
+        #if $settings.restrict_to
+            --restrict-to '${settings.restrict_to}'
+        #end if
+        #if $settings.use_weights
+            --use-weights
+        #end if
+    #end if
+]]></command>
+
+  <inputs>
+    <expand macro="input_object_params"/>
+    <expand macro="output_object_params"/>
+    <param name="output_cluster" type="boolean" checked="true" label="Output cluster in two column text format"/>
+    <conditional name="settings">
+      <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
+      <when value="true"/>
+      <when value="false">
+        <param name="flavor" argument="--flavor" type="select" label="Use the indicated representation">
+          <option value="vtraag" selected="true">vtraag</option>
+          <option value="igraph">igraph</option>
+        </param>
+        <param name="resolution" argument="--resolution" type="float" value="1.0" label="Resolution, high value for more and smaller clusters"/>
+        <param name="resolution_file" argument="--resolution" type="data" format="txt,tsv" optional="true" label="File with resolution, use with parameter iterator. Overrides the resolution setting"/>
+        <param name="restrict_to" argument="--restrict-to" type="text" optional="true" label="Restrict clustering to certain sample categories"/>
+        <param name="key_added" argument="--key-added" type="text" value="louvain" label="Key under which to add the cluster labels (do not change unless you know what you are doing)"/>
+        <param name="use_weights" argument="--use-weights" type="boolean" checked="false" label="Use weights from knn graph"/>
+        <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for random number generator"/>
+      </when>
+    </conditional>
+  </inputs>
+
+  <outputs>
+    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Cluster object"/>
+    <data name="output_txt" format="tsv" from_work_dir="output.tsv" label="${tool.name} on ${on_string}: Cluster table">
+      <filter>output_cluster</filter>
+    </data>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input_obj_file" value="compute_graph.h5"/>
+      <param name="input_format" value="anndata"/>
+      <param name="output_format" value="anndata"/>
+      <param name="output_txt" value="true"/>
+      <param name="default" value="false"/>
+      <param name="flavor" value="vtraag"/>
+      <param name="resolution" value="1.0"/>
+      <param name="random_seed" value="0"/>
+      <output name="output_h5" file="find_cluster.h5" ftype="h5" compare="sim_size"/>
+      <output name="output_txt" file="find_cluster.tsv" ftype="tsv"/>
+    </test>
+  </tests>
+
+  <help><![CDATA[
+===========================================
+Cluster cells into subgroups (`tl.louvain`)
+===========================================
+
+Cluster cells using the Louvain algorithm (Blondel et al, 2008) in the implementation
+of Traag et al,2017. The Louvain algorithm has been proposed for single-cell
+analysis by Levine et al, 2015.
+
+This requires to run `Scanpy ComputeGraph`, first.
+
+It yields `louvain`, generated cluster label.
+
+@HELP@
+
+@VERSION_HISTORY@
+]]></help>
+  <expand macro="citations">
+    <citation type="doi">10.1088/1742-5468/2008/10/P10008</citation>
+    <citation type="doi">10.1016/j.cell.2015.05.047</citation>
+    <citation type="doi">10.5281/zenodo.35117</citation>
+  </expand>
+</tool>