diff scanpy-run-fdg.xml @ 0:96af0059b974 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scanpy-run-fdg.xml	Mon Sep 16 08:23:52 2019 -0400
@@ -0,0 +1,93 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="scanpy_run_fdg" name="Scanpy RunFDG" version="@TOOL_VERSION@+galaxy0">
+  <description>visualise cell clusters using force-directed graph</description>
+  <macros>
+    <import>scanpy_macros2.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[
+ln -s '${input_obj_file}' input.h5 &&
+PYTHONIOENCODING=utf-8 scanpy-cli embed fdg
+    --use-graph '${use_graph}'
+    --key-added '${key_added}'
+#if $embeddings
+    --export-embedding embeddings.csv
+#end if
+#if $settings.default == "false"
+    --random-state ${settings.random_seed}
+    --layout ${settings.layout}
+    #if $settings.init_pos
+        --init-pos '${settings.init_pos}'
+    #end if
+#end if
+    @INPUT_OPTS@
+    @OUTPUT_OPTS@
+
+]]></command>
+
+  <inputs>
+    <expand macro="input_object_params"/>
+    <expand macro="output_object_params"/>
+    <param name="embeddings" type="boolean" checked="true" label="Output embeddings in csv format"/>
+    <param name="use_graph" argument="--use-graph" value="neighbors" type="text"
+           label="Name of the slot that holds the KNN graph"/>
+    <param name="key_added" argument="--key-added" type="text" optional="true"
+           label="Additional suffix to the name of the slot to save the embedding"/>
+
+    <conditional name="settings">
+      <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
+      <when value="true"/>
+      <when value="false">
+        <param name="init_pos" argument="--init-pos" type="text" label="Method to initialise embedding, any key for adata.obsm or choose from the preset methods">
+          <option value="paga">paga</option>
+        </param>
+        <param name="layout" argument="--layout" type="select" label="Graph layout">
+          <option value="fa" selected="true">fa</option>
+          <option value="fr">fr</option>
+          <option value="grid_fr">grid fr</option>
+        </param>
+        <param name="random_seed" argument="--random-state" type="integer" value="0" label="Seed for numpy random number generator"/>
+      </when>
+    </conditional>
+  </inputs>
+
+  <outputs>
+    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: FDG object"/>
+    <data name="output_embed" format="csv" from_work_dir="embeddings.csv" label="${tool.name} on ${on_string}: FDG embeddings">
+      <filter>embeddings</filter>
+    </data>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input_obj_file" value="find_cluster.h5"/>
+      <param name="input_format" value="anndata"/>
+      <param name="output_format" value="anndata"/>
+      <param name="default" value="false"/>
+      <param name="embeddings" value="true"/>
+      <param name="random_seed" value="0"/>
+      <output name="output_h5" file="run_fdg.h5" ftype="h5" compare="sim_size"/>
+      <output name="output_embed" file="run_fdg.embeddings.csv" ftype="csv" compare="sim_size">
+        <assert_contents>
+          <has_n_columns n="2" sep=","/>
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+
+  <help><![CDATA[
+================================================================================
+Embed the neighborhood graph using Force-directed Graph (`scanpy.tl.draw_graph`)
+================================================================================
+
+For making FDG plots, please use `Scanpy PlotEmbed` with the output of this
+tool and enter "draw_graph_{layout}" as the name of the embedding to plot.
+
+It yields `X_draw_graph_{layout}`, FDG coordinates of data.
+
+@HELP@
+
+@VERSION_HISTORY@
+]]></help>
+  <expand macro="citations"/>
+</tool>