diff inspect.xml @ 0:b2a6ce371781 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/inspect.xml	Wed Apr 10 03:25:39 2019 -0400
@@ -0,0 +1,164 @@
+<tool id="anndata_inspect" name="Inspect AnnData" version="@VERSION@+@GALAXY_VERSION@">
+    <description>object</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+@CMD@
+      ]]></command>
+    <configfiles>
+        <configfile name="script_file"><![CDATA[
+@CMD_imports@
+
+adata = ad.read('$input')
+
+#if $inspect.info == 'general'
+with open('$general', 'w') as f:
+    print(adata, file=f)
+#else if $inspect.info == 'X'
+adata.to_df().to_csv('$X', sep='\t')
+#else if $inspect.info == 'obs'
+adata.obs.to_csv('$obs', sep='\t')
+#else if $inspect.info == 'var'
+adata.var.to_csv('$var', sep='\t')
+#else if $inspect.info == 'chunk_X'
+import pandas as pd
+    #if $inspect.chunk.info == 'random'
+X = adata.chunk_X(select=$inspect.chunk.size, replace=$inspect.chunk.replace)
+    #else
+        #set $select = [int(x.strip()) for x in str($inspect.chunk.list).split(',')]
+X = adata.chunk_X(select=$select)
+    #end if
+pd.DataFrame(X).to_csv('$chunk_X', sep='\t')
+#end if
+]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="input" type="data" format="h5ad" label="Annotated data matrix"/>
+        <conditional name="inspect">
+            <param name="info" type="select" label="What to inspect?">
+                <option value="general">General information about the object</option>
+                <option value="X">The full data matrix</option>
+                <option value="chunk_X">A chunk of the data matrix</option>
+                <option value="obs">Key-indexed observations annotation</option>
+                <option value="var">Key-indexed annotation of variables/features</option>
+                <!--<option value="uns">Unstructured annotation</option>!-->
+            </param>
+            <when value="general"/>
+            <when value="X"/>
+            <when value="obs"/>
+            <when value="var"/>
+            <when value="chunk_X">
+                <expand macro="params_chunk_X"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="general" format="txt" label="${tool.name} on ${on_string}: General information">
+            <filter>inspect['info'] == 'general'</filter>
+        </data>
+        <data name="X" format="tabular" label="${tool.name} on ${on_string}: Key-indexed observations annotation (X)">
+            <filter>inspect['info'] == 'X'</filter>
+        </data>
+        <data name="obs" format="tabular" label="${tool.name} on ${on_string}: Key-indexed observations annotation (obs)">
+            <filter>inspect['info'] == 'obs'</filter>
+        </data>
+        <data name="var" format="tabular" label="${tool.name} on ${on_string}: Key-indexed annotation of variables/features (var)">
+            <filter>inspect['info'] == 'var'</filter>
+        </data>
+        <data name="chunk_X" format="tabular" label="${tool.name} on ${on_string}: Observations annotation">
+            <filter>inspect['info'] == 'chunk_X'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="krumsiek11.h5ad"/>
+            <conditional name="inspect">
+                <param name="info" value="general"/>
+            </conditional>
+            <output name="general" value="inspect.general.txt"/>
+        </test>
+        <test>
+            <param name="input" value="krumsiek11.h5ad"/>
+            <conditional name="inspect">
+                <param name="info" value="X"/>
+            </conditional>
+            <assert_stdout>
+                <has_text_matching expression="adata.to_df\(\).to_csv"/>
+            </assert_stdout>
+            <output name="X" value="inspect.X.tabular" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="input" value="krumsiek11.h5ad"/>
+            <conditional name="inspect">
+                <param name="info" value="obs"/>
+            </conditional>
+            <assert_stdout>
+                <has_text_matching expression="adata.obs.to_csv"/>
+            </assert_stdout>
+            <output name="obs" value="inspect.obs.tabular" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="input" value="krumsiek11.h5ad"/>
+            <conditional name="inspect">
+                <param name="info" value="var"/>
+            </conditional>
+            <assert_stdout>
+                <has_text_matching expression="adata.var.to_csv"/>
+            </assert_stdout>
+            <output name="var" value="inspect.var.tabular" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="input" value="krumsiek11.h5ad"/>
+            <conditional name="inspect">
+                <param name="info" value="chunk_X"/>
+                <conditional name="chunk">
+                    <param name="info" value="specified"/>
+                    <param name="list" value="3,5,8"/>
+                </conditional>
+            </conditional>
+            <assert_stdout>
+                <has_text_matching expression="adata.chunk_X"/>
+                <has_text_matching expression="select=\[3, 5, 8\]"/>
+            </assert_stdout>
+            <output name="chunk_X" value="inspect.chunk_X.specified.tabular" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="input" value="krumsiek11.h5ad"/>
+            <conditional name="inspect">
+                <param name="info" value="chunk_X"/>
+                <conditional name="chunk">
+                    <param name="info" value="random"/>
+                    <param name="list" value="10"/>
+                    <param name="replace" value="true"/>
+                </conditional>
+            </conditional>
+            <assert_stdout>
+                <has_text_matching expression="adata.chunk_X"/>
+                <has_text_matching expression="select=10"/>
+                <has_text_matching expression="replace=True"/>
+            </assert_stdout>
+            <output name="chunk_X">
+                <assert_contents>
+                    <has_text_matching expression="0\t1\t2\t3\t4\t5\t6\t7\t8\t9\t10"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This tool inspects a AnnData dataset and returns:
+
+- General information about the object as text
+- The full data matrix (`X`) as a Tabular
+- A chunk of the data matrix as a Tabular, using the `chunk_X method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.chunk_X.html>`__
+- Key-indexed observations annotation (`obs`) as a Tabular
+- Key-indexed annotation of variables/features (`var`) as a Tabular
+
+@HELP@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>