Add Spapros

tools/spapros/.shed.yml

@@ -0,0 +1,19 @@
+name: spapros
+owner: iuc
+description: "Select and evaluate probe sets for targeted spatial transcriptomics."
+homepage_url: https://github.com/theislab/spapros
+long_description: |
+    Spapros is a python package that provides a pipeline for probe set selection and evaluation for targeted spatial transcriptomics data.
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/
+type: unrestricted
+categories:
+- Transcriptomics
+- Sequence Analysis
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "Wrapper for the spapros tool suite: {{ tool_name }}"
+suite:
+  name: "suite_spapros"
+  description: "Spapros - Probe selection and evaluation"
+  long_description: |
+    Spapros is a python package that provides a pipeline for probe set selection and evaluation for targeted spatial transcriptomics data.

tools/spapros/macros.xml

@@ -0,0 +1,97 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.1.5</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@profile@">22.05</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">spapros</requirement>
+            <yield />
+        </requirements>
+    </xml>
+    <xml name="creators">
+        <creator>
+            <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />
+        </creator>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1101/2022.08.16.504115</citation>
+            <citation type="doi">10.1093/gigascience/giaa102</citation>
+        </citations>
+    </xml>
+    <xml name="version_command">
+        <version_command><![CDATA[python -c "import spapros;print('%s' % spapros.__version__ )"]]></version_command>
+    </xml>
+    <token name="@CMD@"><![CDATA[
+cp '$adata' 'anndata.h5ad' &&
+cat '$script_file' > '$hidden_output' &&
+python '$script_file' >> '$hidden_output' &&
+ls . >> '$hidden_output'
+    ]]>
+    </token>
+    <token name="@CMD_imports@"><![CDATA[
+import spapros as sp
+import os
+import pandas as pd
+import scanpy as sc
+import matplotlib as mpl
+import matplotlib.pyplot as plt
+    ]]>
+    </token>
+    <token name="@CMD_plot@"><![CDATA[
+#if $method.set_ids != 'all' and $method.set_ids != '':
+set_ids=[$method.set_ids],
+#end if
+save='plot.$format',
+show=False
+    ]]>
+    </token>
+    <xml name="set_ids">
+        <param name="set_ids" type="text" value="all" optional="true" label="List of probeset ids (comma seperated, e.g., DE,HVG,random)" help="Kepp it with all or empty to select all probeset ids."/>
+    </xml>
+    <xml name="sanitize_query" token_validinitial="string.printable">
+        <sanitizer>
+            <valid initial="@VALIDINITIAL@">
+                <remove value="&apos;" />
+            </valid>
+       </sanitizer>
+    </xml>
+    <xml name="sanitize_vectors" token_validinitial="string.digits">
+        <sanitizer>
+            <valid initial="@VALIDINITIAL@">
+                <add value=","/>
+            </valid>
+        </sanitizer>
+    </xml>
+    <xml name="inputs_anndata">
+        <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
+    </xml>
+    <token name="@CMD_read_inputs@"><![CDATA[
+adata = sc.read_h5ad('anndata.h5ad')
+]]>
+    </token>
+    <xml name="inputs_common_advanced">
+        <section name="advanced_common" title="Advanced Output Options" expanded="false">
+            <param name="show_log" type="boolean" checked="false" label="Output Log?" />
+        </section>
+    </xml>
+    <xml name="param_plot_format">
+        <param name="format" type="select" label="Format for saving figures">
+            <option value="png">png</option>
+            <option value="pdf">pdf</option>
+            <option value="svg">svg</option>
+        </param>
+    </xml>
+    <xml name="param_markerset">
+        <param name="markerset" type="data" format="tabular" label="Markerset tabular file with rows=conditions (e.g., celltypes) and column=features (e.g., genes)" help="This is beeing used to calculate the corelations betweens your probeset features and marker features. Marker features are for example genes that you know are important for your condition (e.g., celltypes)."/>
+        <param name="header_markerset" type="select" optional="false" label="Header in the list of markers?">
+            <option value="included">Header included</option>
+            <option value="not_included">Header not included</option>
+        </param>
+    </xml>
+    <xml name="hidden_outputs">
+        <data name="hidden_output" format="txt" label="Log file" >
+            <filter>advanced_common['show_log']</filter>
+        </data>
+    </xml>
+</macros>