diff seurat_export_cellbrowser.xml @ 0:29112eeaf521 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit fc12e1e90bdc675bd81cf50528afd64ff3dc5c08

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seurat_export_cellbrowser.xml	Mon Mar 04 12:08:58 2019 -0500
@@ -0,0 +1,69 @@
+<tool id="seurat_export_cellbrowser" name="Seurat Export2CellBrowser" version="2.3.1+galaxy0">
+    <description>produces files for UCSC CellBrowser import.</description>
+    <macros>
+        <import>seurat_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version" />
+    <command detect_errors="exit_code"><![CDATA[
+#if $markers_file:
+  cp '$markers_file' markers.csv;
+#end if
+
+seurat-export-cellbrowser.R -i '$rds_input'
+
+#if $markers_file:
+-m markers.csv
+#end if
+
+-o output_html;
+
+cd output_html && tar -cf '$output' *;
+]]></command>
+
+    <inputs>
+        <param name="rds_input" type="data" format="rdata" label="Seurat RDS object" />
+        <param name="markers_file" type="data" format="txt" label="Marker genes file from Seurat" />
+    </inputs>
+
+    <outputs>
+        <data name="output" format="tar" label="${tool.name} on ${on_string}: UCSC CellBrowser bundle"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="rds_input" ftype="rdata" value="out_runtsne.rds"/>
+            <param name="markers_file" ftype="txt" value="out_markers.csv"/>
+            <output name="output" ftype="tar" value="out_cellbrowser_bundle.tar"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.
+It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and
+interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse
+types of single cell data.
+
+This tool converts a Seurat object (hopefully with t-SNE results) and its accompanying marker genes file (optional)
+to a tar that can be feed to the UCSC CellBrowser tool.
+-----
+
+**Inputs**
+
+    * RDS object
+
+-----
+
+**Outputs**
+
+    * Text file
+
+.. _Seurat: https://www.nature.com/articles/nbt.4096
+.. _Satija Lab: https://satijalab.org/seurat/
+
+]]></help>
+      <expand macro="citations" />
+</tool>