# HG changeset patch
# User ebi-gxa
# Date 1594432096 14400
# Node ID 2d121013176ff930b3138960bbaa23c2c2cae78f
# Parent  265dcc5bc1e810cfbd154c5c282c7ac6f0dd1b76
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit bbe3c1f7fd8489951f2d90415fe80dd5cf961ca0

diff -r 265dcc5bc1e8 -r 2d121013176f seurat_macros.xml
--- a/seurat_macros.xml	Mon Nov 25 06:10:49 2019 -0500
+++ b/seurat_macros.xml	Fri Jul 10 21:48:16 2020 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@VERSION@">0.0.6</token>
+    <token name="@VERSION@">0.0.7</token>
     <token name="@SEURAT_VERSION@">3.1.1</token>
     <xml name="requirements">
         <requirements>
@@ -97,6 +97,8 @@
     <token name="@VERSION_HISTORY@"><![CDATA[
 **Version history**
 
+3.1.1_0.0.7: Exposes perplexity and enables tab input.
+
 3.1.1_0.0.6+galaxy0: Moved to Seurat 3.
 
   Find clusters: removed dims-use, k-param, prune-snn.
@@ -121,6 +123,7 @@
               url = {https://github.com/ebi-gene-expression-group/r-seurat-scripts.git},
             }
             </citation>
+            <citation type="doi">10.1101/2020.04.08.032698</citation>
         </citations>
     </xml>
 </macros>
diff -r 265dcc5bc1e8 -r 2d121013176f seurat_read10x.xml
--- a/seurat_read10x.xml	Mon Nov 25 06:10:49 2019 -0500
+++ b/seurat_read10x.xml	Fri Jul 10 21:48:16 2020 -0400
@@ -1,5 +1,5 @@
-<tool id="seurat_read10x" name="Seurat Read10x" version="@SEURAT_VERSION@_@VERSION@+galaxy0">
-<description>Loads 10x data into a serialized seurat R object</description>
+<tool id="seurat_read10x" name="Seurat Read10x" version="@SEURAT_VERSION@+galaxy1">
+<description>Loads Tabular or 10x data into a serialized seurat R object</description>
   <macros>
       <import>seurat_macros.xml</import>
   </macros>
@@ -8,12 +8,19 @@
 <exit_code range="1:" />
 </stdio>
 <command><![CDATA[
-ln -s "$matrix" matrix.mtx;
-ln -s "$genes" genes.tsv;
-ln -s "$barcodes" barcodes.tsv;
+
+#if str($input.format) == "mtx":
+    ln -s "$matrix" matrix.mtx;
+    ln -s "$genes" genes.tsv;
+    ln -s "$barcodes" barcodes.tsv;
+# end if
 
-seurat-read-10x.R -d ./
-
+seurat-read-10x.R
+#if str($input.format) == "mtx":
+ -d ./
+#else
+ -f $input.file
+# end if
 #if $metadata
   --metadata '$metadata'
 #end if
@@ -28,9 +35,20 @@
 
 ]]></command>
 <inputs>
-    <param type="data" name="matrix" help="Raw expression quantification as a sparse matrix in Matrix Market format, where each column is a gene and each row is a barcode/cell." format="txt" label="Expression matrix in sparse matrix format (.mtx)" />
-    <param type="data" name="genes" help="Matrix market column file for genes" label="Gene table" format="tsv,tabular"/>
-    <param type="data" name="barcodes" help="Matrix market row file for genes" label="Barcode/cell table" format="tsv,tabular"/>
+     <conditional name="input" label="Input expression data">
+       <param type="select" name="format" label="Choose the format of the input" help="10X MTX or tabular">
+         <option value="mtx" selected="true">10X-type MTX</option>
+         <option value="tab" selected="true">tab-delimited text</option>
+       </param>
+       <when value="tab">
+         <param type="data" name="file" label="Expression table" help="Tab-delimted expression table" format="tabular"/>
+       </when>
+       <when value="mtx">
+        <param type="data" name="matrix" help="Raw expression quantification as a sparse matrix in Matrix Market format, where each column is a gene and each row is a barcode/cell." format="txt" label="Expression matrix in sparse matrix format (.mtx)" />
+        <param type="data" name="genes" help="Matrix market column file for genes" label="Gene table" format="tsv,tabular"/>
+        <param type="data" name="barcodes" help="Matrix market row file for genes" label="Barcode/cell table" format="tsv,tabular"/>
+       </when>
+     </conditional>
     <param label="Cell Metadata" optional="true" name="metadata" argument="--metadata" type="data" format="tsv,tabular" help="File with metdata for the cells, first column should be cell identifiers as used in the cells 10x file."/>
     <param label="Minimum cells to include features" optional="true" name="min_cells" argument="--min-cells" type="integer" help="Include features detected in at least this many cells. Will subset the counts matrix as well. To reintroduce excluded features, create a new object with a lower cutoff."/>
     <param label="Minimum features to include cells" optional="true" name="min_features" argument="--min-features" type="integer" help="Include cells where at least this many features are detected."/>
@@ -57,9 +75,9 @@
 
   @SEURAT_INTRO@
 
-  **Read 10x-Genomics-formatted mtx directory (`read_10x_mtx`)**
+  **Read expression data from a tabular file or a 10x-Genomics-formatted mtx directory (`read_10x_mtx`)**
 
-  The mtx directory should contain:
+  For mtx, the  directory should contain:
 
   1) Raw expression quantification as a sparse matrix in Matrix Market format, where the each column is a gene and each row is a barcode/cell.
 
@@ -72,9 +90,10 @@
   datasets.
 
   **Inputs**
-      * Raw expression quantification as a sparse matrix in Matrix Market format, where the each column is a gene and each row is a barcode/cell.
-      * A gene table of at least two columns where the first column gives the gene IDs.
-      * A barcode/cell table of at least one column giving the barcode/cell IDs.
+      * A tabular file of expression data OR
+          * Raw expression quantification as a sparse matrix in Matrix Market format, where the each column is a gene and each row is a barcode/cell.
+          * A gene table of at least two columns where the first column gives the gene IDs.
+          * A barcode/cell table of at least one column giving the barcode/cell IDs.
       * Optionally, a file with cell metadata.
 
   **Outputs**