diff seurat_read10x.xml @ 1:265dcc5bc1e8 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f

--- a/seurat_read10x.xml	Wed Apr 03 11:18:21 2019 -0400
+++ b/seurat_read10x.xml	Mon Nov 25 06:10:49 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="seurat_read10x" name="Seurat Read10x" version="2.3.1+galaxy1">
+<tool id="seurat_read10x" name="Seurat Read10x" version="@SEURAT_VERSION@_@VERSION@+galaxy0">
 <description>Loads 10x data into a serialized seurat R object</description>
   <macros>
       <import>seurat_macros.xml</import>
@@ -12,15 +12,32 @@
 ln -s "$genes" genes.tsv;
 ln -s "$barcodes" barcodes.tsv;
 
-seurat-read-10x.R -d ./ -o "$R_seurat_serialized"
+seurat-read-10x.R -d ./
+
+#if $metadata
+  --metadata '$metadata'
+#end if
+#if $min_cells
+  --min-cells '$min_cells'
+#end if
+#if $min_features
+  --min-features '$min_features'
+#end if
+
+@OUTPUT_OBJECT@
+
 ]]></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"/>
+    <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."/>
+    <expand macro="output_object_params"/>
 </inputs>
 <outputs>
-    <data name="R_seurat_serialized" format="rdata" label="${tool.name} on ${on_string}: RData file" />
+    <expand macro="output_files"/>
 </outputs>
 
 <tests>
@@ -28,7 +45,7 @@
        <param name="matrix" ftype="txt" value="test_matrix.txt"/>
        <param name="genes" ftype="txt" value="test_genes.txt"/>
        <param name="barcodes" ftype="txt" value="test_barcodes.txt"/>
-       <output name="R_seurat_serialized" ftype="rdata" value="out_scale.rds" compare="sim_size"/>
+       <output name="rds_seurat_file" ftype="rdata" value="out_scale.rds" compare="sim_size"/>
     </test>
 </tests>
 
@@ -38,10 +55,7 @@
 
   **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. See the `Seurat Guided Clustering tutorial`_ for more information.
+  @SEURAT_INTRO@
 
   **Read 10x-Genomics-formatted mtx directory (`read_10x_mtx`)**
 
@@ -61,6 +75,7 @@
       * 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**
       * R object for Seurat