Mercurial > repos > ebi-gxa > scater_read_10x_results

diff scater-read-10x-results.xml @ 0:da3f394039b5 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
author ebi-gxa
date Wed, 03 Apr 2019 11:40:51 -0400
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scater-read-10x-results.xml	Wed Apr 03 11:40:51 2019 -0400
@@ -0,0 +1,36 @@
+<tool id="scater_read_10x_results" name="Scater read 10x data" version="@TOOL_VERSION@+galaxy0">
+    <description>Loads 10x data into a serialized scater R object</description>
+    <macros>
+        <import>scater_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$matrix' matrix.mtx;
+        ln -s '$genes' genes.tsv;
+        ln -s '$barcodes' barcodes.tsv;
+
+        scater-read-10x-results.R -d ./ -o '$R_scater_serialized'
+    ]]></command>
+    <inputs>
+        <param type="data" name="matrix" format="txt" help="File containing the matrix.mtx, genes.txt, barcodes.txt files provided by 10X. A vector or named vector can be given in order to load several data directories. If a named vector is given, the cell barcode names will be prefixed with the name."/>
+        <param type="data" name="genes" format="tsv" help="File containing the genes.txt, barcodes.txt files provided by 10X. A vector or named vector can be given in order to load several data directories. If a named vector is given, the cell barcode names will be prefixed with the name."/>
+        <param type="data" name="barcodes" format="tsv" help="File containing the barcodes.txt files provided by 10X. A vector or named vector can be given in order to load several data directories. If a named vector is given, the cell barcode names will be prefixed with the name"/>
+    </inputs>
+    <outputs>
+        <data name="R_scater_serialized" format="rdata" label=""/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix" value="matrix.mtx"/>
+            <param name="genes" value="genes.tsv"/>
+            <param name="barcodes" value="barcodes.tsv"/>
+            <output name="R_scater_serialized" file="R_scater_serialized.rds"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP@
+
+@VERSION_HISTORY@
+    ]]></help>
+    <expand macro="citations" />
+</tool>