changeset 0:dae1539a77fa draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0dbd119d68dbe360e8f896f6471dc7692858c4bc-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/matrix-service.xml	Mon Jul 01 19:03:27 2019 -0400
@@ -0,0 +1,108 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="_hca_matrix_downloader" name="Human Cell Atlas Matrix Downloader" version="v0.0.2+galaxy0">
+  <description>retrieves expression matrices and metadata from the Human Cell Atlas.</description>
+  <requirements>
+    <requirement type="package" version="0.0.2">hca-matrix-downloader</requirement>
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[
+
+hca-matrix-downloader -p '${project}' -f mtx -o out -f '${matrix_format}'
+
+#if $matrix_format == "mtx":
+  && hca-mtx-to-10x out.mtx .
+  && gunzip -c out.mtx/cells.tsv.gz > exp_design.tsv
+#end if
+
+]]></command>
+
+  <inputs>
+    <param name="project" type="text" value="Single cell transcriptome analysis of human pancreas" label="Human Cell Atlas project name/label/UUID" help="HCA project identifier, can be project title, project label or project UUID."/>
+    <param name="matrix_format" type="select" label="Choose the format of matrix to download" help="Matrix Market or Loom">
+      <option value="mtx" selected="true">Matrix Market</option>
+      <option value="loom">Loom</option>
+    </param>
+  </inputs>
+
+  <outputs>
+    <data name="matrix_mtx" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string} matrix.mtx">
+      <filter>matrix_format=="mtx"</filter>
+    </data>
+    <data name="genes_tsv" format="tsv" from_work_dir="genes.tsv" label="${tool.name} on ${on_string} genes.tsv">
+      <filter>matrix_format=="mtx"</filter>
+    </data>
+    <data name="barcode_tsv" format="tsv" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string} barcodes.tsv">
+      <filter>matrix_format=="mtx"</filter>
+    </data>
+    <data name="cells_meta_tsv" format="tsv" from_work_dir="exp_design.tsv" label="${tool.name} on ${on_string} exp_design.tsv">
+      <filter>matrix_format=="mtx"</filter>
+    </data>
+    <data name="matrix_loom" format="h5" from_work_dir="out.loom" label="${tool.name} on ${on_string} matrix.loom">
+      <filter>matrix_format=="loom"</filter>
+    </data>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="project" value="Single cell transcriptome analysis of human pancreas"/>
+      <param name="matrix_format" value="mtx"/>
+      <output name="matrix_mtx" file="matrix.mtx" ftype="txt"/>
+      <output name="genes_tsv" file="genes.tsv" ftype="tsv"/>
+      <output name="barcode_tsv" file="barcodes.tsv" ftype="tsv"/>
+      <output name="cells_meta_tsv" file="exp_design.tsv" ftype="tsv"/>
+    </test>
+  </tests>
+
+  <help><![CDATA[
+===========================================================================
+Down expression matrix from HCA projects using HCA DCP's matrix service API
+===========================================================================
+
+The data retrieval tool presented here allows the user to retrieve expression matrices
+and metadata for any public experiment available at Human Cell Atlas data portal.
+
+To use it, simply set the name, or label, or ID for the desired project, which can be
+found at the HCA data browser (https://prod.data.humancellatlas.org/explore/projects),
+and select the desired matrix format (Matrix Market or Loom).
+
+Outputs will be:
+
+- *When "Matrix Market" is seleted, outputs are in 10X-compatible Matrix Market format:*
+
+  1. **Matrix (txt):**
+
+     Contains the expression values for genes (rows) and cells (columns) in raw counts. This
+     text file is formatted as a Matrix Market file, and as such it is accompanied by separate
+     files for the gene identifiers and the cells identifiers.
+
+  2. **Genes (tsv):**
+
+     Identifiers (column repeated) for the genes present in the matrix of expression,
+     in the same order as the matrix rows.
+
+  3. **Barcodes (tsv):**
+
+     Identifiers for the cells of the data matrix. The file is ordered to match the columns
+     of the matrix.
+
+  4. **Experiment Design file (tsv):**
+
+     Contains metadata for the different cells of the experiment.
+
+- *When "Loom" is selected, output is a single Loom HDF5 file:*
+
+  1. **Loom (h5):**
+
+     Contains expression values for genes (rows) and cells (columns) in raw counts, cell
+     metadata table and gene metadata table, in a single HDF5 file with specification defined
+     in http://linnarssonlab.org/loompy/format/index.html.
+
+**Version history**
+
+     0.0.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Teichmann Lab at Wellcome Sanger Institute and
+     Expression Atlas team https://www.ebi.ac.uk/gxa/home  at EMBL-EBI https://www.ebi.ac.uk/.
+
+]]></help>
+  <citations>
+    <citation type="doi">10.7554/eLife.27041</citation>
+  </citations>
+</tool>