changeset 1:90fac5c7e0b7 draft default tip

Deleted selected files

--- a/matrix-service.xml	Mon Jul 01 19:03:27 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,108 +0,0 @@
-<?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>