changeset 1:e7fd6981c0f0 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"

--- a/scanpy-neighbours.xml	Wed Apr 03 11:11:14 2019 -0400
+++ b/scanpy-neighbours.xml	Mon Sep 16 08:18:53 2019 -0400
@@ -1,34 +1,27 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy1">
+<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy0">
   <description>to derive kNN graph</description>
   <macros>
-    <import>scanpy_macros.xml</import>
+    <import>scanpy_macros2.xml</import>
   </macros>
   <expand macro="requirements"/>
   <command detect_errors="exit_code"><![CDATA[
 ln -s '${input_obj_file}' input.h5 &&
-PYTHONIOENCODING=utf-8 scanpy-neighbours.py
-    -i input.h5
-    -f '${input_format}'
-    -o output.h5
-    -F '${output_format}'
-    #if $settings.default == "false"
-        -N '${settings.n_neighbours}'
-        -m '${settings.method}'
-        -s '${settings.random_seed}'
-        #if $settings.use_rep != "auto"
-            -r '${settings.use_rep}'
-        #end if
-        #if $settings.n_pcs
-            -n '${settings.n_pcs}'
-        #end if
-        #if $settings.knn
-            --knn
-        #end if
-        #if $settings.metric
-            -M '${settings.metric}'
-        #end if
+PYTHONIOENCODING=utf-8 scanpy-neighbors
+#if $settings.default == "false"
+    --n-neighbors '${settings.n_neighbours}'
+    --method '${settings.method}'
+    --random-state '${settings.random_seed}'
+    #if $settings.use_rep != "auto"
+        --use-rep '${settings.use_rep}'
     #end if
+    #if $settings.n_pcs
+        --n-pcs '${settings.n_pcs}'
+    #end if
+    ${settings.knn}
+#end if
+    @INPUT_OPTS@
+    @OUTPUT_OPTS@
 ]]></command>
 
   <inputs>
@@ -39,18 +32,17 @@
       <when value="true"/>
       <when value="false">
         <param name="n_neighbours" argument="--n-neighbors" type="integer" value="15" label="Maximum number of neighbours used"/>
-        <param name="use_rep" type="select" label="Use the indicated representation">
-          <option value="X_pca">X_pca, use PCs</option>
+        <param name="use_rep" type="text" label="Use the indicated representation">
+          <option value="X_pca" selected="true">X_pca, use PCs</option>
           <option value="X">X, use normalised expression values</option>
-          <option value="auto" selected="true">Automatically chosen based on problem size</option>
         </param>
         <param name="n_pcs" argument="--n-pcs" type="integer" value="50" optional="true" label="Number of PCs to use"/>
-        <param name="knn" argument="--knn/--no-knn" type="boolean" checked="true" label="Use hard threshold to restrict neighbourhood size (otherwise use a Gaussian kernel to down weight distant neighbours)"/>
+        <param name="knn" argument="--knn" type="boolean" truevalue="" falsevalue="--no-knn" checked="true"
+               label="Use hard threshold to restrict neighbourhood size (otherwise use a Gaussian kernel to down weight distant neighbours)"/>
         <param name="method" argument="--method" type="select" label="Method for calculating connectivity">
           <option value="umap" selected="true">UMAP</option>
           <option value="gauss">Gaussian</option>
         </param>
-        <param name="metric" argument="--metric" type="text" value="euclidean" label="Distance metric"/>
         <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for random number generator"/>
       </when>
     </conditional>
@@ -71,7 +63,6 @@
       <param name="knn" value="true"/>
       <param name="random_seed" value="0"/>
       <param name="method" value="umap"/>
-      <param name="metric" value="euclidean"/>
       <output name="output_h5" file="compute_graph.h5" ftype="h5" compare="sim_size"/>
     </test>
   </tests>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scanpy_macros2.xml	Mon Sep 16 08:18:53 2019 -0400
@@ -0,0 +1,94 @@
+<macros>
+  <token name="@TOOL_VERSION@">1.4.2</token>
+  <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
+  <token name="@VERSION_HISTORY@"><![CDATA[
+**Version history**
+
+1.4.2+galaxy0: Update to scanpy-scripts 0.2.4 (requires scanpy >=1.4.2).
+
+1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files.
+
+1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home  at
+EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
+    ]]></token>
+  <token name="@INPUT_OPTS@">
+    --input-format '${input_format}' input.h5
+  </token>
+  <token name="@OUTPUT_OPTS@">
+    --show-obj stdout --output-format '${output_format}' output.h5
+  </token>
+  <token name="@PLOT_OPTS@">
+#if $fig_title
+    --title '${fig_title}'
+#end if
+    --fig-size '${fig_size}'
+    --fig-dpi ${fig_dpi}
+    --fig-fontsize ${fig_fontsize}
+    ${fig_frame}
+    ./output.png
+  </token>
+  <token name="@EXPORT_MTX_OPTS@">${export_mtx}</token>
+
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="0.2.4.post4">scanpy-scripts</requirement>
+      <yield/>
+    </requirements>
+  </xml>
+
+  <xml name="citations">
+    <citations>
+      <yield />
+      <citation type="doi">10.1186/s13059-017-1382-0</citation>
+      <citation type="bibtex">
+	@misc{githubscanpy-scripts,
+	author = {Ni Huang, EBI Gene Expression Team},
+	year = {2018},
+	title = {Scanpy-scripts: command line interface for Scanpy},
+	publisher = {GitHub},
+	journal = {GitHub repository},
+	url = {https://github.com/ebi-gene-expression-group/scanpy-scripts},
+      }</citation>
+    </citations>
+  </xml>
+
+  <xml name="input_object_params">
+    <param name="input_obj_file" argument="input-object-file" type="data" format="h5" label="Input object in hdf5 format"/>
+    <param name="input_format" argument="--input-format" type="select" label="Format of input object">
+      <option value="anndata" selected="true">AnnData format hdf5</option>
+      <option value="loom">Loom format hdf5</option>
+    </param>
+  </xml>
+
+  <xml name="output_object_params">
+    <param name="output_format" argument="--output-format" type="select" label="Format of output object">
+      <option value="anndata" selected="true">AnnData format hdf5</option>
+      <option value="loom">Loom format hdf5</option>
+    </param>
+  </xml>
+
+  <xml name="output_plot_params">
+    <param name="fig_title" argument="--title" type="text" label="Figure title"/>
+    <param name="fig_size" argument="--fig-size" type="text" value="4,4" label="Figure size as 'width,height', e.g, '7,7'"/>
+    <param name="fig_dpi" argument="--fig-dpi" type="integer" min="1" value="80" label="Figure dpi"/>
+    <param name="fig_fontsize" argument="--fig-fontsize" type="integer" min="0" value="10" label="Figure font size"/>
+    <param name="fig_frame" type="boolean" truevalue="--frameon" falsevalue="--frameoff" checked="false"
+           label="Show plot frame"/>
+  </xml>
+
+  <xml name="export_mtx_params">
+    <param name="export_mtx" argument="--export-mtx" type="boolean" truevalue="--export-mtx ./" falsevalue="" checked="false" label="Save normalised data to 10x mtx format" help="If enabled, it will generate in addition to the main output in Loom or AnnData an export in 10x format of the normalised data."/>
+  </xml>
+
+  <xml name="export_mtx_outputs">
+    <data name="matrix_10x" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string}: 10x matrix">
+      <filter>export_mtx</filter>
+    </data>
+    <data name="genes_10x" format="tsv" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: 10x genes">
+      <filter>export_mtx</filter>
+    </data>
+    <data name="barcodes_10x" format="tsv" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string}: 10x barcodes">
+      <filter>export_mtx</filter>
+    </data>
+  </xml>
+</macros>