# HG changeset patch
# User ebi-gxa
# Date 1584004175 0
# Node ID edb0d2e8ab6641f82e5149d8066854e4481e208a
# Parent  eae21a6c31283283c619c4a2a3953d0a6b2eb845
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"

diff -r eae21a6c3128 -r edb0d2e8ab66 scanpy-scale-data.xml
--- a/scanpy-scale-data.xml	Wed Mar 13 11:50:13 2019 -0400
+++ b/scanpy-scale-data.xml	Thu Mar 12 09:09:35 2020 +0000
@@ -1,44 +1,31 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_scale_data" name="Scanpy ScaleData" version="@TOOL_VERSION@+galaxy1">
+<tool id="scanpy_scale_data" name="Scanpy ScaleData" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@">
   <description>to make expression variance the same for all genes</description>
   <macros>
-    <import>scanpy_macros.xml</import>
+    <import>scanpy_macros2.xml</import>
   </macros>
   <expand macro="requirements"/>
   <command detect_errors="exit_code"><![CDATA[
 ln -s '${input_obj_file}' input.h5 &&
-PYTHONIOENCODING=utf-8 scanpy-scale-data.py
-    -i input.h5
-    -f '${input_format}'
-    -o output.h5
-    -F '${output_format}'
+PYTHONIOENCODING=utf-8 scanpy-scale-data
     #if $scale_max
-        -x '${scale_max}'
+        --max-value '${scale_max}'
     #end if
-    #if $var_to_regress
-        -V '${var_to_regress}'
-    #end if
-    #if $do_log
-        --do-log
-    #end if
-    #if $zero_center
-        --zero-center
-    #end if
+    ${zero_center}
+    @INPUT_OPTS@
+    @OUTPUT_OPTS@
 ]]></command>
 
   <inputs>
     <expand macro="input_object_params"/>
     <expand macro="output_object_params"/>
-    <param name="do_log" argument="--do-log" type="boolean" checked="true" label="Do log(x+1) transformation"/>
-    <param name="zero_center" argument="--zero-center" type="boolean" checked="true" label="Zero center data before scaling"/>
-    <param name="var_to_regress" argument="--var-to-regress" type="text" optional="true" label="Variable(s) to regress out">
-      <option value="n_counts">n_counts</option>
-    </param>
-    <param name="scale_max" argument="--scale-max" type="float" optional="true" label="Truncate to this value after scaling"/>
+    <param name="zero_center" type="boolean" checked="true" truevalue="" falsevalue="--no-zero-center"
+           label="Zero center data before scaling"/>
+    <param name="scale_max" argument="--max-value" type="float" min="0" optional="true" label="Truncate to this value after scaling"/>
   </inputs>
 
   <outputs>
-    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Scaled data"/>
+    <expand macro="output_data_obj" description="Scaled data"/>
   </outputs>
 
   <tests>
@@ -46,7 +33,6 @@
       <param name="input_obj_file" value="find_variable_genes.h5"/>
       <param name="input_format" value="anndata"/>
       <param name="output_format" value="anndata"/>
-      <param name="do_log" value="true"/>
       <param name="zero_center" value="true"/>
       <param name="scale_max" value="10"/>
       <output name="output_h5" file="scale_data.h5" ftype="h5" compare="sim_size"/>
@@ -58,11 +44,7 @@
 
     **What it does**
 
-    Scale data to unit variance and zero mean (`pp.scale`)
-    Regress out unwanted sources of variation (`pp.regress_out`)
-
-    Regress out unwanted sources of variation, using simple linear regression. This is
-    inspired by Seurat's `regressOut` function in R.
+    Scale data to unit variance and (optionally) zero mean (`scanpy.pp.scale`)
 
     @HELP@
 
diff -r eae21a6c3128 -r edb0d2e8ab66 scanpy_macros.xml
--- a/scanpy_macros.xml	Wed Mar 13 11:50:13 2019 -0400
+++ b/scanpy_macros.xml	Thu Mar 12 09:09:35 2020 +0000
@@ -38,9 +38,14 @@
       <yield/>
     </requirements>
   </xml>
+  <token name="@EXPORT_MTX_OPTS@">
+      ${export_mtx}
+  </token>
   <token name="@VERSION_HISTORY@"><![CDATA[
 **Version history**
 
+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>
@@ -87,4 +92,18 @@
     <param name="sort_order" argument="--no-sort-order" type="boolean" checked="true" label="Element with high color-by value plot on top"/>
     <param name="frameoff" argument="--frameoff" type="boolean" checked="false" label="Omit 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 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 ${on_string}: 10x barcodes">
+      <filter>export_mtx</filter>
+    </data>
+  </xml>
 </macros>
diff -r eae21a6c3128 -r edb0d2e8ab66 scanpy_macros2.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scanpy_macros2.xml	Thu Mar 12 09:09:35 2020 +0000
@@ -0,0 +1,142 @@
+<macros>
+  <token name="@TOOL_VERSION@">1.4.3</token>
+  <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
+  <token name="@PROFILE@">18.01</token>
+  <token name="@VERSION_HISTORY@"><![CDATA[
+**Version history**
+
+1.4.3+galaxy10: Update to scanpy-scripts 0.2.10 (running scanpy ==1.4.3) to address bugfixes in run-pca.
+
+1.4.3+galaxy10: Update to scanpy-scripts 0.2.9 (running scanpy ==1.4.3) to address bugfixes in find-variable-genes.
+
+1.4.3+galaxy10: Use profile 18.01 for modules.
+
+1.4.3+galaxy6: Update to scanpy-scripts 0.2.8 (running scanpy ==1.4.3) and wider compatibility with other Galaxy modules. Bug fixes in filtering and plotting improvements.
+
+1.4.3+galaxy0: Update to scanpy-scripts 0.2.5 (running scanpy ==1.4.3).
+
+1.4.2+galaxy0: Update to scanpy-scripts 0.2.4 (requires scanpy >=1.4.2).
+
+1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files.
+
+1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home  at
+EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
+    ]]></token>
+  <token name="@INPUT_OPTS@">
+    --input-format '${input_format}' input.h5
+  </token>
+  <token name="@OUTPUT_OPTS@">
+#if str($output_format).startswith('anndata')
+    --show-obj stdout --output-format anndata output.h5
+#else
+    --show-obj stdout --output-format loom output.h5
+#end if
+  </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="0.2.10">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,h5ad" label="Input object in AnnData/Loom 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_h5ad" selected="true">AnnData format</option>
+      <option value="anndata">AnnData format (h5 for older versions)</option>
+      <option value="loom">Loom format</option>
+      <option value="loom_legacy">Loom format (h5 for older versions)</option>
+    </param>
+  </xml>
+
+  <xml name="output_object_params_no_loom">
+    <param name="output_format" argument="--output-format" type="select" label="Format of output object">
+      <option value="anndata_h5ad" selected="true">AnnData format</option>
+      <option value="anndata">AnnData format (h5 for older versions)</option>
+    </param>
+  </xml>
+
+  <xml name="output_data_obj_no_loom" token_description="operation">
+    <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
+      <filter>output_format == 'anndata_h5ad'</filter>
+    </data>
+    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
+      <filter>output_format == 'anndata'</filter>
+    </data>
+  </xml>
+
+  <xml name="output_data_obj" token_description="operation">
+    <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
+      <filter>output_format == 'anndata_h5ad'</filter>
+    </data>
+    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
+      <filter>output_format == 'anndata'</filter>
+    </data>
+    <data name="output_loom_legacy" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom">
+      <filter>output_format == 'loom_legacy'</filter>
+    </data>
+    <data name="output_loom" format="loom" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom">
+      <filter>output_format == 'loom'</filter>
+    </data>
+  </xml>
+
+  <xml name="output_plot_params">
+    <param name="fig_title" argument="--title" type="text" label="Figure title"/>
+    <param name="fig_size" argument="--fig-size" type="text" value="4,4" label="Figure size as 'width,height', e.g, '7,7'"/>
+    <param name="fig_dpi" argument="--fig-dpi" type="integer" min="1" value="80" label="Figure dpi"/>
+    <param name="fig_fontsize" argument="--fig-fontsize" type="integer" min="0" value="10" label="Figure font size"/>
+    <param name="fig_frame" type="boolean" truevalue="--frameon" falsevalue="--frameoff" checked="false"
+           label="Show plot frame"/>
+  </xml>
+
+  <xml name="export_mtx_params">
+    <param name="export_mtx" argument="--export-mtx" type="boolean" truevalue="--export-mtx ./" falsevalue="" checked="false" label="Save to 10x mtx format" help="If enabled, it will generate in addition to the main output in Loom or AnnData an export in 10x format."/>
+  </xml>
+
+  <xml name="export_mtx_outputs">
+    <data name="matrix_10x" format="txt" from_work_dir="matrix.mtx" label="${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>