Mercurial > repos > ebi-gxa > scanpy_filter_cells

changeset 1:4c806f3f094c draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
author ebi-gxa
date Thu, 12 Mar 2020 09:07:07 +0000
parents cad451be0a2a
children fd03785d0935
files scanpy-filter-cells.xml scanpy_macros.xml scanpy_macros2.xml
diffstat 3 files changed, 219 insertions(+), 29 deletions(-) [+]
line wrap: on
line diff
--- a/scanpy-filter-cells.xml	Wed Mar 13 11:51:56 2019 -0400
+++ b/scanpy-filter-cells.xml	Thu Mar 12 09:07:07 2020 +0000
@@ -1,46 +1,74 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_filter_cells" name="Scanpy FilterCells" version="@TOOL_VERSION@+galaxy0">
+<tool id="scanpy_filter_cells" name="Scanpy FilterCells" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@" >
   <description>based on counts and numbers of genes expressed</description>
   <macros>
-    <import>scanpy_macros.xml</import>
+    <import>scanpy_macros2.xml</import>
   </macros>
   <expand macro="requirements"/>
   <command detect_errors="exit_code"><![CDATA[
 ln -s '${input_obj_file}' input.h5 &&
-PYTHONIOENCODING=utf-8 scanpy-filter-cells.py
-    -i input.h5
-    -f '${input_format}'
-    -o output.h5
-    -F '${output_format}'
-    #if $parameters
-        #set pars = ','.join([str($p['name']) for $p in $parameters])
-        -p '${pars}'
-        #set mins = ','.join([str($p['min']) for $p in $parameters])
-        -l '${mins}'
-        #set maxs = ','.join([str($p['max']) for $p in $parameters])
-        -j '${maxs}'
+PYTHONIOENCODING=utf-8 scanpy-filter-cells
+#if $gene_name
+    --gene-name '${gene_name}'
+#end if
+#if $parameters
+#for $p in $parameters
+    #set $min = $p.min
+    #set $max = $p.max
+    #if $p.name.startswith('pct_')
+      #set $min = float($min) / 100
+      #set $max = float($max) / 100
     #end if
-    #if $subset
-        -s '${subset}'
-    #end if
+    --param 'c:$p.name' $min $max
+#end for
+#end if
+#if $categories
+    #set cats = ' '.join(["--category 'c:{name}' '{negate}{values}'".format(**$c) for $c in $categories])
+    ${cats}
+#end if
+#if $subsets
+    #set subs = ' '.join(["--subset 'c:{name}' '{subset}'".format(**$s) for $s in $subsets])
+    ${subs}
+#end if
+    @INPUT_OPTS@
+    @OUTPUT_OPTS@
+    @EXPORT_MTX_OPTS@
     ]]></command>
 
   <inputs>
     <expand macro="input_object_params"/>
     <expand macro="output_object_params"/>
-    <repeat name="parameters" title="Parameters used to filter cells" min="1">
+
+    <param name="gene_name" type="text" optional="true" label="Name of the column in `anndata.var` that contains gene name"
+           help="Used for flagging mitochondria genes (starting with 'MT-'). Leave empty if gene table already has a boolean column called 'mito' that flags MT genes"/>
+
+    <repeat name="parameters" title="Parameters to select cells to keep" min="1">
       <param name="name" type="text" value="n_genes" label="Name of parameter to filter on" help="for example n_genes or n_counts">
         <option value="n_genes">n_genes</option>
         <option value="n_counts">n_counts</option>
+        <option value="pct_counts_mito">pct_counts_mito (only usable if MT genes are flagged or has been pre-calculated)</option>
       </param>
-      <param name="min" type="float" value="0" min="0" label="Min value"/>
-      <param name="max" type="float" value="1e9" label="Max value"/>
+      <param name="min" type="float" value="0" min="0" label="Min value" help="Cells with value below min will be discarded."/>
+      <param name="max" type="float" value="1e9" label="Max value" help="Cells with value above max will be discarded."/>
     </repeat>
-    <param name="subset" argument="--subset-list" type="data" format="tsv" optional="true" label="List of barcodes"/>
+
+    <repeat name="categories" title="Categories to select cells to keep (unless negate is checked)" min="0">
+      <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/>
+      <param name="values" type="text" value="" label="Comma-separated list of categories" help="Cells with these values in this categorical variable will be kept."/>
+      <param name="negate" type="boolean" truevalue="!" falsevalue="" checked="false" label="Apply as negative filter" help="If enabled, specified categories will be removed rather than retained."/>
+    </repeat>
+
+    <repeat name="subsets" title="Subsets to select cells to keep" min="0">
+      <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/>
+      <param name="subset" type="data" format="tabular" label="List of values to keep" help="A one-column headerless text file is required"/>
+    </repeat>
+    <param name="force_recalc" label="Force recalculation of QC vars" type="boolean" truevalue="--force-recalc" falsevalue="" help="If set, it will recalculate pcts and other existing QC vars, overwriting existing ones."/>
+    <expand macro="export_mtx_params"/>
   </inputs>
 
   <outputs>
-    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Filtered cells"/>
+    <expand macro="output_data_obj" description="Filtered cells"/>
+    <expand macro="export_mtx_outputs"/>
   </outputs>
 
   <tests>
@@ -58,18 +86,19 @@
         <param name="min" value="0"/>
         <param name="max" value="1e9"/>
       </repeat>
-      <output name="output_h5" file="filter_cells.h5" ftype="h5" compare="sim_size"/>
+      <output name="output_h5" file="output.h5" ftype="h5" compare="sim_size"/>
     </test>
   </tests>
 
   <help><![CDATA[
-========================================================================================
-Filter cells outliers based on counts and numbers of genes expressed (`pp.filter_cells`)
-========================================================================================
+===================================================================
+Filter cells based on various QC metrics (`scanpy.pp.filter_cells`)
+===================================================================
 
-For instance, only keep cells with at least `min_counts` counts or
-`min_genes` genes expressed. This is to filter measurement outliers, i.e.,
-"unreliable" observations.
+For instance, only keep cells with at least `min_counts` and at most
+`max_counts` UMI and/or at least `min_genes` expressed genes and/or at most
+`max_mito_percent` mitocondria expression. This is to filter measurement
+outliers, i.e., "unreliable" observations.
 
 @HELP@
 
--- a/scanpy_macros.xml	Wed Mar 13 11:51:56 2019 -0400
+++ b/scanpy_macros.xml	Thu Mar 12 09:07:07 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 ${on_string}: 10x barcodes">
+      <filter>export_mtx</filter>
+    </data>
+  </xml>
 </macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scanpy_macros2.xml	Thu Mar 12 09:07:07 2020 +0000
@@ -0,0 +1,142 @@
+<macros>
+  <token name="@TOOL_VERSION@">1.4.3</token>
+  <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
+  <token name="@PROFILE@">18.01</token>
+  <token name="@VERSION_HISTORY@"><![CDATA[
+**Version history**
+
+1.4.3+galaxy10: Update to scanpy-scripts 0.2.10 (running scanpy ==1.4.3) to address bugfixes in run-pca.
+
+1.4.3+galaxy10: Update to scanpy-scripts 0.2.9 (running scanpy ==1.4.3) to address bugfixes in find-variable-genes.
+
+1.4.3+galaxy10: Use profile 18.01 for modules.
+
+1.4.3+galaxy6: Update to scanpy-scripts 0.2.8 (running scanpy ==1.4.3) and wider compatibility with other Galaxy modules. Bug fixes in filtering and plotting improvements.
+
+1.4.3+galaxy0: Update to scanpy-scripts 0.2.5 (running scanpy ==1.4.3).
+
+1.4.2+galaxy0: Update to scanpy-scripts 0.2.4 (requires scanpy >=1.4.2).
+
+1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files.
+
+1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home  at
+EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
+    ]]></token>
+  <token name="@INPUT_OPTS@">
+    --input-format '${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>