Mercurial > repos > ebi-gxa > seurat_dim_plot

changeset 5:316623eb59bd draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
author ebi-gxa
date Fri, 04 Mar 2022 07:25:13 +0000
parents cfc3d8ee3a64
children 64174ac50d78
files get_test_data.sh seurat_dim_plot.xml seurat_macros.xml
diffstat 3 files changed, 69 insertions(+), 22 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_test_data.sh	Fri Mar 04 07:25:13 2022 +0000
@@ -0,0 +1,51 @@
+#!/usr/bin/env bash
+
+BASENAME_FILE='E-MTAB-6077-3k_features_90_cells'
+
+MTX_LINK='https://drive.google.com/uc?export=download&id=1-1ejn7scP80xsbrG0FtWzsozjg0hhc23'
+RDS_LINK='https://drive.google.com/uc?export=download&id=1KW_GX6xznSUpWRWUykpNaSbAhyClf7_n'
+NORM_LINK='https://drive.google.com/uc?export=download&id=1mvo3ENkBvEAOyWG6ejApzQTPDLX5yBKU'
+FVG_LINK='https://drive.google.com/uc?export=download&id=13Fhruuj-vEEo1WM138ahtAYqfHc7LsaZ'
+SCALED_LINK='https://drive.google.com/uc?export=download&id=18TK8us235LWNajarWDBAtASUXMYAxvw0'
+PCA_LINK='https://drive.google.com/uc?export=download&id=1gf3BTB4dygDsom1TzjsBfgZnZepcoG5c'
+NEIGHBOURS_LINK='https://drive.google.com/uc?export=download&id=1N2lHoKRBZ7pmAYGfghLWB9KUrLA5WoNX'
+CLUSTERS_LINK='https://drive.google.com/uc?export=download&id=1HWxZWHbNUNo4z__9PhhL_CJOLzec_ETa'
+TSNE_LINK='https://drive.google.com/uc?export=download&id=1qsvMr_GkCSp1dyTJt1BZ6cElJwFFX2zO'
+MARKERS_LINK='https://drive.google.com/uc?export=download&id=18OmWNc7mF-4pzH6DQkPp1eKunN4BfvxD'
+
+LOOM_LINK='https://drive.google.com/uc?export=download&id=1qNk5cg8hJG3Nv1ljTKmUEnxTOf11EEZX'
+H5AD_LINK='https://drive.google.com/uc?export=download&id=1YpE0H_t_dkh17P-WBhPijKvRiGP0BlBz'
+SCE_LINK='https://drive.google.com/uc?export=download&id=1UKdyf3M01uAt7oBg93JfmRvNVB_jlUKe'
+
+function get_data {
+  local link=$1
+  local fname=$2
+
+  if [ ! -f $fname ]; then
+    echo "$fname not available locally, downloading.."
+    wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link
+  fi
+}
+
+# get matrix data
+pushd test-data
+get_data $MTX_LINK mtx.zip
+unzip mtx.zip
+rm -f mtx.zip
+
+get_data $RDS_LINK $BASENAME_FILE".rds"
+get_data $NORM_LINK $BASENAME_FILE"-normalised.rds"
+get_data $FVG_LINK $BASENAME_FILE"-fvg.rds"
+get_data $SCALED_LINK $BASENAME_FILE"-scaled.rds"
+get_data $PCA_LINK $BASENAME_FILE"-pca.rds"
+get_data $NEIGHBOURS_LINK $BASENAME_FILE"-neighbours.rds"
+get_data $CLUSTERS_LINK $BASENAME_FILE"-clusters.rds"
+get_data $TSNE_LINK $BASENAME_FILE"-tsne.rds"
+get_data $MARKERS_LINK $BASENAME_FILE"-markers.csv.zip"
+
+unzip $BASENAME_FILE"-markers.csv.zip"
+rm -f $BASENAME_FILE"-markers.csv.zip"
+
+get_data $LOOM_LINK $BASENAME_FILE"_loom.h5"
+get_data $SCE_LINK $BASENAME_FILE"_sce.rds"
+get_data $H5AD_LINK $BASENAME_FILE".h5ad"
--- a/seurat_dim_plot.xml	Fri Nov 27 13:46:57 2020 +0000
+++ b/seurat_dim_plot.xml	Fri Mar 04 07:25:13 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="seurat_dim_plot" name="Seurat Plot dimension reduction" version="@SEURAT_VERSION@+galaxy0">
+<tool id="seurat_dim_plot" name="Seurat Plot dimension reduction" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
     <description>graphs the output of a dimensional reduction technique (PCA by default). Cells are colored by their identity class.</description>
     <macros>
         <import>seurat_macros.xml</import>
@@ -27,22 +27,16 @@
         --label-size $label_size
         #end if
         --do-label $do_label
+        --repel $repel
         #if $group_by
         --group-by $group_by
         #end if
-        #if $plot_title
-        --plot-title '$plot_title'
-        #end if
-        --do-bare $do_bare
         #if $cols_use
         --cols-use '$cols_use'
         #end if
         #if $pt_shape
         --pt-shape '$pt_shape'
         #end if
-        --coord-fixed $coord_fixed
-        --no-axes $no_axes
-        --dark-theme $dark_theme
         #if $plot_order
         --plot-order '$plot_order'
         #end if
@@ -59,14 +53,10 @@
         <param type="float" name="pt_size" value='1' label="Point size" help='Adjust point size for plotting' />
         <param type="float" name="label_size" value='4' label="Label size" help='Sets size of labels'/>
         <param type="boolean" name="do_label" checked="false" label='Label clusters' truevalue="TRUE" falsevalue="FALSE" />
+        <param type="boolean" name="repel" checked="false" label='Repel labels' truevalue="TRUE" falsevalue="FALSE" />
         <param type="text" name="group_by" value='ident' label='Group by' help='Group (color) cells in different ways' />
-        <param type="text" name="plot_title" format="text" label='Plot title' />
-        <param type="boolean" name="do_bare" checked="false" label='Do only minimal formatting' truevalue="TRUE" falsevalue="FALSE" />
         <param type="text" name="cols_use" format="text" label="Colors" help='Comma-separated list of colors, each color corresponds to an identity class. By default, ggplot assigns colors.' />
         <param type="text" name="pt_shape" format="text" label="Cell attribute for shape" help='If NULL, all points are circles (default). You can specify any cell attribute (that can be pulled with FetchData) allowing for both different colors and different shapes on cells.' />
-        <param type="boolean" name="coord_fixed" checked="false" label="Fixed-scaled coordinate system" help='Use a fixed scale coordinate system (for spatial coordinates). Default is FALSE.' truevalue="TRUE" falsevalue="FALSE" />
-        <param type="boolean" name="no_axes" checked="false" label="Remove Axes" help='Setting to TRUE will remove the axes.' truevalue="TRUE" falsevalue="FALSE" />
-        <param type="boolean" name="dark_theme" checked="false" label='Use a dark theme for the plot..' truevalue="TRUE" falsevalue="FALSE" />
         <param type="text" name="plot_order" format="text" label="Ident (clusters) order" help='Comma-separated string specifying the order of plotting for the idents (clusters). This can be useful for crowded plots if points of interest are being buried. Provide either a full list of valid idents or a subset to be plotted last (on top).' />
         <param type="integer" name="png_width" value='1000' label="Figure width" help='Width of png in pixels.' />
         <param type="integer" name="png_height" value='1000' label="Figure height" help='Height of png in pixels.'/>
@@ -76,9 +66,12 @@
     </outputs>
     <tests>
         <test>
-            <param name="rds_seurat_file" value="cluster_seurat.rds" ftype="rdata" />
-            <param name="do_bare" value="True" />
-            <output name="output_image_file" file="pcatest.png" compare="sim_size" delta="5000000" />
+            <param name="rds_seurat_file" value="E-MTAB-6077-3k_features_90_cells-tsne.rds" ftype="rdata" />
+            <output name="output_image_file" >
+              <assert_contents>
+                <has_size value="18122" delta="2000"/>
+              </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[
--- a/seurat_macros.xml	Fri Nov 27 13:46:57 2020 +0000
+++ b/seurat_macros.xml	Fri Mar 04 07:25:13 2022 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@VERSION@">0.0.8</token>
-    <token name="@SEURAT_VERSION@">3.1.2</token>
+    <token name="@VERSION@">0.3.0</token>
+    <token name="@SEURAT_VERSION@">3.2.3</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">seurat-scripts</requirement>
@@ -96,7 +96,10 @@
 
     <token name="@VERSION_HISTORY@"><![CDATA[
 **Version history**
-3.1.2_0.0.8: Upd ate metadata parsing
+
+3.2.3+galaxy0: Moves to Seurat 3.2.3 and introduce convert method, improving format interconversion support.
+
+3.1.2_0.0.8: Update metadata parsing
 
 3.1.1_0.0.7: Exposes perplexity and enables tab input.
 
@@ -105,9 +108,9 @@
   Find clusters: removed dims-use, k-param, prune-snn.
 
 2.3.1+galaxy0: Improved documentation and further exposition of all script's options. Pablo Moreno, Jonathan Manning and Ni Huang, Expression Atlas team https://www.ebi.ac.uk/gxa/home  at
-EMBL-EBI https://www.ebi.ac.uk/. Parts obtained from wrappers from Christophe Antoniewski(https://github.com/drosofff) and Lea Bellenger(https://github.com/bellenger-l).
+EMBL-EBI https://www.ebi.ac.uk/. Parts obtained from wrappers from Christophe Antoniewski(github.com/drosofff) and Lea Bellenger(github.com/bellenger-l).
 
-0.0.1: Initial contribution. Maria Doyle, https://github.com/mblue9.
+0.0.1: Initial contribution. Maria Doyle (github.com/mblue9).
       ]]></token>
 
 
@@ -124,7 +127,7 @@
               url = {https://github.com/ebi-gene-expression-group/r-seurat-scripts.git},
             }
             </citation>
-            <citation type="doi">10.1101/2020.04.08.032698</citation>
+            <citation type="doi">10.1038/s41592-021-01102-w</citation>
         </citations>
     </xml>
 </macros>