| Previous changeset 4:cfc3d8ee3a64 (2020-11-27) Next changeset 6:64174ac50d78 (2024-03-02) |
|
Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a" |
|
modified:
seurat_dim_plot.xml seurat_macros.xml |
|
added:
get_test_data.sh |
| b |
| diff -r cfc3d8ee3a64 -r 316623eb59bd get_test_data.sh --- /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" |
| b |
| diff -r cfc3d8ee3a64 -r 316623eb59bd seurat_dim_plot.xml --- 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[ |
| b |
| diff -r cfc3d8ee3a64 -r 316623eb59bd seurat_macros.xml --- 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> |