| Previous changeset 0:f6f189ce4ebc (2019-04-03) Next changeset 2:b946c0c60d4c (2019-10-25) |
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Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142" |
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modified:
scanpy-run-tsne.xml |
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added:
scanpy_macros2.xml |
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| diff -r f6f189ce4ebc -r 2e74fd7b5f45 scanpy-run-tsne.xml --- a/scanpy-run-tsne.xml Wed Apr 03 11:10:51 2019 -0400 +++ b/scanpy-run-tsne.xml Mon Sep 16 08:17:58 2019 -0400 |
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| @@ -2,45 +2,45 @@ <tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy1"> <description>visualise cell clusters using tSNE</description> <macros> - <import>scanpy_macros.xml</import> + <import>scanpy_macros2.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ ln -s '${input_obj_file}' input.h5 && -PYTHONIOENCODING=utf-8 scanpy-run-tsne.py - -i input.h5 - -f '${input_format}' - -o output.h5 - -F '${output_format}' - #if $embeddings - --output-embeddings-file embeddings.csv +PYTHONIOENCODING=utf-8 scanpy-run-tsne +#if $use_rep != "auto" + --use-rep '${use_rep}' +#end if +#if $key_added + --key-added '${key_added}' +#end if +#if $embeddings + --export-embedding embeddings.csv +#end if +#if $settings.default == "false" + #if $settings.perplexity_file + --perplexity \$( cat $settings.perplexity_file ) + #else + --perplexity '${settings.perplexity}' #end if - #if $settings.default == "false" - #if $settings.perplexity_file - --perplexity \$( cat $settings.perplexity_file ) - #else - --perplexity '${settings.perplexity}' - #end if - --early-exaggeration '${settings.early_exaggeration}' - --learning-rate '${settings.learning_rate}' - #if $settings.use_rep != "auto" - -r '${settings.use_rep}' - #end if - #if $settings.n_pc - -n '${settings.n_pc}' - #end if - #if not $settings.fast_tsne - --no-fast-tsne - #end if - #if $settings.n_job - --n-jobs '${settings.n_job}' - #end if - #if $settings.random_seed is not None - -s '${settings.random_seed}' - #end if + --early-exaggeration '${settings.early_exaggeration}' + --learning-rate '${settings.learning_rate}' + #if $settings.n_pc + --n-pcs ${settings.n_pc} + #end if + #if not $settings.fast_tsne + --no-fast-tsne #end if + #if $settings.n_job + --n-jobs ${settings.n_job} + #end if + #if $settings.random_seed is not None + --random-state ${settings.random_seed} + #end if +#end if + @INPUT_OPTS@ + @OUTPUT_OPTS@ -@PLOT_OPTS@ ]]></command> <inputs> @@ -48,15 +48,18 @@ <expand macro="output_object_params"/> <param name="embeddings" type="boolean" checked="true" label="Output embeddings in csv format"/> + <param name="use_rep" argument="--use-rep" type="select" label="Use the indicated representation"> + <option value="X_pca">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="key_added" argument="--key-added" type="text" optional="true" + label="Additional suffix to the name of the slot to save the embedding"/> + <conditional name="settings"> <param name="default" type="boolean" checked="true" label="Use programme defaults"/> <when value="true"/> <when value="false"> - <param name="use_rep" argument="--use-rep" type="select" label="Use the indicated representation"> - <option value="X_pca">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="perplexity" argument="--perplexity" type="float" value="30" label="The perplexity is related to the number of nearest neighbours, select a value between 5 and 50"/> <param name="perplexity_file" argument="--perplexity" type="data" format="txt,tsv" label="The perplexity is related to the number of nearest neighbours" help="For use with the parameter iterator. Overrides the persplexity option above" optional="true"/> <param name="early_exaggeration" argument="--early-exaggeration" type="float" value="12" label="Controls the tightness within and between clusters"/> @@ -68,21 +71,10 @@ </when> </conditional> - <conditional name="do_plotting"> - <param name="plot" type="boolean" checked="false" label="Make tSNE plot"/> - <when value="true"> - <expand macro="output_plot_params"/> - <param name="color_by" argument="--color-by" type="text" value="louvain" label="Color by attributes, comma separated strings"/> - </when> - <when value="false"/> - </conditional> </inputs> <outputs> <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: tSNE object"/> - <data name="output_png" format="png" from_work_dir="output.png" label="${tool.name} on ${on_string}: tSNE plot"> - <filter>do_plotting['plot']</filter> - </data> <data name="output_embed" format="csv" from_work_dir="embeddings.csv" label="${tool.name} on ${on_string}: tSNE embeddings"> <filter>embeddings</filter> </data> @@ -96,10 +88,7 @@ <param name="default" value="false"/> <param name="embeddings" value="true"/> <param name="random_seed" value="0"/> - <param name="plot" value="true"/> - <param name="color_by" value="louvain"/> <output name="output_h5" file="run_tsne.h5" ftype="h5" compare="sim_size"/> - <output name="output_png" file="run_tsne.png" ftype="png" compare="sim_size"/> <output name="output_embed" file="run_tsne.embeddings.csv" ftype="csv" compare="sim_size"> <assert_contents> <has_n_columns n="2" sep=","/> @@ -109,9 +98,12 @@ </tests> <help><![CDATA[ -================================================================== -t-distributed stochastic neighborhood embedding (tSNE) (`tl.tsne`) -================================================================== +========================================================================= +t-distributed stochastic neighborhood embedding (tSNE) (`scanpy.tl.tsne`) +========================================================================= + +For making TSNE plots, please use `Scanpy PlotEmbed` with the output of this tool and enter "tsne" as the +name of the embedding to plot. t-distributed stochastic neighborhood embedding (tSNE) (Maaten et al, 2008) has been proposed for visualizating single-cell data by (Amir et al, 2013). Here, by default, |
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| diff -r f6f189ce4ebc -r 2e74fd7b5f45 scanpy_macros2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy_macros2.xml Mon Sep 16 08:17:58 2019 -0400 |
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| @@ -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> |