| Previous changeset 0:305d0cbe0ffd (2019-04-03) Next changeset 2:d88a29e2eba6 (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-find-variable-genes.xml |
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added:
scanpy_macros2.xml |
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| diff -r 305d0cbe0ffd -r b089f4a55e6b scanpy-find-variable-genes.xml --- a/scanpy-find-variable-genes.xml Wed Apr 03 11:12:05 2019 -0400 +++ b/scanpy-find-variable-genes.xml Mon Sep 16 08:19:34 2019 -0400 |
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| @@ -2,47 +2,51 @@ <tool id="scanpy_find_variable_genes" name="Scanpy FindVariableGenes" version="@TOOL_VERSION@+galaxy0"> <description>based on normalised dispersion of expression</description> <macros> - <import>scanpy_macros.xml</import> + <import>scanpy_macros2.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ ln -s '${input_obj_file}' input.h5 && -PYTHONIOENCODING=utf-8 scanpy-find-variable-genes.py -i input.h5 - -f '${input_format}' - -o output.h5 - -F '${output_format}' - --flavor '${flavor}' - -b '${n_bin}' - #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}' - #end if - #if $n_top_gene - -n '${n_top_gene}' - #end if +PYTHONIOENCODING=utf-8 scanpy-find-variable-genes + --flavor '${method.flavor}' +#if $method.flavor == 'seurat' + --mean-limits ${method.min_mean} ${method.max_mean} + --disp-limits ${method.min_disp} ${method.max_disp} +#else + --n-top-genes ${method.n_top_gene} +#end if + --n-bins '${n_bin}' + ${filter} + @INPUT_OPTS@ + @OUTPUT_OPTS@ ]]></command> <inputs> <expand macro="input_object_params"/> <expand macro="output_object_params"/> - <param name="flavor" argument="--flavor" type="select" value="seurat" label="Flavor of computing normalised dispersion"> - <option value="seurat">Seurat</option> - <option value="cell_ranger">Cell-ranger</option> - </param> - <repeat name="parameters" min="1" title="Parameters used to find variable genes"> - <param name="name" type="select" label="Name of parameter to filter on"> - <option value="mean">Mean of expression</option> - <option value="disp">Dispersion of expression</option> + <conditional name="method"> + <param name="flavor" argument="--flavor" type="select" label="Flavor of computing normalised dispersion"> + <option value="seurat" selected="true">Seurat</option> + <option value="cell_ranger">Cell-ranger</option> </param> - <param name="min" type="float" value="0" label="Min value"/> - <param name="max" type="float" value="1e9" label="Max value"/> - </repeat> + <when value="seurat"> + <param name="min_mean" argument="--min-mean" type="float" min="0" value="0.0125" + label="Min value for normalised mean expression (in log1p scale)"/> + <param name="max_mean" argument="--max-mean" type="float" min="0" value="3" + label="Max value for normalised mean expresssion (in log1p scale)"/> + <param name="min_disp" argument="--min-disp" type="float" min="0" value="0.5" + label="Min value for dispersion of expression"/> + <param name="max_disp" argument="--max-disp" type="float" min="0" value="50" + label="Max value for dispersion of expresssion"/> + </when> + <when value="cell_ranger"> + <param name="n_top_gene" argument="--n-top-genes" type="integer" value="2000" + label="Number of top variable genes to keep"/> + </when> + </conditional> <param name="n_bin" argument="--n-bins" type="integer" value="20" label="Number of bins for binning the mean expression"/> - <param name="n_top_gene" argument="--n-top-genes" type="integer" optional="true" label="Number of top variable genes to keep"/> + <param name="filter" argument="--subset" type="boolean" truevalue="--subset" falsevalue="" checked="false" + label="Remove genes not marked as highly variable"/> </inputs> <outputs> @@ -56,26 +60,20 @@ <param name="output_format" value="anndata"/> <param name="flavor" value="seurat"/> <param name="n_bin" value="20"/> - <repeat name="parameters"> - <param name="name" value="mean"/> - <param name="min" value="0.0125"/> - <param name="max" value="3"/> - </repeat> - <repeat name="parameters"> - <param name="name" value="disp"/> - <param name="min" value="0.5"/> - <param name="max" value="1e9"/> - </repeat> + <param name="min_mean" value="0.0125"/> + <param name="max_mean" value="3"/> + <param name="min_disp" value="0.5"/> + <param name="max_disp" value="1e9"/> <output name="output_h5" file="find_variable_genes.h5" ftype="h5" compare="sim_size"/> </test> </tests> <help><![CDATA[ -============================================================ -Extract highly variable genes (`pp.filter_genes_dispersion`) -============================================================ +============================================================== +Mark highly variable genes (`scanpy.pp.highly_variable_genes`) +============================================================== -Depending on `flavor`, this reproduces the R-implementations of Seurat and Cell Ranger. +Depending on `flavor`, this reproduces the R-implementations of Seurat or Cell Ranger. The normalized dispersion is obtained by scaling with the mean and standard deviation of the dispersions for genes falling into a given bin for mean |
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| diff -r 305d0cbe0ffd -r b089f4a55e6b scanpy_macros2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy_macros2.xml Mon Sep 16 08:19:34 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> |