| Next changeset 1:b089f4a55e6b (2019-09-16) |
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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 9bf9a6e46a330890be932f60d1d996dd166426c4 |
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added:
scanpy-find-variable-genes.xml scanpy_macros.xml |
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| diff -r 000000000000 -r 305d0cbe0ffd scanpy-find-variable-genes.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy-find-variable-genes.xml Wed Apr 03 11:12:05 2019 -0400 |
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| @@ -0,0 +1,93 @@ +<?xml version="1.0" encoding="utf-8"?> +<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> + </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 +]]></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> + </param> + <param name="min" type="float" value="0" label="Min value"/> + <param name="max" type="float" value="1e9" label="Max value"/> + </repeat> + <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"/> + </inputs> + + <outputs> + <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Variable genes"/> + </outputs> + + <tests> + <test> + <param name="input_obj_file" value="normalise_data.h5"/> + <param name="input_format" value="anndata"/> + <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> + <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`) +============================================================ + +Depending on `flavor`, this reproduces the R-implementations of Seurat and 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 +expression of genes. This means that for each bin of mean expression, highly +variable genes are selected. + +@HELP@ + +@VERSION_HISTORY@ +]]></help> + <expand macro="citations"> + <citation type="doi">10.1038/nbt.3192</citation> + <citation type="doi">10.1038/ncomms14049</citation> + </expand> +</tool> |
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| diff -r 000000000000 -r 305d0cbe0ffd scanpy_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy_macros.xml Wed Apr 03 11:12:05 2019 -0400 |
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| @@ -0,0 +1,109 @@ +<macros> + <token name="@TOOL_VERSION@">1.3.2</token> + <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token> + <token name="@PLOT_OPTS@"> +#if $do_plotting.plot + -P output.png + --projectio $do_plotting.projection + --components $do_plotting.components + #if $do_plotting.color_by + --color-by $do_plotting.color_by + #end if + #if $do_plotting.groups + --group $do_plotting.groups + #end if + #if $do_plotting.use_raw + --use-raw + #end if + #if $do_plotting.palette + --palette $do_plotting.palette + #end if + #if $do_plotting.edges + --edges + #end if + #if $do_plotting.arrows + --arrows + #end if + #if not $do_plotting.sort_order + --no-sort-order + #end if + #if $do_plotting.frameoff + --frameoff + #end if +#end if + </token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.0.5">scanpy-scripts</requirement> + <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> + <xml name="citations"> + <citations> + <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> + <yield /> + </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, current support is incomplete</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, current support is defective</option> + </param> + </xml> + <xml name="output_plot_params"> + <param name="color_by" argument="--color-by" type="text" value="n_genes" label="Color by attributes, comma separated strings"/> + <param name="groups" argument="--groups" type="text" optional="ture" label="Restrict plotting to named groups, comma separated strings"/> + <param name="projection" argument="--projection" type="select" label="Plot projection"> + <option value="2d" selected="true">2D</option> + <option value="3d">3D</option> + </param> + <param name="components" argument="--components" type="text" value="1,2" label="Components to plot, comma separated integers"/> + <param name="palette" argument="--palette" type="text" optional="true" label="Palette"/> + <param name="use_raw" argument="--use-raw" type="boolean" checked="false" label="Use raw attributes if present"/> + <param name="edges" argument="--edges" type="boolean" checked="false" label="Show edges"/> + <param name="arrows" argument="--arrows" type="boolean" checked="false" label="Show arrows"/> + <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> |