| Next changeset 1:0ac2f9f2313b (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-run-umap.xml scanpy_macros.xml |
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| diff -r 000000000000 -r 88c1516e25e0 scanpy-run-umap.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy-run-umap.xml Wed Apr 03 11:10:27 2019 -0400 |
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| @@ -0,0 +1,133 @@ +<?xml version="1.0" encoding="utf-8"?> +<tool id="scanpy_run_umap" name="Scanpy RunUMAP" version="@TOOL_VERSION@+galaxy1"> + <description>visualise cell clusters using UMAP</description> + <macros> + <import>scanpy_macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +ln -s '${input_obj_file}' input.h5 && +PYTHONIOENCODING=utf-8 scanpy-run-umap.py + -i input.h5 + -f '${input_format}' + -o output.h5 + -F '${output_format}' + #if $embeddings + --output-embeddings-file embeddings.csv + #end if + #if $settings.default == "false" + -n '${settings.n_components}' + --min-dist '${settings.min_dist}' + --spread '${settings.spread}' + --alpha '${settings.alpha}' + --gamma '${settings.gamma}' + --negative-sample-rate '${settings.negative_sample_rate}' + #if $settings.init_pos + --init-pos '${settings.init_pos}' + #end if + #if $settings.maxiter + --maxiter '${settings.maxiter}' + #end if + #if $settings.a + -a '${settings.a}' + #end if + #if $settings.b + -b '${settings.b}' + #end if + #if $settings.random_seed is not None + -s '${settings.random_seed}' + #end if + #end if + +@PLOT_OPTS@ +]]></command> + + <inputs> + <expand macro="input_object_params"/> + <expand macro="output_object_params"/> + <param name="embeddings" type="boolean" checked="true" label="Output embeddings in csv format"/> + <conditional name="settings"> + <param name="default" type="boolean" checked="true" label="Use programme defaults"/> + <when value="true"/> + <when value="false"> + <param name="n_components" argument="--n-components" type="integer" value="2" label="The number of dimensions of the embedding"/> + <param name="min_dist" argument="--min-dist" type="float" value="0.5" label="The effective minimum distance between embedded points"/> + <param name="spread" argument="--spread" type="float" value="1.0" label="The effective spread of embedded points"/> + <param name="alpha" argument="--alpha" type="float" value="1.0" label="Initial learning rate"/> + <param name="gamma" argument="--gamma" type="float" value="1.0" label="Weighting applied to negative samples"/> + <param name="negative_sample_rate" argument="--negative-sample-rate" type="integer" value="5" label="The ratio of negative to positive edge in optimisation"/> + <param name="init_pos" argument="--init-pos" type="text" label="Method to initialise embedding, any key for adata.obsm or choose from the preset methods"> + <option value="spectral" selected="true">spectral</option> + <option value="paga">paga</option> + <option value="random">random</option> + </param> + <param name="maxiter" argument="--maxiter" type="integer" optional="true" label="Number of iterations of optimisation"/> + <param name="a" argument="-a" type="float" optional="true" label="More specific parameter controlling embedding, automatically determined from --min-dist and --spread if unset"/> + <param name="b" argument="-b" type="float" optional="true" label="More specific parameter controlling embedding, automatically determined from --min-dist and --spread if unset"/> + <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for numpy random number generator"/> + </when> + </conditional> + <conditional name="do_plotting"> + <param name="plot" type="boolean" checked="false" label="Make UMAP 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 ${on_string}: UMAP object"/> + <data name="output_png" format="png" from_work_dir="output.png" label="${tool.name} on ${on_string}: UMAP plot"> + <filter>do_plotting['plot']</filter> + </data> + <data name="output_embed" format="csv" from_work_dir="embeddings.csv" label="${tool.name} on ${on_string}: UMAP embeddings"> + <filter>embeddings</filter> + </data> + </outputs> + + <tests> + <test> + <param name="input_obj_file" value="find_cluster.h5"/> + <param name="input_format" value="anndata"/> + <param name="output_format" value="anndata"/> + <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_umap.h5" ftype="h5" compare="sim_size"/> + <output name="output_png" file="run_umap.png" ftype="png" compare="sim_size"/> + <output name="output_embed" file="run_umap.embeddings.csv" ftype="csv" compare="sim_size"> + <assert_contents> + <has_n_columns n="2" sep=","/> + </assert_contents> + </output> + </test> + </tests> + + <help><![CDATA[ +======================================================== +Embed the neighborhood graph using UMAP (`tl.umap`) +======================================================== + +UMAP (Uniform Manifold Approximation and Projection) is a manifold learning +technique suitable for visualizing high-dimensional data. Besides tending to +be faster than tSNE, it optimizes the embedding such that it best reflects +the topology of the data, which we represent throughout Scanpy using a +neighborhood graph. tSNE, by contrast, optimizes the distribution of +nearest-neighbor distances in the embedding such that these best match the +distribution of distances in the high-dimensional space. We use the +implementation of `umap-learn <https://github.com/lmcinnes/umap>`__ +(McInnes et al, 2018). For a few comparisons of UMAP with tSNE, see this `preprint +<https://doi.org/10.1101/298430>`__. + +It yields `X_umap`, UMAP coordinates of data. + +@HELP@ + +@VERSION_HISTORY@ +]]></help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r 88c1516e25e0 scanpy_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy_macros.xml Wed Apr 03 11:10:27 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> |