| Previous changeset 0:3d242b0d97d0 (2019-04-03) Next changeset 2:53e6944bd162 (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-neighbours.xml |
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added:
scanpy_macros2.xml |
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| diff -r 3d242b0d97d0 -r e7fd6981c0f0 scanpy-neighbours.xml --- a/scanpy-neighbours.xml Wed Apr 03 11:11:14 2019 -0400 +++ b/scanpy-neighbours.xml Mon Sep 16 08:18:53 2019 -0400 |
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| @@ -1,34 +1,27 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy1"> +<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy0"> <description>to derive kNN graph</description> <macros> - <import>scanpy_macros.xml</import> + <import>scanpy_macros2.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ ln -s '${input_obj_file}' input.h5 && -PYTHONIOENCODING=utf-8 scanpy-neighbours.py - -i input.h5 - -f '${input_format}' - -o output.h5 - -F '${output_format}' - #if $settings.default == "false" - -N '${settings.n_neighbours}' - -m '${settings.method}' - -s '${settings.random_seed}' - #if $settings.use_rep != "auto" - -r '${settings.use_rep}' - #end if - #if $settings.n_pcs - -n '${settings.n_pcs}' - #end if - #if $settings.knn - --knn - #end if - #if $settings.metric - -M '${settings.metric}' - #end if +PYTHONIOENCODING=utf-8 scanpy-neighbors +#if $settings.default == "false" + --n-neighbors '${settings.n_neighbours}' + --method '${settings.method}' + --random-state '${settings.random_seed}' + #if $settings.use_rep != "auto" + --use-rep '${settings.use_rep}' #end if + #if $settings.n_pcs + --n-pcs '${settings.n_pcs}' + #end if + ${settings.knn} +#end if + @INPUT_OPTS@ + @OUTPUT_OPTS@ ]]></command> <inputs> @@ -39,18 +32,17 @@ <when value="true"/> <when value="false"> <param name="n_neighbours" argument="--n-neighbors" type="integer" value="15" label="Maximum number of neighbours used"/> - <param name="use_rep" type="select" label="Use the indicated representation"> - <option value="X_pca">X_pca, use PCs</option> + <param name="use_rep" type="text" label="Use the indicated representation"> + <option value="X_pca" selected="true">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="n_pcs" argument="--n-pcs" type="integer" value="50" optional="true" label="Number of PCs to use"/> - <param name="knn" argument="--knn/--no-knn" type="boolean" checked="true" label="Use hard threshold to restrict neighbourhood size (otherwise use a Gaussian kernel to down weight distant neighbours)"/> + <param name="knn" argument="--knn" type="boolean" truevalue="" falsevalue="--no-knn" checked="true" + label="Use hard threshold to restrict neighbourhood size (otherwise use a Gaussian kernel to down weight distant neighbours)"/> <param name="method" argument="--method" type="select" label="Method for calculating connectivity"> <option value="umap" selected="true">UMAP</option> <option value="gauss">Gaussian</option> </param> - <param name="metric" argument="--metric" type="text" value="euclidean" label="Distance metric"/> <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for random number generator"/> </when> </conditional> @@ -71,7 +63,6 @@ <param name="knn" value="true"/> <param name="random_seed" value="0"/> <param name="method" value="umap"/> - <param name="metric" value="euclidean"/> <output name="output_h5" file="compute_graph.h5" ftype="h5" compare="sim_size"/> </test> </tests> |
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| diff -r 3d242b0d97d0 -r e7fd6981c0f0 scanpy_macros2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy_macros2.xml Mon Sep 16 08:18:53 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> |