| Next changeset 1:17eca8cc832a (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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added:
scanpy-run-dpt.xml scanpy_macros.xml scanpy_macros2.xml |
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| diff -r 000000000000 -r f57f57c459d8 scanpy-run-dpt.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy-run-dpt.xml Mon Sep 16 08:24:32 2019 -0400 |
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| @@ -0,0 +1,83 @@ +<?xml version="1.0" encoding="utf-8"?> +<tool id="scanpy_run_dpt" name="Scanpy DPT" version="@TOOL_VERSION@+galaxy0"> + <description>diffusion pseudotime inference</description> + <macros> + <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-cli dpt + --n-dcs $n_dcs + --root '${root_attr}' '${root_value}' +#if $n_branchings > 0 + --n-branchings ${n_branchings} + --min-group-size ${min_group_size} +#end if +#if $use_graph + --use-graph '${use_graph}' +#end if +#if $key_added + --key-added '${key_added}' +#end if + @INPUT_OPTS@ + @OUTPUT_OPTS@ +]]></command> + + <inputs> + <expand macro="input_object_params"/> + <expand macro="output_object_params"/> + + <param name="n_dcs" argument="--n-dcs" type="integer" min="2" value="10" + label="Number of diffusion components to use"/> + <param name="n_branchings" argument="--n-branchings" min="0" type="integer" value="0" + label="Number of branchings to detect"/> + <param name="min_group_size" argument="--min-group-size" type="float" min="0" max="1" value="0" + label="The fraction of total cells under which further splitting is skipped during recursive splitting of branches" + help="Ignored when `Number of branchings to detect` is 0"/> + <param name="root_attr" argument="--root {attr} value" type="text" + label="Name of attribute that defines clustering"/> + <param name="root_value" argument="--root attr {value}" type="text" + label="Name of the clustering that defines the root cell type"/> + <param name="use_graph" argument="--use-graph" value="neighbors" type="text" + label="Name of the slot that holds the KNN graph"/> + <param name="key_added" argument="--key-added" type="text" optional="true" + label="Additional suffix to the name of the slot to save the calculated trajectory"/> + </inputs> + + <outputs> + <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: dpt object"/> + </outputs> + + <tests> + <test> + <param name="input_obj_file" value="diffmap.h5"/> + <param name="input_format" value="anndata"/> + <param name="output_format" value="anndata"/> + <param name="n_dcs" value="10"/> + <param name="root_attr" value="leiden"/> + <param name="root_value" value="1"/> + <param name="use_graph" value="neighbors"/> + <output name="output_h5" file="paga.h5" ftype="h5" compare="sim_size"/> + </test> + </tests> + + <help><![CDATA[ +================================================ +Calculate Diffusion Pseudotime (`scanpy.tl.dpt`) +================================================ + +Calculate diffusion pseudotime from single cell KNN graphs. + +This requires to run `Scanpy DiffusionMap` and `Scanpy FindCluster`, first. + +It yields `dpt_pseudotime`, diffusion pseudotime as an attribute for each cell. + +@HELP@ + +@VERSION_HISTORY@ +]]></help> + <expand macro="citations"> + <citation type="doi">10.1186/s13059-019-1663-x</citation> + </expand> +</tool> |
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| diff -r 000000000000 -r f57f57c459d8 scanpy_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy_macros.xml Mon Sep 16 08:24:32 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 ${on_string}: 10x barcodes"> + <filter>export_mtx</filter> + </data> + </xml> +</macros> |
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| diff -r 000000000000 -r f57f57c459d8 scanpy_macros2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy_macros2.xml Mon Sep 16 08:24:32 2019 -0400 |
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| @@ -0,0 +1,94 @@ +<macros> + <token name="@TOOL_VERSION@">1.4.2</token> + <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token> + <token name="@VERSION_HISTORY@"><![CDATA[ +**Version history** + +1.4.2+galaxy0: Update to scanpy-scripts 0.2.4 (requires scanpy >=1.4.2). + +1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files. + +1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at +EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute. + ]]></token> + <token name="@INPUT_OPTS@"> + --input-format '${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> |