| Next changeset 1:f1298838e93b (2020-09-10) |
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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 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty" |
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added:
scanpy-integrate-harmony.xml scanpy_macros.xml scanpy_macros2.xml |
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| diff -r 000000000000 -r 8b3a52fbb482 scanpy-integrate-harmony.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy-integrate-harmony.xml Mon Sep 07 13:10:56 2020 +0000 |
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| @@ -0,0 +1,134 @@ +<?xml version="1.0" encoding="utf-8"?> +<tool id="scanpy_integrate_harmony" name="Scanpy Harmony" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> + <description>adjust principal components for variables that might introduce batch effect</description> + <macros> + <import>scanpy_macros2.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +#if $batch_key + ln -s '${input_obj_file}' input.h5 && + PYTHONIOENCODING=utf-8 scanpy-integrate harmony + --batch-key '${batch_key}' + #if $basis + --basis '${basis}' + #end if + --adjusted-basis '${adjusted_basis}' + #if not $settings.default + #if $settings.theta + --theta '${settings.theta}' + #end if + #if $settings.lambda + --lambda '${settings.lambda}' + #end if + #if $settings.sigma + --sigma '${settings.sigma}' + #end if + #if $settings.nclust + --nclust '${settings.nclust}' + #end if + #if $settings.tau + --tau '${settings.tau}' + #end if + #if $settings.block_size + --block-size '${settings.block_size}' + #end if + #if $settings.max_iter_cluster + --max-iter-cluster '${settings.max_iter_cluster}' + #end if + #if $settings.max_iter_harmony + --max-iter-harmony '${settings.max_iter_harmony}' + #end if + #if $settings.epsilon_cluster + --epsilon-cluster '${settings.epsilon_cluster}' + #end if + #if $settings.epsilon_harmony + --epsilon-harmony '${settings.epsilon_harmony}' + #end if + #if $settings.random_state + --random-state '${settings.random_state}' + #end if + #end if + @INPUT_OPTS@ + @OUTPUT_OPTS@ +#else + echo "No batch variables passed, simply passing original input as output unchanged."; + cp '${input_obj_file}' '${output_h5}' +#end if +]]></command> + + <inputs> + <expand macro="input_object_params"/> + <expand macro="output_object_params"/> + <param name="batch_key" type="text" argument="--batch-key" label="The name of the column in adata.obs that differentiates among experiments/batches."> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param name="basis" argument="--basis" type="text" value='X_pca' label="The name of the field in adata.obsm where the PCA table is stored. Defaults to 'X_pca', which is the default for sc.tl.pca()."> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + </param> + <param name="adjusted_basis" argument="--adjusted-basis" type="text" value='X_pca_harmony' label="he name of the field in adata.obsm where the adjusted PCA table will be stored after running this function."> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + </param> + <conditional name="settings"> + <param name="default" type="boolean" checked="true" label="Use programme defaults"/> + <when value="true"/> + <when value="false"> + <param name="theta" argument="--theta" type="float" value="2.0" + label="Diversity clustering penalty parameter" help="theta=0 does not encourage any diversity. Larger values of theta result in more diverse clusters." /> + <param name="lambda" argument="--lambda" type="float" min="0" value="1.0" + label="Ridge regression penalty parameter" help="Lambda must be strictly positive. Smaller values result in more aggressive correction." /> + <param name="sigma" argument="--sigma" type="float" value="0.1" + label="Ridge regression penalty parameter" help="Width of soft kmeans clusters. Sigma scales the distance from a cell to cluster centroids. Larger values of sigma result in cells assigned to more clusters. Smaller values of sigma make soft kmeans cluster approach hard clustering." /> + <param name="nclust" argument="--nclust" type="integer" value="" optional="true" + label="Number of clusters in model." help="nclust=1 equivalent to simple linear regression." /> + <param name="tau" argument="--tau" type="integer" value="0" + label="Protection against overclustering small datasets with large ones." help="'tau is the expected number of cells per cluster." /> + <param name="block_size" argument="--block-size" type="float" value="0.05" + label="What proportion of cells to update during clustering" min="0" max="1" help="Between 0 to 1, default 0.05. Larger values may be faster but less accurate." /> + <param name="max_iter_cluster" argument="--max-iter-cluster" type="integer" value="20" + label="Maximum number of rounds to run clustering at each round of Harmony" /> + <param name="max_iter_harmony" argument="--max-iter-harmony" type="integer" value="10" + label="Maximum number of rounds to run Harmony. One round of Harmony involves one clustering and one correction step." /> + <param name="epsilon_cluster" argument="--epsilon-cluster" type="float" value="0.00001" + label="Convergence tolerance for clustering round of Harmony" help="Set to -Inf to never stop early." /> + <param name="epsilon_harmony" argument="--epsilon-harmony" type="float" value="0.00001" + label="Convergence tolerance for Harmony." help="Set to -Inf to never stop early." /> + <param name="random_state" argument="--random-state" type="integer" value="0" + label="Seed for random number generator." /> + </when> + </conditional> + </inputs> + + <outputs> + <expand macro="output_data_obj" description="Batch-corrected for ${batch_key}"/> + </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="batch_key" value="louvain"/> + <output name="output_h5" file="harmony.h5" ftype="h5" compare="sim_size"/> + </test> + </tests> + + <help><![CDATA[ + .. class:: infomark + + **What it does** + + Uses harmonypy [Korunsky19] to integrate different experiments at the principal components level. + + @HELP@ + + @VERSION_HISTORY@ +]]></help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r 8b3a52fbb482 scanpy_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy_macros.xml Mon Sep 07 13:10:56 2020 +0000 |
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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 ${on_string}: 10x barcodes"> + <filter>export_mtx</filter> + </data> + </xml> +</macros> |
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| diff -r 000000000000 -r 8b3a52fbb482 scanpy_macros2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy_macros2.xml Mon Sep 07 13:10:56 2020 +0000 |
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| @@ -0,0 +1,146 @@ +<macros> + <token name="@TOOL_VERSION@">1.6.0</token> + <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token> + <token name="@PROFILE@">18.01</token> + <token name="@VERSION_HISTORY@"><![CDATA[ +**Version history** + +1.6.0+galaxy0: Update to scanpy-scripts 0.2.13 (running scanpy ==1.6.0) to incorporate new options, code simplifications, and batch integration methods. Jonathan Manning, Expression Atlas team https://www.ebi.ac.uk/gxa/home at +EMBL-EBI https://www.ebi.ac.uk/ + +1.4.3+galaxy10: Update to scanpy-scripts 0.2.10 (running scanpy ==1.4.3) to address bugfixes in run-pca. + +1.4.3+galaxy10: Update to scanpy-scripts 0.2.9 (running scanpy ==1.4.3) to address bugfixes in find-variable-genes. + +1.4.3+galaxy10: Use profile 18.01 for modules. + +1.4.3+galaxy6: Update to scanpy-scripts 0.2.8 (running scanpy ==1.4.3) and wider compatibility with other Galaxy modules. Bug fixes in filtering and plotting improvements. + +1.4.3+galaxy0: Update to scanpy-scripts 0.2.5 (running scanpy ==1.4.3). + +1.4.2+galaxy0: Update to scanpy-scripts 0.2.4 (requires scanpy >=1.4.2). + +1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files. + +1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at +EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute. + ]]></token> + <token name="@INPUT_OPTS@"> + --input-format '${input_format}' input.h5 + </token> + <token name="@OUTPUT_OPTS@"> +#if str($output_format).startswith('anndata') + --show-obj stdout --output-format anndata output.h5 +#else + --show-obj stdout --output-format loom output.h5 +#end if + </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="0.3.0">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> + <citation type="doi">10.1101/2020.04.08.032698</citation> + </citations> + </xml> + + <xml name="input_object_params"> + <param name="input_obj_file" argument="input-object-file" type="data" format="h5,h5ad" label="Input object in AnnData/Loom 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_h5ad" selected="true">AnnData format</option> + <option value="anndata">AnnData format (h5 for older versions)</option> + <option value="loom">Loom format</option> + <option value="loom_legacy">Loom format (h5 for older versions)</option> + </param> + </xml> + + <xml name="output_object_params_no_loom"> + <param name="output_format" argument="--output-format" type="select" label="Format of output object"> + <option value="anndata_h5ad" selected="true">AnnData format</option> + <option value="anndata">AnnData format (h5 for older versions)</option> + </param> + </xml> + + <xml name="output_data_obj_no_loom" token_description="operation"> + <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData"> + <filter>output_format == 'anndata_h5ad'</filter> + </data> + <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData"> + <filter>output_format == 'anndata'</filter> + </data> + </xml> + + <xml name="output_data_obj" token_description="operation"> + <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData"> + <filter>output_format == 'anndata_h5ad'</filter> + </data> + <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData"> + <filter>output_format == 'anndata'</filter> + </data> + <data name="output_loom_legacy" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom"> + <filter>output_format == 'loom_legacy'</filter> + </data> + <data name="output_loom" format="loom" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom"> + <filter>output_format == 'loom'</filter> + </data> + </xml> + + <xml name="output_plot_params"> + <param name="fig_title" argument="--title" type="text" label="Figure title"/> + <param name="fig_size" argument="--fig-size" type="text" value="4,4" label="Figure size as 'width,height', e.g, '7,7'"/> + <param name="fig_dpi" argument="--fig-dpi" type="integer" min="1" value="80" label="Figure dpi"/> + <param name="fig_fontsize" argument="--fig-fontsize" type="integer" min="0" value="10" label="Figure font size"/> + <param name="fig_frame" type="boolean" truevalue="--frameon" falsevalue="--frameoff" checked="false" + label="Show plot frame"/> + </xml> + + <xml name="export_mtx_params"> + <param name="export_mtx" argument="--export-mtx" type="boolean" truevalue="--export-mtx ./" falsevalue="" checked="false" label="Save to 10x mtx format" help="If enabled, it will generate in addition to the main output in Loom or AnnData an export in 10x format."/> + </xml> + + <xml name="export_mtx_outputs"> + <data name="matrix_10x" format="txt" from_work_dir="matrix.mtx" label="${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> |