Mercurial > repos > ebi-gxa > scanpy_scale_data
changeset 1:edb0d2e8ab66 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
| author | ebi-gxa |
|---|---|
| date | Thu, 12 Mar 2020 09:09:35 +0000 |
| parents | eae21a6c3128 |
| children | 9b07e1cf91d2 |
| files | scanpy-scale-data.xml scanpy_macros.xml scanpy_macros2.xml |
| diffstat | 3 files changed, 173 insertions(+), 30 deletions(-) [+] |
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--- a/scanpy-scale-data.xml Wed Mar 13 11:50:13 2019 -0400 +++ b/scanpy-scale-data.xml Thu Mar 12 09:09:35 2020 +0000 @@ -1,44 +1,31 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_scale_data" name="Scanpy ScaleData" version="@TOOL_VERSION@+galaxy1"> +<tool id="scanpy_scale_data" name="Scanpy ScaleData" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@"> <description>to make expression variance the same for all genes</description> <macros> - <import>scanpy_macros.xml</import> + <import>scanpy_macros2.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ ln -s '${input_obj_file}' input.h5 && -PYTHONIOENCODING=utf-8 scanpy-scale-data.py - -i input.h5 - -f '${input_format}' - -o output.h5 - -F '${output_format}' +PYTHONIOENCODING=utf-8 scanpy-scale-data #if $scale_max - -x '${scale_max}' + --max-value '${scale_max}' #end if - #if $var_to_regress - -V '${var_to_regress}' - #end if - #if $do_log - --do-log - #end if - #if $zero_center - --zero-center - #end if + ${zero_center} + @INPUT_OPTS@ + @OUTPUT_OPTS@ ]]></command> <inputs> <expand macro="input_object_params"/> <expand macro="output_object_params"/> - <param name="do_log" argument="--do-log" type="boolean" checked="true" label="Do log(x+1) transformation"/> - <param name="zero_center" argument="--zero-center" type="boolean" checked="true" label="Zero center data before scaling"/> - <param name="var_to_regress" argument="--var-to-regress" type="text" optional="true" label="Variable(s) to regress out"> - <option value="n_counts">n_counts</option> - </param> - <param name="scale_max" argument="--scale-max" type="float" optional="true" label="Truncate to this value after scaling"/> + <param name="zero_center" type="boolean" checked="true" truevalue="" falsevalue="--no-zero-center" + label="Zero center data before scaling"/> + <param name="scale_max" argument="--max-value" type="float" min="0" optional="true" label="Truncate to this value after scaling"/> </inputs> <outputs> - <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Scaled data"/> + <expand macro="output_data_obj" description="Scaled data"/> </outputs> <tests> @@ -46,7 +33,6 @@ <param name="input_obj_file" value="find_variable_genes.h5"/> <param name="input_format" value="anndata"/> <param name="output_format" value="anndata"/> - <param name="do_log" value="true"/> <param name="zero_center" value="true"/> <param name="scale_max" value="10"/> <output name="output_h5" file="scale_data.h5" ftype="h5" compare="sim_size"/> @@ -58,11 +44,7 @@ **What it does** - Scale data to unit variance and zero mean (`pp.scale`) - Regress out unwanted sources of variation (`pp.regress_out`) - - Regress out unwanted sources of variation, using simple linear regression. This is - inspired by Seurat's `regressOut` function in R. + Scale data to unit variance and (optionally) zero mean (`scanpy.pp.scale`) @HELP@
--- a/scanpy_macros.xml Wed Mar 13 11:50:13 2019 -0400 +++ b/scanpy_macros.xml Thu Mar 12 09:09:35 2020 +0000 @@ -38,9 +38,14 @@ <yield/> </requirements> </xml> + <token name="@EXPORT_MTX_OPTS@"> + ${export_mtx} + </token> <token name="@VERSION_HISTORY@"><![CDATA[ **Version history** +1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files. + 1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute. ]]></token> @@ -87,4 +92,18 @@ <param name="sort_order" argument="--no-sort-order" type="boolean" checked="true" label="Element with high color-by value plot on top"/> <param name="frameoff" argument="--frameoff" type="boolean" checked="false" label="Omit frame"/> </xml> + <xml name="export_mtx_params"> + <param name="export_mtx" argument="--export-mtx" type="boolean" truevalue="--export-mtx ./" falsevalue="" checked="false" label="Save normalised data to 10x format" help="If enabled, it will generate in addition to the main output in Loom or AnnData an export in 10x format of the normalised data."/> + </xml> + <xml name="export_mtx_outputs"> + <data name="matrix_10x" format="txt" from_work_dir="matrix.mtx" label="${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 ${on_string}: 10x barcodes"> + <filter>export_mtx</filter> + </data> + </xml> </macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy_macros2.xml Thu Mar 12 09:09:35 2020 +0000 @@ -0,0 +1,142 @@ +<macros> + <token name="@TOOL_VERSION@">1.4.3</token> + <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token> + <token name="@PROFILE@">18.01</token> + <token name="@VERSION_HISTORY@"><![CDATA[ +**Version history** + +1.4.3+galaxy10: Update to scanpy-scripts 0.2.10 (running scanpy ==1.4.3) to address bugfixes in run-pca. + +1.4.3+galaxy10: Update to scanpy-scripts 0.2.9 (running scanpy ==1.4.3) to address bugfixes in find-variable-genes. + +1.4.3+galaxy10: Use profile 18.01 for modules. + +1.4.3+galaxy6: Update to scanpy-scripts 0.2.8 (running scanpy ==1.4.3) and wider compatibility with other Galaxy modules. Bug fixes in filtering and plotting improvements. + +1.4.3+galaxy0: Update to scanpy-scripts 0.2.5 (running scanpy ==1.4.3). + +1.4.2+galaxy0: Update to scanpy-scripts 0.2.4 (requires scanpy >=1.4.2). + +1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files. + +1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at +EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute. + ]]></token> + <token name="@INPUT_OPTS@"> + --input-format '${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="0.2.10">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,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>