Mercurial > repos > ebi-gxa > scanpy_find_markers
view scanpy_macros2.xml @ 21:a6a896082cd7 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 858a2398f1dbbd60110867c593c237358c794615-dirty"
author | ebi-gxa |
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date | Mon, 12 Apr 2021 14:41:34 +0000 |
parents | 9fe7e2da8fe6 |
children | 7042ce140caa |
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<macros> <token name="@TOOL_VERSION@">1.7.2</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** 1.7.2+galaxy0: Upate to scanpy-scripts 0.3.3 (running scanpy ==1.7.2) to incorporate fix for object output from PAGA plotting, to allow PAGA init of FDG. 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="0.3.3">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> <citation type="doi">10.1038/s41592-021-01102-w</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>