Mercurial > repos > ebi-gxa > scanpy_run_fdg
view scanpy_macros.xml @ 5:f5bc7d1b32fd draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 367d978e52fac9467a804009c5013f53c06765f0
author | ebi-gxa |
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date | Tue, 26 Nov 2019 05:52:47 -0500 |
parents | 96af0059b974 |
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<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>