Mercurial > repos > ebi-gxa > scanpy_run_tsne
view scanpy_macros.xml @ 0:5494c27c5880 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
author | ebi-gxa |
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date | Wed, 13 Mar 2019 11:50:56 -0400 |
parents | |
children | 80a4c2939242 |
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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="@VERSION_HISTORY@"><![CDATA[ **Version history** 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> </macros>