Mercurial > repos > ebi-gxa > scanpy_normalise_data
changeset 0:19805a556cd6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty
author | ebi-gxa |
---|---|
date | Wed, 13 Mar 2019 11:49:12 -0400 |
parents | |
children | 5704635cef67 |
files | scanpy-normalise-data.xml scanpy_macros.xml |
diffstat | 2 files changed, 148 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy-normalise-data.xml Wed Mar 13 11:49:12 2019 -0400 @@ -0,0 +1,58 @@ +<?xml version="1.0" encoding="utf-8"?> +<tool id="scanpy_normalise_data" name="Scanpy NormaliseData" version="@TOOL_VERSION@+galaxy0"> + <description>to make all cells having the same total expression</description> + <macros> + <import>scanpy_macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +ln -s '${input_obj_file}' input.h5 && +PYTHONIOENCODING=utf-8 scanpy-normalise-data.py + -i input.h5 + -f '${input_format}' + -o output.h5 + -F '${output_format}' + -s '${scale_factor}' + #if $save_raw + '${save_raw}' + #end if +]]></command> + + <inputs> + <expand macro="input_object_params"/> + <expand macro="output_object_params"/> + <param name="scale_factor" argument="--scale-factor" type="float" value="1e4" label="Target number to normalise to"/> + <param name="save_raw" argument="--save-raw" type="boolean" truevalue="--save-raw" falsevalue="" checked="true" label="Save pre-normalised data"/> + </inputs> + + <outputs> + <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Normalized data" /> + </outputs> + + <tests> + <test> + <param name="input_obj_file" value="filter_genes.h5"/> + <param name="input_format" value="anndata"/> + <param name="output_format" value="anndata"/> + <param name="scale_factor" value="1e4"/> + <param name="save_raw" value="false"/> + <output name="output_h5" file="normalise_data.h5" ftype="h5" compare="sim_size"/> + </test> + </tests> + + <help><![CDATA[ +========================================================= +Normalize total counts per cell (`pp.normalize_per_cell`) +========================================================= + +Normalize each cell by total counts over all genes, so that every cell has +the same total count after normalization. + +Similar functions are used, for example, by Seurat, Cell Ranger or SPRING. + +@HELP@ + +@VERSION_HISTORY@ +]]></help> + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy_macros.xml Wed Mar 13 11:49:12 2019 -0400 @@ -0,0 +1,90 @@ +<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>