| Previous changeset 0:1dda36e73482 (2019-04-03) Next changeset 2:059f8d2e8be1 (2019-10-25) |
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Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142" |
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modified:
scanpy-normalise-data.xml |
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added:
scanpy_macros2.xml |
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| diff -r 1dda36e73482 -r e541f264fad2 scanpy-normalise-data.xml --- a/scanpy-normalise-data.xml Wed Apr 03 11:07:51 2019 -0400 +++ b/scanpy-normalise-data.xml Mon Sep 16 08:11:56 2019 -0400 |
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| @@ -2,33 +2,34 @@ <tool id="scanpy_normalise_data" name="Scanpy NormaliseData" version="@TOOL_VERSION@+galaxy1"> <description>to make all cells having the same total expression</description> <macros> - <import>scanpy_macros.xml</import> + <import>scanpy_macros2.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ ln -s '${input_obj_file}' input.h5 && -PYTHONIOENCODING=utf-8 scanpy-normalise-data.py - -i input.h5 - -f '${input_format}' - -o output.h5 - -F '${output_format}' - -s '${scale_factor}' - #if $save_raw - '${save_raw}' - #end if - @EXPORT_MTX_OPTS@ +PYTHONIOENCODING=utf-8 scanpy-normalise-data + --normalize-to ${scale_factor} + --fraction ${fraction} + --save-raw ${save_raw} + @INPUT_OPTS@ + @OUTPUT_OPTS@ ]]></command> <inputs> <expand macro="input_object_params"/> <expand macro="output_object_params"/> - <param name="scale_factor" argument="--scale-factor" type="float" value="1e4" label="Target number to normalise to" help="Aimed counts per cell after normalisation, default: 1e4"/> - <param name="save_raw" argument="--save-raw" type="boolean" truevalue="--save-raw" falsevalue="" checked="true" label="Save pre-normalised data" help="Save raw quantification in log scale before normalisation."/> + <param name="scale_factor" argument="--normalize-to" type="float" value="1e4" min="0" + label="Target number to normalise to" help="Aimed counts per cell after normalisation."/> + <param name="fraction" argument="--fraction" type="float" value="1" min="0" max="1" + label="Exclude top expressed genes until the remaining account for no greater than specified fraction of total counts" + help="Only non-excluded genes will sum up the target number."/> + <param name="save_raw" argument="--save-raw" type="boolean" truevalue="yes" falsevalue="no" checked="true" + label="Save normalised data in `.raw`" help="The saved normalised data are log1p transformed."/> <expand macro="export_mtx_params"/> </inputs> <outputs> - <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Normalized data" /> + <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Normalised data"/> <expand macro="export_mtx_outputs"/> </outputs> @@ -44,12 +45,13 @@ </tests> <help><![CDATA[ -========================================================= -Normalize total counts per cell (`pp.normalize_per_cell`) -========================================================= +============================================================= +Normalise total counts per cell (`scanpy.pp.normalize_total`) +============================================================= -Normalize each cell by total counts over all genes, so that every cell has -the same total count after normalization. +Normalise each cell by total counts over all genes (excluding top expressed +genes if so required), so that every cell has the same total count after +normalisation. Similar functions are used, for example, by Seurat, Cell Ranger or SPRING. |
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| diff -r 1dda36e73482 -r e541f264fad2 scanpy_macros2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy_macros2.xml Mon Sep 16 08:11:56 2019 -0400 |
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| @@ -0,0 +1,94 @@ +<macros> + <token name="@TOOL_VERSION@">1.4.2</token> + <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token> + <token name="@VERSION_HISTORY@"><![CDATA[ +**Version history** + +1.4.2+galaxy0: Update to scanpy-scripts 0.2.4 (requires scanpy >=1.4.2). + +1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files. + +1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at +EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute. + ]]></token> + <token name="@INPUT_OPTS@"> + --input-format '${input_format}' input.h5 + </token> + <token name="@OUTPUT_OPTS@"> + --show-obj stdout --output-format '${output_format}' output.h5 + </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="0.2.4.post4">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" 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</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</option> + </param> + </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 normalised data 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 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> |