| Next changeset 1:3faf577f3e40 (2019-09-16) |
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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 9bf9a6e46a330890be932f60d1d996dd166426c4 |
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added:
scanpy-read-10x.xml scanpy_macros.xml |
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| diff -r 000000000000 -r 572b6e3b2aff scanpy-read-10x.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy-read-10x.xml Wed Apr 03 11:11:38 2019 -0400 |
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| @@ -0,0 +1,66 @@ +<?xml version="1.0" encoding="utf-8"?> +<tool id="scanpy_read_10x" name="Scanpy Read10x" version="@TOOL_VERSION@+galaxy0"> + <description>into hdf5 object handled by scanpy</description> + <macros> + <import>scanpy_macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +ln -s '${matrix}' matrix.mtx && +ln -s '${genes}' genes.tsv && +ln -s '${barcodes}' barcodes.tsv && +PYTHONIOENCODING=utf-8 scanpy-read-10x.py + -d ./ + -o read_10x.h5 + -F '${output_format}' + -v '${var_names}' +]]></command> + + <inputs> + <param name="matrix" type="data" format="txt" label="Expression matrix in sparse matrix format (.mtx)"/> + <param name="genes" type="data" format="tsv,tabular" label="Gene table"/> + <param name="barcodes" type="data" format="tsv,tabular" label="Barcode/cell table"/> + <expand macro="output_object_params"/> + <param name="var_names" type="select" label="Attribute used as annotation index"> + <option value="gene_ids" selected="true">Gene ID</option> + <option value="gene_symbols">Gene symbol</option> + </param> + </inputs> + + <outputs> + <data name="output_h5" format="h5" from_work_dir="read_10x.h5" label="${tool.name} on ${on_string}: ${output_format}"/> + </outputs> + + <tests> + <test> + <param name="matrix" value="matrix.mtx"/> + <param name="genes" value="genes.tsv"/> + <param name="barcodes" value="barcodes.tsv"/> + <param name="output_format" value="anndata"/> + <output name="output_h5" file="read_10x.h5" ftype="h5" compare="sim_size"/> + </test> + </tests> + + <help><![CDATA[ +========================================================== +Read 10x-Genomics-formatted mtx directory (`read_10x_mtx`) +========================================================== + +The mtx directory should contain: + +1) Raw expression quantification as a sparse matrix in Matrix Market format, where the each column is a gene and each row is a barcode/cell. + +2) A gene table of at least two columns where the first column gives the gene IDs. + +3) A barcode/cell table of at least one column giving the barcode/cell IDs. + +The above-mentioned files can be obtained by running `EBI SCXA Data Retrieval` +with a dataset accession. + + +@HELP@ + +@VERSION_HISTORY@ +]]></help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r 572b6e3b2aff scanpy_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy_macros.xml Wed Apr 03 11:11:38 2019 -0400 |
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| @@ -0,0 +1,109 @@ +<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> |