| Previous changeset 0:ce27ae8a36cd (2019-04-03) Next changeset 2:e232ea3fff07 (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-find-cluster.xml |
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added:
scanpy_macros2.xml |
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| diff -r ce27ae8a36cd -r ee181563bae7 scanpy-find-cluster.xml --- a/scanpy-find-cluster.xml Wed Apr 03 11:09:12 2019 -0400 +++ b/scanpy-find-cluster.xml Mon Sep 16 08:13:51 2019 -0400 |
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| @@ -2,55 +2,68 @@ <tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy1"> <description>based on community detection on KNN graph</description> <macros> - <import>scanpy_macros.xml</import> + <import>scanpy_macros2.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ ln -s '${input_obj_file}' input.h5 && -PYTHONIOENCODING=utf-8 scanpy-find-cluster.py - -i input.h5 - -f '${input_format}' - -o output.h5 - -F '${output_format}' - #if $output_cluster - --output-text-file output.tsv - #end if - #if $settings.default == "false" - --flavor '${settings.flavor}' +PYTHONIOENCODING=utf-8 scanpy-find-cluster + ${method} +#if $settings.default == "false" + --use-graph '${settings.use_graph}' + #if $settings.key_added --key-added '${settings.key_added}' - -s '${settings.random_seed}' - #if $settings.flavor == "vtraag" and $settings.resolution_file - --resolution \$( cat $settings.resolution_file ) - #elif $settings.flavor == "vtraag" - --resolution '${settings.resolution}' - #end if - #if $settings.restrict_to - --restrict-to '${settings.restrict_to}' - #end if - #if $settings.use_weights - --use-weights - #end if + #end if + #if $settings.resolution_file + --resolution \$( cat $settings.resolution_file ) + #elif $settings.resolution + --resolution '${settings.resolution}' + #end if + #if $settings.restrict_to + --restrict-to '${settings.restrict_to}' #end if + #if $settings.use_weights + --use-weights + #end if + --random-state '${settings.random_seed}' + ${settings.directed} +#end if +#if $output_cluster + --export-cluster output.tsv +#end if + @INPUT_OPTS@ + @OUTPUT_OPTS@ ]]></command> <inputs> <expand macro="input_object_params"/> <expand macro="output_object_params"/> <param name="output_cluster" type="boolean" checked="true" label="Output cluster in two column text format"/> + + <param name="method" type="select" label="Clustering algorithm"> + <option value="louvain" selected="true">Louvain</option> + <option value="leiden">Leiden</option> + </param> + <conditional name="settings"> <param name="default" type="boolean" checked="true" label="Use programme defaults"/> <when value="true"/> <when value="false"> - <param name="flavor" argument="--flavor" type="select" label="Use the indicated representation"> - <option value="vtraag" selected="true">vtraag</option> - <option value="igraph">igraph</option> - </param> - <param name="resolution" argument="--resolution" type="float" value="1.0" label="Resolution, high value for more and smaller clusters"/> - <param name="resolution_file" argument="--resolution" type="data" format="txt,tsv" optional="true" label="File with resolution, use with parameter iterator. Overrides the resolution setting"/> - <param name="restrict_to" argument="--restrict-to" type="text" optional="true" label="Restrict clustering to certain sample categories"/> - <param name="key_added" argument="--key-added" type="text" value="louvain" label="Key under which to add the cluster labels (do not change unless you know what you are doing)"/> + <param name="use_graph" argument="--use-graph" value="neighbors" type="text" + label="Name of the slot that holds the KNN graph"/> + <param name="key_added" argument="--key-added" type="text" optional="true" + label="Additional suffix to the name of the slot to save the calculated trajectory"/> + + <param name="resolution" argument="--resolution" type="float" min="0.0" value="1.0" + label="Resolution, high value for more and smaller clusters"/> + <param name="resolution_file" argument="--resolution" type="data" format="txt,tsv" optional="true" + label="File with resolution, use with parameter iterator. Overrides the resolution setting"/> + <param name="restrict_to" argument="--restrict-to" type="text" optional="true" + label="Restrict clustering to certain sample categories"/> <param name="use_weights" argument="--use-weights" type="boolean" checked="false" label="Use weights from knn graph"/> <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for random number generator"/> + <param name="directed" argument="--directed" type="boolean" truevalue="--directed" falsevalue="--undirected" checked="true" + label="Interpret the adjacency matrix as directed graph."/> </when> </conditional> </inputs> @@ -69,7 +82,6 @@ <param name="output_format" value="anndata"/> <param name="output_txt" value="true"/> <param name="default" value="false"/> - <param name="flavor" value="vtraag"/> <param name="resolution" value="1.0"/> <param name="random_seed" value="0"/> <output name="output_h5" file="find_cluster.h5" ftype="h5" compare="sim_size"/> @@ -78,17 +90,18 @@ </tests> <help><![CDATA[ -=========================================== -Cluster cells into subgroups (`tl.louvain`) -=========================================== +====================================================================== +Cluster cells into subgroups (`scanpy.tl.louvain`, `scanpy.tl.leiden`) +====================================================================== -Cluster cells using the Louvain algorithm (Blondel et al, 2008) in the implementation -of Traag et al,2017. The Louvain algorithm has been proposed for single-cell -analysis by Levine et al, 2015. +Cluster cells using the Louvain algorithm (Blondel et al, 2008) in the +implementation of Traag et al, 2017, or the Leiden algorithm (Traag et al, +2019). The Louvain algorithm has been proposed for single-cell analysis by +Levine et al, 2015. This requires to run `Scanpy ComputeGraph`, first. -It yields `louvain`, generated cluster label. +It by default yields `louvain` or `leiden`, generated cluster label. @HELP@ @@ -97,6 +110,7 @@ <expand macro="citations"> <citation type="doi">10.1088/1742-5468/2008/10/P10008</citation> <citation type="doi">10.1016/j.cell.2015.05.047</citation> + <citation type="doi">10.1038/s41598-019-41695-z</citation> <citation type="doi">10.5281/zenodo.35117</citation> </expand> </tool> |
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| diff -r ce27ae8a36cd -r ee181563bae7 scanpy_macros2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy_macros2.xml Mon Sep 16 08:13:51 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> |