Mercurial > repos > ebi-gxa > scanpy_find_cluster
diff scanpy-find-cluster.xml @ 1:ee181563bae7 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
author | ebi-gxa |
---|---|
date | Mon, 16 Sep 2019 08:13:51 -0400 |
parents | ce27ae8a36cd |
children | d5290f98fde4 |
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--- 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 @@ -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>