| Previous changeset 12:b456d129066d (2020-06-05) Next changeset 14:25e479cd340e (2020-09-10) |
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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 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty" |
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modified:
scanpy-find-cluster.xml scanpy_macros2.xml |
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| diff -r b456d129066d -r c46750e2e4a4 scanpy-find-cluster.xml --- a/scanpy-find-cluster.xml Fri Jun 05 08:55:05 2020 -0400 +++ b/scanpy-find-cluster.xml Mon Sep 07 13:06:07 2020 +0000 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy11" profile="@PROFILE@"> +<tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>based on community detection on KNN graph</description> <macros> <import>scanpy_macros2.xml</import> @@ -10,7 +10,10 @@ PYTHONIOENCODING=utf-8 scanpy-find-cluster ${method} #if $settings.default == "false" - --use-graph '${settings.use_graph}' + --neighbors-key '${settings.neighbors_key}' + #if $settings.layer + --layer '${settings.layer}' + #end if #if $settings.key_added --key-added '${settings.key_added}' #end if @@ -49,8 +52,10 @@ <param name="default" type="boolean" checked="true" label="Use programme defaults"/> <when value="true"/> <when value="false"> - <param name="use_graph" argument="--use-graph" value="neighbors" type="text" + <param name="neighbors_key" argument="--neighbors-key" value="neighbors" type="text" label="Name of the slot that holds the KNN graph"/> + <param name="layer" argument="--layer" value="" type="text" + label="Key from adata.layers whose value will be used to perform tests on. (Default: use .X)"/> <param name="key_added" argument="--key-added" type="text" optional="true" label="Additional suffix to the name of the slot to save the calculated clustering"/> |
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| diff -r b456d129066d -r c46750e2e4a4 scanpy_macros2.xml --- a/scanpy_macros2.xml Fri Jun 05 08:55:05 2020 -0400 +++ b/scanpy_macros2.xml Mon Sep 07 13:06:07 2020 +0000 |
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| @@ -1,10 +1,13 @@ <macros> - <token name="@TOOL_VERSION@">1.4.3</token> + <token name="@TOOL_VERSION@">1.6.0</token> <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token> <token name="@PROFILE@">18.01</token> <token name="@VERSION_HISTORY@"><![CDATA[ **Version history** +1.6.0+galaxy0: Update to scanpy-scripts 0.2.13 (running scanpy ==1.6.0) to incorporate new options, code simplifications, and batch integration methods. Jonathan Manning, Expression Atlas team https://www.ebi.ac.uk/gxa/home at +EMBL-EBI https://www.ebi.ac.uk/ + 1.4.3+galaxy10: Update to scanpy-scripts 0.2.10 (running scanpy ==1.4.3) to address bugfixes in run-pca. 1.4.3+galaxy10: Update to scanpy-scripts 0.2.9 (running scanpy ==1.4.3) to address bugfixes in find-variable-genes. @@ -46,7 +49,7 @@ <xml name="requirements"> <requirements> - <requirement type="package" version="0.2.10">scanpy-scripts</requirement> + <requirement type="package" version="0.3.0">scanpy-scripts</requirement> <yield/> </requirements> </xml> |