| Previous changeset 11:1ab80fc6f667 (2020-06-05) Next changeset 13:af4ee7300107 (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-run-dpt.xml scanpy_macros2.xml |
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| diff -r 1ab80fc6f667 -r 820493156c4a scanpy-run-dpt.xml --- a/scanpy-run-dpt.xml Fri Jun 05 09:11:11 2020 -0400 +++ b/scanpy-run-dpt.xml Mon Sep 07 13:10:11 2020 +0000 |
| [ |
| @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_run_dpt" name="Scanpy DPT" version="@TOOL_VERSION@+galaxy11" profile="@PROFILE@"> +<tool id="scanpy_run_dpt" name="Scanpy DPT" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>diffusion pseudotime inference</description> <macros> <import>scanpy_macros2.xml</import> @@ -15,11 +15,14 @@ --min-group-size ${min_group_size} #end if #if $use_graph - --use-graph '${use_graph}' + --neighbors-key '${use_graph}' #end if #if $key_added --key-added '${key_added}' #end if +#if not $allow_kendall_tau_shift + --disallow-kendall-tau-shift +#end if @INPUT_OPTS@ @OUTPUT_OPTS@ ]]></command> @@ -39,10 +42,11 @@ label="Name of attribute that defines clustering"/> <param name="root_value" argument="--root attr {value}" type="text" label="Name of the clustering that defines the root cell type"/> - <param name="use_graph" argument="--use-graph" value="neighbors" type="text" + <param name="use_graph" argument="--neighbors-key" 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 pseudo-time"/> + <param name="allow_kendall_tau_shift" type="boolean" checked="true" label="Allow Kendall Tau shift" help="If a very small branch is detected upon splitting, shift away from maximum correlation in Kendall tau criterion of [Haghverdi16] to stabilize the splitting" /> </inputs> <outputs> @@ -55,10 +59,10 @@ <param name="input_format" value="anndata"/> <param name="output_format" value="anndata"/> <param name="n_dcs" value="10"/> - <param name="root_attr" value="leiden"/> + <param name="root_attr" value="louvain"/> <param name="root_value" value="1"/> <param name="use_graph" value="neighbors"/> - <output name="output_h5" file="paga.h5" ftype="h5" compare="sim_size"/> + <output name="output_h5" file="dpt.h5" ftype="h5" compare="sim_size"/> </test> </tests> |
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| diff -r 1ab80fc6f667 -r 820493156c4a scanpy_macros2.xml --- a/scanpy_macros2.xml Fri Jun 05 09:11:11 2020 -0400 +++ b/scanpy_macros2.xml Mon Sep 07 13:10:11 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> |