| Previous changeset 10:ed2231b3edff (2020-06-05) Next changeset 12:607408d09a36 (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-paga.xml scanpy_macros2.xml |
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| diff -r ed2231b3edff -r a1a7650c5cf2 scanpy-run-paga.xml --- a/scanpy-run-paga.xml Fri Jun 05 09:12:40 2020 -0400 +++ b/scanpy-run-paga.xml Mon Sep 07 14:01:54 2020 +0000 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_run_paga" name="Scanpy PAGA" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@"> +<tool id="scanpy_run_paga" name="Scanpy PAGA" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>trajectory inference</description> <macros> <import>scanpy_macros2.xml</import> @@ -9,12 +9,15 @@ ln -s '${input_obj_file}' input.h5 && PYTHONIOENCODING=utf-8 scanpy-cli paga --groups '${groups}' -#if $use_graph - --use-graph '${use_graph}' +#if $neighbors_key + --neighbors-key '${neighbors_key}' #end if #if $key_added --key-added '${key_added}' #end if +#if $use_rna_velocity + --use-rna-velocity +#end if @INPUT_OPTS@ @OUTPUT_OPTS@ ]]></command> @@ -24,8 +27,9 @@ <expand macro="output_object_params"/> <param name="groups" argument="--groups" type="text" label="Name of the clustering"/> - <param name="use_graph" argument="--use-graph" value="neighbors" type="text" label="Name of the slot that holds the KNN graph"/> + <param name="neighbors_key" 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 trajectory"/> + <param name="use_rna_velocity" type="boolean" checked="false" label="Use RNA velocity to orient edges in the abstracted graph and estimate transitions." help=" Requires that adata.uns contains a directed single-cell graph with key velocity_graph. This feature might be subject to change in the future."/> </inputs> <outputs> @@ -34,11 +38,11 @@ <tests> <test> - <param name="input_obj_file" value="compute_graph.h5"/> + <param name="input_obj_file" value="find_cluster.h5"/> <param name="input_format" value="anndata"/> <param name="output_format" value="anndata"/> - <param name="groups" value="leiden"/> - <param name="use_graph" value="neighbors"/> + <param name="groups" value="louvain"/> + <param name="neighbors_key" value="neighbors"/> <output name="output_h5" file="paga.h5" ftype="h5" compare="sim_size"/> </test> </tests> |
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| diff -r ed2231b3edff -r a1a7650c5cf2 scanpy_macros2.xml --- a/scanpy_macros2.xml Fri Jun 05 09:12:40 2020 -0400 +++ b/scanpy_macros2.xml Mon Sep 07 14:01:54 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> |