Mercurial > repos > ebi-gxa > scanpy_compute_graph
changeset 11:232937b5bb8f draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 121972f836fc6f5a60390abcdc1e2fe904b79072"
| author | ebi-gxa |
|---|---|
| date | Fri, 05 Jun 2020 09:12:59 -0400 |
| parents | 3bce5710a90b |
| children | c78c930e3263 |
| files | scanpy-neighbours.xml scanpy_macros2.xml |
| diffstat | 2 files changed, 12 insertions(+), 5 deletions(-) [+] |
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--- a/scanpy-neighbours.xml Thu Mar 12 05:18:41 2020 -0400 +++ b/scanpy-neighbours.xml Fri Jun 05 09:12:59 2020 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@"> +<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy11" profile="@PROFILE@"> <description>to derive kNN graph</description> <macros> <import>scanpy_macros2.xml</import> @@ -9,7 +9,11 @@ ln -s '${input_obj_file}' input.h5 && PYTHONIOENCODING=utf-8 scanpy-neighbors #if $settings.default == "false" - --n-neighbors '${settings.n_neighbours}' + #if $settings.n_neighbors_file + --n-neighbors \$( cat $settings.n_neighbors_file ) + #elif $settings.n_neighbors + --n-neighbors '${settings.n_neighbors}' + #end if --method '${settings.method}' --random-state '${settings.random_seed}' #if $settings.use_rep != "auto" @@ -31,14 +35,16 @@ <param name="default" type="boolean" checked="true" label="Use programme defaults"/> <when value="true"/> <when value="false"> - <param name="n_neighbours" argument="--n-neighbors" type="integer" value="15" label="Maximum number of neighbours used"/> + <param name="n_neighbors" argument="--n-neighbors" type="integer" value="15" label="Maximum number of neighbors used"/> + <param name="n_neighbors_file" argument="--n-neighbors" type="data" format="txt,tsv" optional="true" + label="File with n_neighbours, use with parameter iterator. Overrides the n_neighbors setting"/> <param name="use_rep" type="text" label="Use the indicated representation"> <option value="X_pca" selected="true">X_pca, use PCs</option> <option value="X">X, use normalised expression values</option> </param> <param name="n_pcs" argument="--n-pcs" type="integer" value="50" optional="true" label="Number of PCs to use"/> <param name="knn" argument="--knn" type="boolean" truevalue="" falsevalue="--no-knn" checked="true" - label="Use hard threshold to restrict neighbourhood size (otherwise use a Gaussian kernel to down weight distant neighbours)"/> + label="Use hard threshold to restrict neighbourhood size (otherwise use a Gaussian kernel to down weight distant neighbors)"/> <param name="method" argument="--method" type="select" label="Method for calculating connectivity"> <option value="umap" selected="true">UMAP</option> <option value="gauss">Gaussian</option> @@ -58,7 +64,7 @@ <param name="input_format" value="anndata"/> <param name="output_format" value="anndata"/> <param name="default" value="false"/> - <param name="n_neighbours" value="15"/> + <param name="n_neighbors" value="15"/> <param name="n_pcs" value="50"/> <param name="knn" value="true"/> <param name="random_seed" value="0"/>
--- a/scanpy_macros2.xml Thu Mar 12 05:18:41 2020 -0400 +++ b/scanpy_macros2.xml Fri Jun 05 09:12:59 2020 -0400 @@ -64,6 +64,7 @@ journal = {GitHub repository}, url = {https://github.com/ebi-gene-expression-group/scanpy-scripts}, }</citation> + <citation type="doi">10.1101/2020.04.08.032698</citation> </citations> </xml>