Mercurial > repos > ebi-gxa > scanpy_compute_graph
diff scanpy-neighbours.xml @ 1:e7fd6981c0f0 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 08:18:53 -0400 |
parents | 3d242b0d97d0 |
children | 4f9811ccc575 |
line wrap: on
line diff
--- a/scanpy-neighbours.xml Wed Apr 03 11:11:14 2019 -0400 +++ b/scanpy-neighbours.xml Mon Sep 16 08:18:53 2019 -0400 @@ -1,34 +1,27 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy1"> +<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy0"> <description>to derive 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 '${input_obj_file}' input.h5 && -PYTHONIOENCODING=utf-8 scanpy-neighbours.py - -i input.h5 - -f '${input_format}' - -o output.h5 - -F '${output_format}' - #if $settings.default == "false" - -N '${settings.n_neighbours}' - -m '${settings.method}' - -s '${settings.random_seed}' - #if $settings.use_rep != "auto" - -r '${settings.use_rep}' - #end if - #if $settings.n_pcs - -n '${settings.n_pcs}' - #end if - #if $settings.knn - --knn - #end if - #if $settings.metric - -M '${settings.metric}' - #end if +PYTHONIOENCODING=utf-8 scanpy-neighbors +#if $settings.default == "false" + --n-neighbors '${settings.n_neighbours}' + --method '${settings.method}' + --random-state '${settings.random_seed}' + #if $settings.use_rep != "auto" + --use-rep '${settings.use_rep}' #end if + #if $settings.n_pcs + --n-pcs '${settings.n_pcs}' + #end if + ${settings.knn} +#end if + @INPUT_OPTS@ + @OUTPUT_OPTS@ ]]></command> <inputs> @@ -39,18 +32,17 @@ <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="use_rep" type="select" label="Use the indicated representation"> - <option value="X_pca">X_pca, use PCs</option> + <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> - <option value="auto" selected="true">Automatically chosen based on problem size</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/--no-knn" type="boolean" checked="true" label="Use hard threshold to restrict neighbourhood size (otherwise use a Gaussian kernel to down weight distant neighbours)"/> + <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)"/> <param name="method" argument="--method" type="select" label="Method for calculating connectivity"> <option value="umap" selected="true">UMAP</option> <option value="gauss">Gaussian</option> </param> - <param name="metric" argument="--metric" type="text" value="euclidean" label="Distance metric"/> <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for random number generator"/> </when> </conditional> @@ -71,7 +63,6 @@ <param name="knn" value="true"/> <param name="random_seed" value="0"/> <param name="method" value="umap"/> - <param name="metric" value="euclidean"/> <output name="output_h5" file="compute_graph.h5" ftype="h5" compare="sim_size"/> </test> </tests>