| Previous changeset 12:c78c930e3263 (2020-09-07) Next changeset 14:a57b128ea4f6 (2020-09-29) |
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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 e572b5425460d57f1bd13ab6374674c1c6801ab3-dirty" |
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modified:
scanpy-neighbours.xml |
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| diff -r c78c930e3263 -r e6c989a9211c scanpy-neighbours.xml --- a/scanpy-neighbours.xml Mon Sep 07 14:02:36 2020 +0000 +++ b/scanpy-neighbours.xml Thu Sep 24 13:26:39 2020 +0000 |
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| @@ -1,19 +1,32 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> +<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>to derive kNN graph</description> <macros> <import>scanpy_macros2.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ +#from pathlib import Path +#if $settings.n_neighbors_file + #set n_neighbors = Path($settings.n_neighbors_file.__str__).read_text().strip() +#elif $settings.n_neighbors + #set n_neighbors = $settings.n_neighbors.__str__.strip() +#end if + ln -s '${input_obj_file}' input.h5 && PYTHONIOENCODING=utf-8 scanpy-neighbors #if $settings.default == "false" - #if $settings.n_neighbors_file - --n-neighbors \$( cat $settings.n_neighbors_file ) - #elif $settings.n_neighbors - --n-neighbors '${settings.n_neighbors}' + #if $n_neighbors + --n-neighbors $n_neighbors #end if + #if $settings.key_added + #set key_added = $settings.key_added + #if $n_neighbors + #set key_added = $key_added.replace('N_NEIGHBORS', $n_neighbors.__str__) + #end if + --key-added '${key_added}' + #end if + --method '${settings.method}' --metric '${settings.metric}' --random-state '${settings.random_seed}' @@ -36,6 +49,8 @@ <param name="default" type="boolean" checked="true" label="Use programme defaults"/> <when value="true"/> <when value="false"> + <param name="key_added" argument="--key-added" type="text" optional="true" label="Key added" + help="If not specified, the neighbors data is stored in .uns[‘neighbors’], distances and connectivities are stored in .obsp[‘distances’] and .obsp[‘connectivities’] respectively. If specified, the neighbors data is added to .uns[key_added], distances are stored in .obsp[key_added+’_distances’] and connectivities in .obsp[key_added+’_connectivities’]." value='neighbours' /> <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"/> |