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comparison scanpy-neighbours.xml @ 15:3cf0177ed87e draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit fda35ff3ea8609c4bb5e1fd9e58ba70cd5b5a997-dirty"
author ebi-gxa
date Wed, 30 Sep 2020 11:16:35 +0000
parents a57b128ea4f6
children 087a7edb0995
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14:a57b128ea4f6 15:3cf0177ed87e
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> 2 <tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@">
3 <description>to derive kNN graph</description> 3 <description>to derive kNN graph</description>
4 <macros> 4 <macros>
5 <import>scanpy_macros2.xml</import> 5 <import>scanpy_macros2.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
49 <conditional name="settings"> 49 <conditional name="settings">
50 <param name="default" type="boolean" checked="true" label="Use programme defaults"/> 50 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
51 <when value="true"/> 51 <when value="true"/>
52 <when value="false"> 52 <when value="false">
53 <param name="key_added" argument="--key-added" type="text" optional="true" label="Key added" 53 <param name="key_added" argument="--key-added" type="text" optional="true" label="Key added"
54 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' /> 54 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='' />
55 <param name="n_neighbors" argument="--n-neighbors" type="integer" value="15" label="Maximum number of neighbors used"/> 55 <param name="n_neighbors" argument="--n-neighbors" type="integer" value="15" label="Maximum number of neighbors used"/>
56 <param name="n_neighbors_file" argument="--n-neighbors" type="data" format="txt,tsv" optional="true" 56 <param name="n_neighbors_file" argument="--n-neighbors" type="data" format="txt,tsv" optional="true"
57 label="File with n_neighbours, use with parameter iterator. Overrides the n_neighbors setting"/> 57 label="File with n_neighbours, use with parameter iterator. Overrides the n_neighbors setting"/>
58 <param name="use_rep" type="select" label="Use the indicated representation"> 58 <param name="use_rep" type="select" label="Use the indicated representation">
59 <option value="X_pca" selected="true">X_pca, use PCs</option> 59 <option value="X_pca" selected="true">X_pca, use PCs</option>