Mercurial > repos > ebi-gxa > scanpy_run_tsne

comparison scanpy-run-tsne.xml @ 22:8b0d6f6f44c8 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 4332e90fa9f269bf4a8b912366eeace9c040b4c4-dirty"
author ebi-gxa
date Fri, 23 Jul 2021 08:32:50 +0000
parents 2c6340dad187
children a147dce191e9
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21:c4868b59cf7f 22:8b0d6f6f44c8
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> 2 <tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
3 <description>visualise cell clusters using tSNE</description> 3 <description>visualise cell clusters using tSNE</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"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 #set embeddings_tsv='embeddings.tsv' 9 #set embeddings_tsv='embeddings.tsv'
10 ln -s '${input_obj_file}' input.h5 && 10 ln -s '${input_obj_file}' input.h5 &&
11 PYTHONIOENCODING=utf-8 scanpy-run-tsne 11 PYTHONIOENCODING=utf-8 scanpy-run-tsne
12 #if $use_rep != "auto" 12 #if $use_rep
13 --use-rep '${use_rep}' 13 --use-rep '${use_rep}'
14 #end if 14 #end if
15 #if $embeddings 15 #if $embeddings
16 --export-embedding embeddings.tsv 16 --export-embedding embeddings.tsv
17 #end if 17 #end if
62 <inputs> 62 <inputs>
63 <expand macro="input_object_params"/> 63 <expand macro="input_object_params"/>
64 <expand macro="output_object_params"/> 64 <expand macro="output_object_params"/>
65 <param name="embeddings" type="boolean" checked="true" label="Output embeddings in tsv format"/> 65 <param name="embeddings" type="boolean" checked="true" label="Output embeddings in tsv format"/>
66 66
67 <param name="use_rep" argument="--use-rep" type="select" label="Use the indicated representation"> 67 <param name="use_rep" argument="--use-rep" type="text" optional="true" label="Use the indicated representation" help="Use the indicated representation. 'X' (for the content of .X, usuaally normalised expression values) or any key for .obsm (e.g. X_pca for PCA) is valid. If not set, the representation is chosen automatically: For .n_vars less than 50, .X is used, otherwise ‘X_pca’ is used. If ‘X_pca’ is not present, it’s computed with default parameters."/>
68 <option value="X_pca">X_pca, use PCs</option>
69 <option value="X">X, use normalised expression values</option>
70 <option value="auto" selected="true">Automatically chosen based on problem size</option>
71 </param>
72 <conditional name="settings"> 68 <conditional name="settings">
73 <param name="default" type="boolean" checked="true" label="Use programme defaults"/> 69 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
74 <when value="true"/> 70 <when value="true"/>
75 <when value="false"> 71 <when value="false">
76 <param name="key_added" argument="--key-added" type="text" optional="true" 72 <param name="key_added" argument="--key-added" type="text" optional="true"