Mercurial > repos > ebi-gxa > scanpy_run_tsne

comparison scanpy-run-tsne.xml @ 16:9d2b6c6f9e07 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 c02d457c74016980672e64832e6cad31d703edcd-dirty"
author ebi-gxa
date Tue, 29 Sep 2020 14:10:52 +0000
parents b5e1939cc155
children 2c6340dad187
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15:b5e1939cc155 16:9d2b6c6f9e07
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@+galaxy1" profile="@PROFILE@"> 2 <tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy2" 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 #from pathlib import Path
10 #set embeddings_tsv='embeddings.tsv' 9 #set embeddings_tsv='embeddings.tsv'
11 ln -s '${input_obj_file}' input.h5 && 10 ln -s '${input_obj_file}' input.h5 &&
12 PYTHONIOENCODING=utf-8 scanpy-run-tsne 11 PYTHONIOENCODING=utf-8 scanpy-run-tsne
13 #if $use_rep != "auto" 12 #if $use_rep != "auto"
14 --use-rep '${use_rep}' 13 --use-rep '${use_rep}'
16 #if $embeddings 15 #if $embeddings
17 --export-embedding embeddings.tsv 16 --export-embedding embeddings.tsv
18 #end if 17 #end if
19 #if $settings.default == "false" 18 #if $settings.default == "false"
20 #if $settings.perplexity_file 19 #if $settings.perplexity_file
21 #set perplexity = Path($settings.perplexity_file.__str__).read_text().strip() 20 #set f = open($settings.perplexity_file.__str__)
21 #set perplexity = f.read().strip()
22 #silent f.close
22 #elif $settings.perplexity 23 #elif $settings.perplexity
23 #set perplexity = $settings.perplexity.__str__.strip() 24 #set perplexity = $settings.perplexity.__str__.strip()
24 #end if 25 #end if
25 #if $perplexity 26 #if $perplexity
26 --perplexity '$perplexity' 27 --perplexity '$perplexity'
98 <test> 99 <test>
99 <param name="input_obj_file" value="find_cluster.h5"/> 100 <param name="input_obj_file" value="find_cluster.h5"/>
100 <param name="input_format" value="anndata"/> 101 <param name="input_format" value="anndata"/>
101 <param name="output_format" value="anndata"/> 102 <param name="output_format" value="anndata"/>
102 <param name="default" value="false"/> 103 <param name="default" value="false"/>
104 <param name="perplexity_file" value="perplexity.txt"/>
105 <param name="embeddings" value="true"/>
106 <param name="random_seed" value="0"/>
107 <output name="output_h5" file="run_tsne.h5" ftype="h5" compare="sim_size"/>
108 <output name="output_embed" file="run_tsne.embeddings.tsv" ftype="tabular" compare="sim_size">
109 <assert_contents>
110 <has_n_columns n="3"/>
111 </assert_contents>
112 </output>
113 </test>
114 <test>
115 <param name="input_obj_file" value="find_cluster.h5"/>
116 <param name="input_format" value="anndata"/>
117 <param name="output_format" value="anndata"/>
118 <param name="default" value="false"/>
119 <param name="perplexity" value="30"/>
103 <param name="embeddings" value="true"/> 120 <param name="embeddings" value="true"/>
104 <param name="random_seed" value="0"/> 121 <param name="random_seed" value="0"/>
105 <output name="output_h5" file="run_tsne.h5" ftype="h5" compare="sim_size"/> 122 <output name="output_h5" file="run_tsne.h5" ftype="h5" compare="sim_size"/>
106 <output name="output_embed" file="run_tsne.embeddings.tsv" ftype="tabular" compare="sim_size"> 123 <output name="output_embed" file="run_tsne.embeddings.tsv" ftype="tabular" compare="sim_size">
107 <assert_contents> 124 <assert_contents>