Mercurial > repos > ebi-gxa > scanpy_run_umap

comparison scanpy-run-umap.xml @ 15:135e8cacb57e 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 e572b5425460d57f1bd13ab6374674c1c6801ab3-dirty"
author ebi-gxa
date Thu, 17 Sep 2020 16:30:12 +0000
parents f53bb2c1fa07
children 3a7b97ddf3ff
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14:62c31dc2e5d5 15:135e8cacb57e
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_run_umap" name="Scanpy RunUMAP" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> 2 <tool id="scanpy_run_umap" name="Scanpy RunUMAP" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
3 <description>visualise cell clusters using UMAP</description> 3 <description>visualise cell clusters using UMAP</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 ln -s '${input_obj_file}' input.h5 && 9 ln -s '${input_obj_file}' input.h5 &&
10 PYTHONIOENCODING=utf-8 scanpy-run-umap 10 PYTHONIOENCODING=utf-8 scanpy-run-umap
11 --neighbors-key '${use_graph}' 11 #set neighbors_key = $use_graph.replace('INPUT_OBJ', $input_obj_file.__getattr__('name'))
12 #set embeddings_tsv='embeddings.tsv'
13 --neighbors-key '${neighbors_key}'
14 #if $key_added
15 #if $neighbors_key
16 #set key_added = $key_added.replace('NEIGHBORS_KEY', $neighbors_key.__str__)
17 #set embeddings_tsv="embeddings_" + $key_added.__str__ + ".tsv"
18 #end if
12 --key-added '${key_added}' 19 --key-added '${key_added}'
20 #end if
13 #if $embeddings 21 #if $embeddings
14 --export-embedding embeddings.tsv 22 --export-embedding embeddings.tsv
15 #end if 23 #end if
16 #if $settings.default == "false" 24 #if $settings.default == "false"
17 --n-components ${settings.n_components} 25 --n-components ${settings.n_components}
28 --maxiter ${settings.maxiter} 36 --maxiter ${settings.maxiter}
29 #end if 37 #end if
30 #end if 38 #end if
31 @INPUT_OPTS@ 39 @INPUT_OPTS@
32 @OUTPUT_OPTS@ 40 @OUTPUT_OPTS@
41 #if $embeddings
42 #if $embeddings_tsv != 'embeddings.tsv'
43 && mv '${embeddings_tsv}' embeddings.tsv
44 #end if
45 #end if
33 46
34 ]]></command> 47 ]]></command>
35 48
36 <inputs> 49 <inputs>
37 <expand macro="input_object_params"/> 50 <expand macro="input_object_params"/>