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comparison scanpy-run-diffmap.xml @ 12:26e1a99e3c0f 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 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
author ebi-gxa
date Mon, 07 Sep 2020 14:02:22 +0000
parents 713e94af9d6c
children e2ca1846080f
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11:f10df597ed6d 12:26e1a99e3c0f
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_run_diffmap" name="Scanpy DiffusionMap" version="@TOOL_VERSION@+galaxy11" profile="@PROFILE@"> 2 <tool id="scanpy_run_diffmap" name="Scanpy DiffusionMap" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
3 <description>calculate diffusion components</description> 3 <description>calculate diffusion components</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-cli embed diffmap 10 PYTHONIOENCODING=utf-8 scanpy-cli embed diffmap
11 --n-comps ${n_comps} 11 --n-comps ${n_comps}
12 #if $use_graph 12 #if $use_graph
13 --use-graph '${use_graph}' 13 --neighbors-key '${use_graph}'
14 #end if 14 #end if
15 #if $key_added 15 #if $key_added
16 --key-added '${key_added}' 16 --key-added '${key_added}'
17 #end if 17 #end if
18 $export_embed 18 $export_embed
27 <param name="n_comps" argument="--n-comps" type="integer" min="2" value="10" 27 <param name="n_comps" argument="--n-comps" type="integer" min="2" value="10"
28 label="Number of diffusion components to calculate"/> 28 label="Number of diffusion components to calculate"/>
29 <param name="export_embed" argument="--export-embedding" type="boolean" checked="false" 29 <param name="export_embed" argument="--export-embedding" type="boolean" checked="false"
30 truevalue="--export-embedding embed.tsv" falsevalue="" 30 truevalue="--export-embedding embed.tsv" falsevalue=""
31 label="Export embeddings as a tab-separated text table"/> 31 label="Export embeddings as a tab-separated text table"/>
32 <param name="use_graph" argument="--use-graph" value="neighbors" type="text" 32 <param name="use_graph" argument="--neighbors-key" value="neighbors" type="text"
33 label="Name of the slot that holds the KNN graph"/> 33 label="Name of the slot that holds the KNN graph"/>
34 <param name="key_added" argument="--key-added" type="text" optional="true" 34 <param name="key_added" argument="--key-added" type="text" optional="true"
35 label="Additional suffix to the name of the slot to save the calculated diffusion map"/> 35 label="Additional suffix to the name of the slot to save the calculated diffusion map"/>
36 </inputs> 36 </inputs>
37 37
42 </data> 42 </data>
43 </outputs> 43 </outputs>
44 44
45 <tests> 45 <tests>
46 <test> 46 <test>
47 <param name="input_obj_file" value="diffmap.h5"/> 47 <param name="input_obj_file" value="find_cluster.h5"/>
48 <param name="input_format" value="anndata"/> 48 <param name="input_format" value="anndata"/>
49 <param name="output_format" value="anndata"/> 49 <param name="output_format" value="anndata"/>
50 <param name="n_dcs" value="10"/> 50 <param name="n_dcs" value="10"/>
51 <param name="root_attr" value="leiden"/> 51 <param name="root_attr" value="louvain"/>
52 <param name="root_value" value="1"/> 52 <param name="root_value" value="1"/>
53 <param name="use_graph" value="neighbors"/> 53 <param name="use_graph" value="neighbors"/>
54 <output name="output_h5" file="paga.h5" ftype="h5" compare="sim_size"/> 54 <output name="output_h5" file="diffmap.h5" ftype="h5" compare="sim_size"/>
55 </test> 55 </test>
56 </tests> 56 </tests>
57 57
58 <help><![CDATA[ 58 <help><![CDATA[
59 ==================================================== 59 ====================================================