Mercurial > repos > ebi-gxa > anndata_ops

comparison anndata_operations.xml @ 2:ba18139e7400 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 400799f99ee36ad12b990b1ccabf4be16a26c003
author ebi-gxa
date Mon, 25 Nov 2019 14:37:55 -0500
parents 086d850271a2
children d586ebb8ff43
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1:339d205356c6 2:ba18139e7400
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="anndata_ops" name="AnnData Operations" version="0.0.1+galaxy0"> 2 <tool id="anndata_ops" name="AnnData Operations" version="0.0.1+galaxy1">
3 <description>modifies metadata and flags genes</description> 3 <description>modifies metadata and flags genes</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"/>
51 adata.write('output.h5', compression='gzip') 51 adata.write('output.h5', compression='gzip')
52 </configfile> 52 </configfile>
53 </configfiles> 53 </configfiles>
54 54
55 <inputs> 55 <inputs>
56 <param name="input_obj_file" argument="input-object-file" type="data" format="h5" label="Input object in hdf5 AnnData format"/> 56 <param name="input_obj_file" argument="input-object-file" type="data" format="h5,h5ad" label="Input object in hdf5 AnnData format"/>
57 <expand macro="output_object_params_no_loom"/>
57 <repeat name="modifications" title="Change field names in AnnData observations" min="0"> 58 <repeat name="modifications" title="Change field names in AnnData observations" min="0">
58 <param name="from_obs" type="text" label="Original name" help="Name in observations that you want to change"> 59 <param name="from_obs" type="text" label="Original name" help="Name in observations that you want to change">
59 <sanitizer> 60 <sanitizer>
60 <valid initial="string.printable"/> 61 <valid initial="string.printable"/>
61 </sanitizer> 62 </sanitizer>
69 </repeat> 70 </repeat>
70 <param name="top_genes" label="Number of top genes" value='50' help="to calculate percentage of the flagged genes in that number of top genes. Used by sc.pp.calculate_qc_metrics (integer)." type="integer"/> 71 <param name="top_genes" label="Number of top genes" value='50' help="to calculate percentage of the flagged genes in that number of top genes. Used by sc.pp.calculate_qc_metrics (integer)." type="integer"/>
71 </inputs> 72 </inputs>
72 73
73 <outputs> 74 <outputs>
74 <data name="output" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: anndata with metadata changes."/> 75 <expand macro="output_data_obj_no_loom" description="metadata changes on"/>
75 </outputs> 76 </outputs>
76 77
77 <tests> 78 <tests>
78 <test> 79 <test>
79 <param name="input_obj_file" value="find_cluster.h5"/> 80 <param name="input_obj_file" value="find_cluster.h5"/>
80 <param name="input_format" value="anndata"/> 81 <param name="input_format" value="anndata"/>
81 <param name="color_by" value="louvain"/> 82 <param name="color_by" value="louvain"/>
82 <output name="output" file="output.h5" ftype="h5" compare="sim_size"/> 83 <output name="output_h5ad" file="output.h5" ftype="h5" compare="sim_size"/>
83 </test> 84 </test>
84 </tests> 85 </tests>
85 86
86 <help><![CDATA[ 87 <help><![CDATA[
87 ============================= 88 =============================