Mercurial > repos > ebi-gxa > anndata_ops

comparison anndata_operations.xml @ 11:f0a29f4b9be9 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 e2ec0706fd62528e5198e3c050d91ab0ee6cd4da"
author ebi-gxa
date Fri, 12 Jun 2020 09:19:22 -0400
parents 54f1212d26ac
children f1a1cf7c0153
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10:54f1212d26ac 11:f0a29f4b9be9
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="0.0.3+galaxy0" profile="@PROFILE@"> 2 <tool id="anndata_ops" name="AnnData Operations" version="0.0.3+galaxy1" profile="@PROFILE@">
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"/>
33 import anndata 33 import anndata
34 from numpy import all 34 from numpy import all
35 import logging 35 import logging
36 36
37 adata = sc.read('input.h5') 37 adata = sc.read('input.h5')
38
39 #if $copy_adata_to_raw:
40 adata.raw = adata
41 #end if
38 42
39 gene_name = '${gene_symbols_field}' 43 gene_name = '${gene_symbols_field}'
40 qc_vars = list() 44 qc_vars = list()
41 45
42 #for $i, $s in enumerate($modifications) 46 #for $i, $s in enumerate($modifications)
126 </configfiles> 130 </configfiles>
127 131
128 <inputs> 132 <inputs>
129 <param name="input_obj_file" argument="input-object-file" type="data" format="h5,h5ad" label="Input object in hdf5 AnnData format"/> 133 <param name="input_obj_file" argument="input-object-file" type="data" format="h5,h5ad" label="Input object in hdf5 AnnData format"/>
130 <expand macro="output_object_params_no_loom"/> 134 <expand macro="output_object_params_no_loom"/>
135 <param name="copy_adata_to_raw" type="boolean" label="Copy AnnData to .raw" help="If activated, it will do 'adata.raw = adata'" checked="false"/>
131 <repeat name="modifications" title="Change field names in AnnData observations" min="0"> 136 <repeat name="modifications" title="Change field names in AnnData observations" min="0">
132 <param name="from_obs" type="text" label="Original name" help="Name in observations that you want to change"> 137 <param name="from_obs" type="text" label="Original name" help="Name in observations that you want to change">
133 <sanitizer> 138 <sanitizer>
134 <valid initial="string.printable"/> 139 <valid initial="string.printable"/>
135 </sanitizer> 140 </sanitizer>