anndata_manipulate: manipulate.xml annotate

annotate manipulate.xml @ 16:e0161aea7682 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata commit 7511ac8af2d638d0ad54f196b5ab3657c7577aa5

author	iuc
date	Wed, 10 Dec 2025 16:59:25 +0000
parents	9402539a3aea
children

rev	line source
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	1 <tool id="anndata_manipulate" name="Manipulate AnnData" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	2 <description>object</description>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	3 <macros>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	4 <import>macros.xml</import>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	5 <xml name="param_join">
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	6 <param name="join" type="select" label="The connecting string between name and integer">
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	7 <option value="-">-</option>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	8 <option value="_">_</option>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	9 <option value=" "> </option>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	10 <option value="/">/</option>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	11 </param>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	12 </xml>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	13 </macros>
13 3aa539e5b254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit c1d84c1850c53deccc384de3960d2cec37bb2869 iuc parents: 12 diff changeset	14 <expand macro="bio_tools"/>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	15 <expand macro="requirements"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	16 <expand macro="version_command"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	17 <command detect_errors="exit_code"><![CDATA[
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	18 @CMD@
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	19 ]]></command>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	20 <configfiles>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	21 <configfile name="script_file"><![CDATA[
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	22 @CMD_imports@
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	23
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	24 adata = ad.read_h5ad('$input')
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	25
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	26 #if $manipulate.function == 'concatenate'
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	27 #for i, filepath in enumerate($manipulate.other_adatas)
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	28 adata_$i = ad.read_h5ad('$filepath')
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	29 #end for
7 1cd7d1a94481 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 033c2d20a0c73cd84c5c3aee73ae224183a9c1c2" iuc parents: 6 diff changeset	30 adata = adata.concatenate(
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	31 #for i, filepath in enumerate($manipulate.other_adatas)
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	32 adata_$i,
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	33 #end for
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	34 join='$manipulate.join',
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	35 #if str($manipulate.index_unique) != ''
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	36 index_unique='$manipulate.index_unique',
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	37 #else
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	38 index_unique=None,
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	39 #end if
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	40 #if str($manipulate.uns_merge) != 'None'
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	41 uns_merge='$manipulate.uns_merge',
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	42 #else
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	43 uns_merge=None,
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	44 #end if
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	45 batch_key='$manipulate.batch_key')
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	46
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	47 #else if $manipulate.function == 'var_names_make_unique'
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	48 adata.var_names_make_unique(join='$manipulate.join')
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	49
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	50 #else if $manipulate.function == 'obs_names_make_unique'
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	51 adata.obs_names_make_unique(join='$manipulate.join')
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	52
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	53 #else if $manipulate.function == 'rename_categories'
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	54 #set $categories = [x.strip() for x in str($manipulate.categories).split(',')]
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	55 #if $manipulate.update_key.new_key == 'no':
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	56 adata.rename_categories(
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	57 key='$manipulate.key',
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	58 categories=$categories)
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	59 #else
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	60 if '$manipulate.key' in adata.obs:
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	61 print("changing key in obs")
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	62 adata.obs['$manipulate.key_name'] = adata.obs['$manipulate.key']
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	63 adata.rename_categories(
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	64 key='$manipulate.key_name',
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	65 categories=$categories)
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	66 elif '$manipulate.key' in adata.var:
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	67 print("changing key in var")
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	68 adata.var['$manipulate.key_name'] = adata.var['$manipulate.key']
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	69 adata.rename_categories(
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	70 key='$manipulate.key_name',
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	71 categories=$categories)
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	72 else:
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	73 print("chanigng key in uns")
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	74 adata.uns['$manipulate.key_name'] = adata.uns['$manipulate.key']
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	75 adata.rename_categories(
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	76 key='$manipulate.key_name',
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	77 categories=$categories)
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	78 #end if
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	79
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	80 #else if $manipulate.function == 'remove_keys'
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	81 #if $manipulate.obs_keys
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	82 #set $keys = [x.strip() for x in str($manipulate.obs_keys).split(',')]
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	83 adata.obs = adata.obs.drop(columns=$keys)
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	84 #end if
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	85
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	86 #if $manipulate.var_keys
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	87 #set $keys = [x.strip() for x in str($manipulate.var_keys).split(',')]
16 e0161aea7682 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata commit 7511ac8af2d638d0ad54f196b5ab3657c7577aa5 iuc parents: 14 diff changeset	88 adata.var = adata.var.drop(columns=$keys)
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	89 #end if
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	90
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	91 #else if $manipulate.function == 'flag_genes'
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	92 ## adapted from anndata operations
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	93 #for $flag in $manipulate.gene_flags
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	94 #if str($flag.col_in) != '':
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	95 k_cat = adata.var['${flag.col_in}'].str.startswith('${flag.startswith}')
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	96 #else:
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	97 k_cat = adata.var_names.str.startswith('${flag.startswith}')
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	98 #end if
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	99 if k_cat.sum() > 0:
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	100 adata.var['${flag.col_out}'] = k_cat
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	101 else:
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	102 print(f'No genes starting with {'${flag.startswith}'} found.')
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	103 #end for
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	104
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	105 #else if $manipulate.function == 'rename_obs':
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	106 adata.obs['${to_obs}'] = adata.obs['${from_obs}']
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	107 #if not $keep_original:
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	108 del adata.obs['${from_obs}']
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	109 #end if
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	110
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	111 #else if $manipulate.function == 'rename_var':
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	112 adata.var['${to_var}'] = adata.var['${from_var}']
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	113 #if not $keep_original:
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	114 del adata.var['${from_var}']
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	115 #end if
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	116
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	117 #else if $manipulate.function == 'strings_to_categoricals'
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	118 adata.strings_to_categoricals()
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	119
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	120 #else if $manipulate.function == 'transpose'
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	121 adata = adata.transpose()
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	122
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	123 #else if $manipulate.function == 'add_annotation'
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	124 import pandas as pd
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	125 extra_annot_t = pd.read_csv('$manipulate.new_annot', sep='\t').reset_index(drop=True)
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	126 #if $manipulate.var_obs == 'var'
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	127 var_index = adata.var_names
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	128 var = pd.concat([adata.var.reset_index(drop=True), extra_annot_t], axis=1)
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	129 var.index = var_index
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	130 adata.var = var
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	131 #else if $manipulate.var_obs == 'obs'
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	132 obs_index = adata.obs.index
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	133 obs = pd.concat([adata.obs.reset_index(drop=True), extra_annot_t], axis=1)
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	134 obs.index = obs_index
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	135 adata.obs = obs
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	136 #end if
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	137
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	138 #else if $manipulate.function == 'split_on_obs'
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	139 import os
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	140 res_dir = "output_split"
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	141 os.makedirs(res_dir, exist_ok=True)
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	142 for s,field_value in enumerate(adata.obs["${manipulate.key}"].unique()):
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	143 ad_s = adata[adata.obs.${manipulate.key} == field_value]
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	144 ad_s.write(f"{res_dir}/${manipulate.key}_{s}.h5ad", compression='gzip')
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	145
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	146 #else if $manipulate.function == 'copy_obs'
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	147 source_adata = ad.read_h5ad('$source_adata')
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	148 #for $key in $manipulate.keys
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	149 if '$key.source_key' in source_adata.obs:
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	150 #if str($key.target_key) == '':
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	151 adata.obs['$key.source_key'] = source_adata.obs['$key.source_key']
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	152 #else
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	153 adata.obs['$key.target_key'] = source_adata.obs['$key.source_key']
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	154 #end if
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	155 else:
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	156 print(f"Obs column {'{$key.source_key}'} not found in source AnnData.")
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	157 #end for
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	158
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	159 #else if $manipulate.function == 'copy_uns'
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	160 source_adata = ad.read_h5ad('$source_adata')
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	161 #for $key in $manipulate.keys
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	162 if '$key.source_key' in source_adata.uns:
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	163 #if str($key.target_key) == '':
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	164 adata.uns['$key.source_key'] = source_adata.uns['$key.source_key']
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	165 #else
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	166 adata.uns['$key.target_key'] = source_adata.uns['$key.source_key']
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	167 #end if
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	168 else:
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	169 print(f"Uns key {'{$key.source_key}'} not found in source AnnData.")
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	170 #end for
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	171
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	172 #else if $manipulate.function == 'copy_embed'
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	173 source_adata = ad.read_h5ad('$source_adata')
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	174 #for $key in $manipulate.keys
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	175 if '$key.source_key' in source_adata.obsm:
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	176 #if $key.target_key is None
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	177 adata.obsm['$key.source_key'] = source_adata.obsm['$key.source_key']
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	178 #else
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	179 adata.obsm['$key.target_key'] = source_adata.obsm['$key.source_key']
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	180 #end if
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	181 else:
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	182 print(f"Embedding key {'{$key.source_key}'} not found in source AnnData.")
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	183 #end for
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	184
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	185 #else if $manipulate.function == 'copy_layers'
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	186 source_adata = ad.read_h5ad('$source_adata')
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	187 #for $key in $manipulate.keys
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	188 if '$key.source_key' in source_adata.layers:
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	189 #if $key.target_key is None
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	190 adata.layers['$key.source_key'] = source_adata.layers['$key.source_key']
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	191 #else
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	192 adata.layers['$key.target_key'] = source_adata.layers['$key.source_key']
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	193 #end if
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	194 else:
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	195 print(f"Layer {'{$key.source_key}'} not found in source AnnData.")
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	196 #end for
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	197
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	198 #else if $manipulate.function == 'copy_X'
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	199 source_adata = ad.read_h5ad('$source_adata')
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	200 #if $target_key is None
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	201 adata.X = source_adata.X
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	202 #else
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	203 adata.layers['$target_key'] = source_adata.X
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	204 #end if
2 a28cc202e9f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 1 diff changeset	205
a28cc202e9f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 1 diff changeset	206 #else if $manipulate.function == 'save_raw'
a28cc202e9f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 1 diff changeset	207 adata.raw = adata
a28cc202e9f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 1 diff changeset	208
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	209 #end if
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	210
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	211 #if $manipulate.function != 'split_on_obs'
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	212 adata.write('anndata.h5ad', compression='gzip')
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	213 print(adata)
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	214 #end if
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	215
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	216 ]]></configfile>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	217 </configfiles>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	218 <inputs>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	219 <param name="input" type="data" format="h5ad" label="Annotated data matrix"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	220 <conditional name="manipulate">
6 ef824f3d03d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85" iuc parents: 2 diff changeset	221 <param name="function" type="select" label="Function to manipulate the object">
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	222 <option value="concatenate">Concatenate along the observations axis</option>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	223 <option value="obs_names_make_unique">Makes the obs index unique by appending '1', '2', etc</option>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	224 <option value="var_names_make_unique">Makes the var index unique by appending '1', '2', etc</option>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	225 <option value="rename_categories">Rename categories of annotation</option>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	226 <option value="remove_keys">Remove keys from obs or var annotations</option>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	227 <option value="flag_genes">Flag genes start with a pattern</option><!--adapted from EBI anndata operations tool -->
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	228 <option value="rename_obs">Rename fileds in AnnData observations</option><!--adapted from EBI anndata operations tool -->
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	229 <option value="rename_var">Rename fileds in AnnData variables</option><!--adapted from EBI anndata operations tool -->
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	230 <option value="strings_to_categoricals">Transform string annotations to categoricals</option>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	231 <option value="transpose">Transpose the data matrix, leaving observations and variables interchanged</option>
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	232 <option value="add_annotation">Add new annotation(s) for observations or variables</option>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	233 <option value="split_on_obs">Split the AnnData object into multiple AnnData objects based on the values of a given obs key</option><!--adapted from EBI anndata operations tool-->
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	234 <option value="copy_obs">Copy observation keys from a different anndata object</option>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	235 <option value="copy_uns">Copy uns keys from a different anndata object</option>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	236 <option value="copy_embed">Copy embeddings from a different anndata object</option>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	237 <option value="copy_layers">Copy layers from a different anndata object</option>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	238 <option value="copy_X">Copy data matrix (.X) from a different anndata object</option>
2 a28cc202e9f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 1 diff changeset	239 <option value="save_raw">Freeze the current state into the 'raw' attribute</option>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	240 </param>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	241 <when value="concatenate">
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	242 <param name="other_adatas" type="data" format="h5ad" multiple="true" label="Annotated data matrix to add"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	243 <param name="join" type="select" label="Join method">
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	244 <option value="inner">Intersection of variables</option>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	245 <option value="outer">Union of variables</option>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	246 </param>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	247 <param name="batch_key" type="text" value="batch" label="Key to add the batch annotation to obs"/>
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	248 <param name="uns_merge" type="select" label="Strategy to use for merging entries of uns" help="These strategies are applied recusivley.">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	249 <option value="None" selected="true">The default. The concatenated object will just have an empty dict for uns</option>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	250 <option value="same">Only entries which have the same value in all AnnData objects are kept</option>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	251 <option value="unique">Only entries which have one unique value in all AnnData objects are kept</option>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	252 <option value="first">The first non-missing value is used</option>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	253 <option value="only">A value is included if only one of the AnnData objects has a value at this path</option>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	254 </param>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	255 <param name="index_unique" type="select" label="Separator to join the existing index names with the batch category" help="Leave it empty to keep existing indices">
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	256 <option value="-">-</option>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	257 <option value="_">_</option>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	258 <option value=" "> </option>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	259 <option value="/">/</option>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	260 </param>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	261 </when>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	262 <when value="obs_names_make_unique">
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	263 <expand macro="param_join"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	264 </when>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	265 <when value="var_names_make_unique">
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	266 <expand macro="param_join"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	267 </when>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	268 <when value="rename_categories">
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	269 <param name="key" type="text" value="" label="Key for observations or variables annotation" help="Annotation key in obs or var"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	270 <param name="categories" type="text" value="" label="Comma-separated list of new categories" help="It should be the same number as the old categories"/>
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	271 <conditional name="update_key">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	272 <param name="new_key" type="select" label="Add categories to a new key?" help="If Yes, a new key will be created with the new categories, otherwise the old key will be updated">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	273 <option value="yes">Yes</option>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	274 <option value="no" selected="true">No</option>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	275 </param>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	276 <when value="yes">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	277 <param name="key_name" type="text" value="" optional="false" label="Key name">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	278 <expand macro="sanitize_query"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	279 </param>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	280 </when>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	281 <when value="no"></when>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	282 </conditional>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	283 </when>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	284 <when value="remove_keys">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	285 <param name="obs_keys" type="text" value="" optional="true" label="Keys/fields to remove from observations (obs)">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	286 <expand macro="sanitize_query"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	287 </param>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	288 <param name="var_keys" type="text" value="" optional="true" label="Keys/fields to remove from variables (var)">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	289 <expand macro="sanitize_query"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	290 </param>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	291 </when>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	292 <when value="flag_genes">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	293 <repeat name="gene_flags" title="Flag genes that start with these names">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	294 <param name="startswith" type="text" label="Text that you expect the genes to be flagged to start with" help="For example, 'MT-' for mito genes">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	295 <sanitizer invalid_char="">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	296 <valid initial="string.ascii_letters,string.digits,string.punctuation">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	297 <remove value="'" />
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	298 </valid>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	299 </sanitizer>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	300 </param>
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	301 <param name="col_in" value='' optional="true" type="text" label="Column in .var to use" help="By default it uses the var_names (normally gene symbols)">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	302 <expand macro="sanitize_query"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	303 </param>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	304 <param name="col_out" type="text" label="Name of the column in var.names where this boolean flag is stored" help="For example, name this column as 'mito' for mitochondrial genes.">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	305 <expand macro="sanitize_query"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	306 </param>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	307 </repeat>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	308 </when>
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	309 <when value="rename_obs">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	310 <param name="from_obs" type="text" label="Name of the observations field that you want to change">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	311 <expand macro="sanitize_query"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	312 </param>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	313 <param name="to_obs" type="text" label="New name of the field in the observations">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	314 <expand macro="sanitize_query"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	315 </param>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	316 <param name="keep_original" type="boolean" checked="false" label="Keep original" help="If activated, it will also keep the original column"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	317 </when>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	318 <when value="rename_var">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	319 <param name="from_var" type="text" label="Name of the variables field that you want to change">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	320 <expand macro="sanitize_query"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	321 </param>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	322 <param name="to_var" type="text" label="New name of the filed in the variables">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	323 <expand macro="sanitize_query"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	324 </param>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	325 <param name="keep_original" type="boolean" checked="false" label="Keep original" help="If activated, it will also keep the original column"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	326 </when>
7 1cd7d1a94481 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 033c2d20a0c73cd84c5c3aee73ae224183a9c1c2" iuc parents: 6 diff changeset	327 <when value="strings_to_categoricals" ></when>
1cd7d1a94481 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 033c2d20a0c73cd84c5c3aee73ae224183a9c1c2" iuc parents: 6 diff changeset	328 <when value="transpose" ></when>
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	329 <when value="add_annotation">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	330 <param name="var_obs" type="select" label="What to annotate?">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	331 <option value="var">Variables (var)</option>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	332 <option value="obs">Observations (obs)</option>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	333 </param>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	334 <param name="new_annot" type="data" format="tabular" label="Table with new annotations"
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	335 help="The new table should have the same number of rows and the same order as obs or var. The key names should be in the header (1st line)"/>
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	336 </when>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	337 <when value="split_on_obs">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	338 <param name="key" type="text" label="The obs key to split on" help="For example, if you want to split on cluster annotation, you can use the key 'louvain'. The output will be a collection of anndata objects">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	339 <sanitizer invalid_char="">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	340 <valid initial="string.ascii_letters,string.digits,string.punctuation">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	341 <remove value="'" />
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	342 </valid>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	343 </sanitizer>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	344 </param>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	345 </when>
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	346 <when value="save_raw"></when>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	347 <when value="copy_obs">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	348 <param name="source_adata" type="data" format="h5ad" label="Source anndata object" help="Ideally the source AnnData object should contain the same set of genes and cells."/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	349 <repeat name="keys" title="Keys from obs to copy" min="1">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	350 <param name="source_key" type="text" optional="true" label="Column to be copied from the source anndata" help="louvain, batch, etc. Provide one key at a time.">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	351 <expand macro="sanitize_query"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	352 </param>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	353 <param name="target_key" type="text" optional="true" label="Target column name" help="Warning! Provide a new key name to avoid rewriting. Leave empty to copy to the same key.">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	354 <expand macro="sanitize_query"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	355 </param>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	356 </repeat>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	357 </when>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	358 <when value="copy_uns">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	359 <param name="source_adata" type="data" format="h5ad" label="Source anndata object" help="Ideally the source AnnData object should contain the same set of genes and cells."/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	360 <repeat name="keys" title="Keys from uns to copy" min="1">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	361 <param name="source_key" type="text" optional="true" label="Uns key to be copied from the source anndata" help="hvg, neighbors, etc. Provide one key at a time.">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	362 <expand macro="sanitize_query"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	363 </param>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	364 <param name="target_key" type="text" optional="true" label="Target key name" help="Warning! Provide a new key name to avoid rewriting. Leave empty to copy to the same key.">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	365 <expand macro="sanitize_query"/>
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	366 </param>
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	367 </repeat>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	368 </when>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	369 <when value="copy_embed">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	370 <param name="source_adata" type="data" format="h5ad" label="Source anndata object" help="Ideally the source AnnData object should contain the same set of genes and cells."/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	371 <repeat name="keys" title="Keys from embeddings to copy" min="1">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	372 <param name="source_key" type="text" label="Key to be copied from the source anndata" help="tSNE, UMAP, etc. Provide one key at a time.">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	373 <expand macro="sanitize_query"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	374 </param>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	375 <param name="target_key" type="text" optional="true" label="Target key name" help="Warning! Provide a new key name to avoid rewriting. Leave empty to copy to the same key.">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	376 <expand macro="sanitize_query"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	377 </param>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	378 </repeat>
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	379 </when>
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	380 <when value="copy_layers">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	381 <param name="source_adata" type="data" format="h5ad" label="Source anndata object" help="Ideally the source AnnData object should contain the same set of genes and cells."/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	382 <repeat name="keys" title="Layers to copy" min="1">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	383 <param name="source_key" type="text" label="Layer to be copied from the source anndata">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	384 <expand macro="sanitize_query"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	385 </param>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	386 <param name="target_key" type="text" optional="true" label="Target layer name" help="Warning! give a new key name to avoid rewriting. Leave empty to copy to the same key.">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	387 <expand macro="sanitize_query"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	388 </param>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	389 </repeat>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	390 </when>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	391 <when value="copy_X">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	392 <param name="source_adata" type="data" format="h5ad" label="Source anndata object" help="Ideally the source AnnData object should contain the same set of genes and cells."/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	393 <param name="target_key" type="text" optional="true" label="Give a target layer name or leave empty to overwrite .X" help="Warning! give a new key name to avoid rewriting. Leave empty to copy to the .X of the current anndata">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	394 <expand macro="sanitize_query"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	395 </param>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	396 </when>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	397 </conditional>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	398 </inputs>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	399 <outputs>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	400 <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${manipulate.function}) on ${on_string}">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	401 <filter>manipulate['function'] != 'split_on_obs'</filter>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	402 </data>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	403 <collection name="output_h5ad_split" type="list" label="${tool.name} (${manipulate.function}) on ${on_string} Collection">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	404 <discover_datasets pattern="(?P<designation>.+)\.h5" directory="output_split" format="h5ad" visible="true"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	405 <filter>manipulate['function'] == 'split_on_obs'</filter>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	406 </collection>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	407 </outputs>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	408 <tests>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	409 <test expect_num_outputs="1">
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	410 <!-- test 1 -->
8 f1b4b1591958 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6497f5415b57bedd849b876883574b3f0050741a" iuc parents: 7 diff changeset	411 <param name="input" value="import.csv.h5ad"/>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	412 <conditional name="manipulate">
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	413 <param name="function" value="concatenate"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	414 <param name="other_adatas" value="import.csv.h5ad"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	415 <param name="join" value="inner"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	416 <param name="batch_key" value="batch"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	417 <param name="index_unique" value="-"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	418 </conditional>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	419 <assert_stdout>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	420 <has_text_matching expression="adata_0"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	421 <has_text_matching expression="adata.concatenate"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	422 <has_text_matching expression="join='inner'"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	423 <has_text_matching expression="index_unique='-'"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	424 <has_text_matching expression="batch_key='batch'"/>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	425 <has_text_matching expression="6 × 2"/>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	426 </assert_stdout>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	427 <output name="anndata" ftype="h5ad">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	428 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	429 <has_h5_keys keys="obs/batch"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	430 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	431 </output>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	432 </test>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	433 <test expect_num_outputs="1">
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	434 <!-- test 2 -->
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	435 <param name="input" value="krumsiek11.h5ad"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	436 <conditional name="manipulate">
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	437 <param name="function" value="obs_names_make_unique"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	438 <param name="join" value="-"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	439 </conditional>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	440 <assert_stdout>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	441 <has_text_matching expression="adata.obs_names_make_unique$join='-'$"/>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	442 <has_text_matching expression="500 × 11"/>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	443 </assert_stdout>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	444 <output name="anndata" ftype="h5ad">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	445 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	446 <has_h5_keys keys="obs/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	447 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	448 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	449 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	450 </output>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	451 </test>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	452 <test expect_num_outputs="1">
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	453 <!-- test 3 -->
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	454 <param name="input" value="krumsiek11.h5ad"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	455 <conditional name="manipulate">
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	456 <param name="function" value="var_names_make_unique"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	457 <param name="join" value="-"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	458 </conditional>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	459 <assert_stdout>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	460 <has_text_matching expression="adata.var_names_make_unique$join='-'$"/>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	461 <has_text_matching expression="500 × 11"/>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	462 </assert_stdout>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	463 <output name="anndata" ftype="h5ad">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	464 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	465 <has_h5_keys keys="obs/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	466 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	467 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	468 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	469 </output>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	470 </test>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	471 <test expect_num_outputs="1">
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	472 <!-- test 4 -->
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	473 <param name="input" value="krumsiek11.h5ad"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	474 <conditional name="manipulate">
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	475 <param name="function" value="rename_categories"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	476 <param name="key" value="cell_type"/>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	477 <param name="categories" value="ery, mk, mo, progenitor"/>
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	478 <conditional name="update_key">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	479 <param name="new_key" value="no"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	480 </conditional>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	481 </conditional>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	482 <assert_stdout>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	483 <has_text_matching expression="adata.rename_categories"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	484 <has_text_matching expression="key='cell_type'"/>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	485 <has_text_matching expression="categories=\['ery', 'mk', 'mo', 'progenitor'\]"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	486 <has_text_matching expression="500 × 11"/>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	487 </assert_stdout>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	488 <output name="anndata" ftype="h5ad">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	489 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	490 <has_h5_keys keys="obs/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	491 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	492 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	493 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	494 </output>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	495 </test>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	496 <test expect_num_outputs="1">
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	497 <!-- test 5 -->
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	498 <param name="input" value="krumsiek11.h5ad"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	499 <conditional name="manipulate">
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	500 <param name="function" value="strings_to_categoricals"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	501 </conditional>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	502 <assert_stdout>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	503 <has_text_matching expression="adata.strings_to_categoricals"/>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	504 <has_text_matching expression="500 × 11"/>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	505 </assert_stdout>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	506 <output name="anndata" ftype="h5ad">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	507 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	508 <has_h5_keys keys="obs/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	509 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	510 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	511 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	512 </output>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	513 </test>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	514 <test expect_num_outputs="1">
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	515 <!-- test 6 -->
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	516 <param name="input" value="krumsiek11.h5ad"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	517 <conditional name="manipulate">
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	518 <param name="function" value="transpose"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	519 </conditional>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	520 <assert_stdout>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	521 <has_text_matching expression="adata.transpose"/>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	522 <has_text_matching expression="11 × 500"/>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	523 </assert_stdout>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	524 <output name="anndata" ftype="h5ad">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	525 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	526 <has_h5_keys keys="var/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	527 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	528 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	529 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	530 </output>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	531 </test>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	532 <test expect_num_outputs="1">
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	533 <!-- test 7 -->
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	534 <param name="input" value="krumsiek11.h5ad"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	535 <conditional name="manipulate">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	536 <param name="function" value="add_annotation"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	537 <param name="var_obs" value="var"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	538 <param name="new_annot" value="var_add_annotation.tabular"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	539 </conditional>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	540 <assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	541 <has_text_matching expression="500 × 11"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	542 </assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	543 <output name="anndata" ftype="h5ad">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	544 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	545 <has_h5_keys keys="obs/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	546 <has_h5_keys keys="var/annot1"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	547 <has_h5_keys keys="var/annot2"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	548 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	549 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	550 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	551 </output>
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	552 </test>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	553 <test expect_num_outputs="1">
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	554 <!-- test 8 -->
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	555 <param name="input" value="krumsiek11.h5ad"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	556 <conditional name="manipulate">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	557 <param name="function" value="add_annotation"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	558 <param name="var_obs" value="obs"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	559 <param name="new_annot" value="obs_add_annotation.tabular"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	560 </conditional>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	561 <assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	562 <has_text_matching expression="500 × 11"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	563 </assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	564 <output name="anndata" ftype="h5ad">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	565 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	566 <has_h5_keys keys="obs/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	567 <has_h5_keys keys="obs/annot1"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	568 <has_h5_keys keys="obs/annot2"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	569 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	570 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	571 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	572 </output>
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	573 </test>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	574 <test expect_num_outputs="1">
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	575 <!-- test 9 -->
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	576 <param name="input" value="krumsiek11.h5ad"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	577 <conditional name="manipulate">
2 a28cc202e9f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 1 diff changeset	578 <param name="function" value="save_raw"/>
a28cc202e9f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 1 diff changeset	579 </conditional>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	580 <assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	581 <has_text_matching expression="500 × 11"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	582 </assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	583 <output name="anndata" ftype="h5ad">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	584 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	585 <has_h5_keys keys="obs/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	586 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	587 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	588 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	589 </output>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	590 </test>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	591 <test expect_num_outputs="1">
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	592 <!-- test 10 remove_keys -->
16 e0161aea7682 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata commit 7511ac8af2d638d0ad54f196b5ab3657c7577aa5 iuc parents: 14 diff changeset	593 <param name="input" value="flagged.h5ad"/>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	594 <conditional name="manipulate">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	595 <param name="function" value="remove_keys"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	596 <param name="obs_keys" value="cell_type"/>
16 e0161aea7682 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata commit 7511ac8af2d638d0ad54f196b5ab3657c7577aa5 iuc parents: 14 diff changeset	597 <param name="var_keys" value="GF"/>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	598 </conditional>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	599 <assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	600 <has_text_matching expression="500 × 11"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	601 </assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	602 <output name="anndata" ftype="h5ad">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	603 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	604 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	605 <has_h5_keys keys="uns/iroot"/>
16 e0161aea7682 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata commit 7511ac8af2d638d0ad54f196b5ab3657c7577aa5 iuc parents: 14 diff changeset	606 <has_h5_keys keys="var/Gata_TF"/>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	607 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	608 </output>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	609 </test>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	610 <test expect_num_outputs="1">
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	611 <!-- test 11 flag_genes -->
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	612 <param name="input" value="krumsiek11.h5ad"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	613 <conditional name="manipulate">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	614 <param name="function" value="flag_genes"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	615 <repeat name="gene_flags">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	616 <param name="startswith" value="Gata"/>
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	617 <param name="col_out" value="Gata_TF"/>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	618 </repeat>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	619 <repeat name="gene_flags">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	620 <param name="startswith" value="Gf"/>
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	621 <param name="col_out" value="GF"/>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	622 </repeat>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	623 </conditional>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	624 <assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	625 <has_text_matching expression="500 × 11"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	626 </assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	627 <output name="anndata" ftype="h5ad">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	628 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	629 <has_h5_keys keys="var/Gata_TF"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	630 <has_h5_keys keys="var/GF"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	631 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	632 </output>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	633 </test>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	634 <test expect_num_outputs="1">
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	635 <!-- test 12 split_on_obs -->
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	636 <param name="input" value="krumsiek11.h5ad"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	637 <conditional name="manipulate">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	638 <param name="function" value="split_on_obs"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	639 <param name="key" value="cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	640 </conditional>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	641 <output_collection name="output_h5ad_split" type="list">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	642 <element name="cell_type_0">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	643 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	644 <has_h5_keys keys="obs/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	645 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	646 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	647 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	648 </element>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	649 <element name="cell_type_1">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	650 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	651 <has_h5_keys keys="obs/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	652 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	653 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	654 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	655 </element>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	656 <element name="cell_type_2">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	657 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	658 <has_h5_keys keys="obs/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	659 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	660 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	661 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	662 </element>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	663 <element name="cell_type_3">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	664 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	665 <has_h5_keys keys="obs/cell_type"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	666 <has_h5_keys keys="uns/highlights"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	667 <has_h5_keys keys="uns/iroot"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	668 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	669 </element>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	670 </output_collection>
2 a28cc202e9f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 1 diff changeset	671 </test>
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	672 <test expect_num_outputs="1">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	673 <!-- test 13 rename categories with new key -->
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	674 <param name="input" value="krumsiek11.h5ad"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	675 <conditional name="manipulate">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	676 <param name="function" value="rename_categories"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	677 <param name="key" value="cell_type"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	678 <param name="categories" value="ery, mk, mo, progenitor"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	679 <conditional name="update_key">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	680 <param name="new_key" value="yes"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	681 <param name="key_name" value="new_cell_type"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	682 </conditional>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	683 </conditional>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	684 <assert_stdout>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	685 <has_text_matching expression="adata.rename_categories"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	686 <has_text_matching expression="key='new_cell_type'"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	687 <has_text_matching expression="categories=\['ery', 'mk', 'mo', 'progenitor'\]"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	688 <has_text_matching expression="changing key in obs"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	689 <has_text_matching expression="500 × 11"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	690 </assert_stdout>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	691 <output name="anndata" ftype="h5ad">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	692 <assert_contents>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	693 <has_h5_keys keys="obs/cell_type"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	694 <has_h5_keys keys="obs/new_cell_type"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	695 <has_h5_keys keys="uns/highlights"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	696 <has_h5_keys keys="uns/iroot"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	697 </assert_contents>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	698 </output>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	699 </test>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	700 <test expect_num_outputs="1">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	701 <!-- test 14 flag_genes with a key -->
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	702 <param name="input" value="flag_new_key.h5ad"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	703 <conditional name="manipulate">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	704 <param name="function" value="flag_genes"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	705 <repeat name="gene_flags">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	706 <param name="startswith" value="ENSG"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	707 <param name="col_in" value="gene_ids"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	708 <param name="col_out" value="ensembl"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	709 </repeat>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	710 </conditional>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	711 <assert_stdout>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	712 <has_text_matching expression="199 × 199"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	713 </assert_stdout>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	714 <output name="anndata" ftype="h5ad">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	715 <assert_contents>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	716 <has_h5_keys keys="var/ensembl"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	717 </assert_contents>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	718 </output>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	719 </test>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	720 <test expect_num_outputs="1">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	721 <!-- test 15 copy_obs -->
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	722 <param name="input" value="krumsiek11.h5ad"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	723 <conditional name="manipulate">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	724 <param name="function" value="copy_obs"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	725 <param name="source_adata" value="krumsiek11.h5ad"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	726 <repeat name="keys">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	727 <param name="source_key" value="cell_type"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	728 <param name="target_key" value="new_cell_type"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	729 </repeat>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	730 </conditional>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	731 <assert_stdout>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	732 <has_text_matching expression="adata.obs\['new_cell_type'\] = source_adata.obs\['cell_type'\]"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	733 <has_text_matching expression="500 × 11"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	734 </assert_stdout>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	735 <output name="anndata" ftype="h5ad">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	736 <assert_contents>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	737 <has_h5_keys keys="obs/cell_type"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	738 <has_h5_keys keys="obs/new_cell_type"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	739 <has_h5_keys keys="uns/highlights"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	740 <has_h5_keys keys="uns/iroot"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	741 </assert_contents>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	742 </output>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	743 </test>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	744 <test expect_num_outputs="1">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	745 <!-- test 16 copy_uns -->
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	746 <param name="input" value="krumsiek11.h5ad"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	747 <conditional name="manipulate">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	748 <param name="function" value="copy_uns"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	749 <param name="source_adata" value="krumsiek11.h5ad"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	750 <repeat name="keys">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	751 <param name="source_key" value="iroot"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	752 <param name="target_key" value="new_iroot"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	753 </repeat>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	754 </conditional>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	755 <assert_stdout>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	756 <has_text_matching expression="adata.uns\['new_iroot'\] = source_adata.uns\['iroot'\]"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	757 <has_text_matching expression="500 × 11"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	758 </assert_stdout>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	759 <output name="anndata" ftype="h5ad">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	760 <assert_contents>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	761 <has_h5_keys keys="obs/cell_type"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	762 <has_h5_keys keys="uns/highlights"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	763 <has_h5_keys keys="uns/iroot"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	764 <has_h5_keys keys="uns/new_iroot"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	765 </assert_contents>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	766 </output>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	767 </test>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	768 <test expect_num_outputs="1">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	769 <!-- test 17 copy_embed -->
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	770 <param name="input" value="tl.umap.h5ad"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	771 <conditional name="manipulate">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	772 <param name="function" value="copy_embed"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	773 <param name="source_adata" value="tl.umap.h5ad"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	774 <repeat name="keys">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	775 <param name="source_key" value="X_pca"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	776 <param name="target_key" value="new_X_pca"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	777 </repeat>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	778 </conditional>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	779 <assert_stdout>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	780 <has_text_matching expression="adata.obsm\['new_X_pca'\] = source_adata.obsm\['X_pca'\]"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	781 <has_text_matching expression="100 × 800"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	782 </assert_stdout>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	783 <output name="anndata" ftype="h5ad">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	784 <assert_contents>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	785 <has_h5_keys keys="obs/paul15_clusters"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	786 <has_h5_keys keys="uns/neighbors"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	787 <has_h5_keys keys="uns/iroot"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	788 <has_h5_keys keys="obsm/X_pca"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	789 <has_h5_keys keys="obsm/new_X_pca"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	790 <has_h5_keys keys="obsm/X_umap"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	791 <has_h5_keys keys="layers/count"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	792 <has_h5_keys keys="obsp/connectivities"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	793 <has_h5_keys keys="obsp/distances"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	794 </assert_contents>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	795 </output>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	796 </test>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	797 <test expect_num_outputs="1">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	798 <!-- test 18 copy_layers -->
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	799 <param name="input" value="tl.umap.h5ad"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	800 <conditional name="manipulate">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	801 <param name="function" value="copy_layers"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	802 <param name="source_adata" value="tl.umap.h5ad"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	803 <repeat name="keys">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	804 <param name="source_key" value="count"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	805 <param name="target_key" value="new_count"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	806 </repeat>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	807 </conditional>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	808 <assert_stdout>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	809 <has_text_matching expression="adata.layers\['new_count'\] = source_adata.layers\['count'\]"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	810 <has_text_matching expression="100 × 800"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	811 </assert_stdout>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	812 <output name="anndata" ftype="h5ad">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	813 <assert_contents>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	814 <has_h5_keys keys="obs/paul15_clusters"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	815 <has_h5_keys keys="uns/neighbors"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	816 <has_h5_keys keys="uns/iroot"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	817 <has_h5_keys keys="obsm/X_pca"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	818 <has_h5_keys keys="obsm/X_umap"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	819 <has_h5_keys keys="layers/count"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	820 <has_h5_keys keys="layers/new_count"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	821 <has_h5_keys keys="obsp/connectivities"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	822 <has_h5_keys keys="obsp/distances"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	823 </assert_contents>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	824 </output>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	825 </test>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	826 <test expect_num_outputs="1">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	827 <!-- test 19 copy_X -->
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	828 <param name="input" value="tl.umap.h5ad"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	829 <conditional name="manipulate">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	830 <param name="function" value="copy_X"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	831 <param name="source_adata" value="tl.umap.h5ad"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	832 <param name="target_key" value="new_X"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	833 </conditional>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	834 <assert_stdout>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	835 <has_text_matching expression="adata.layers\['new_X'\] = source_adata.X"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	836 <has_text_matching expression="100 × 800"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	837 </assert_stdout>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	838 <output name="anndata" ftype="h5ad">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	839 <assert_contents>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	840 <has_h5_keys keys="obs/paul15_clusters"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	841 <has_h5_keys keys="uns/neighbors"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	842 <has_h5_keys keys="uns/iroot"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	843 <has_h5_keys keys="obsm/X_pca"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	844 <has_h5_keys keys="obsm/X_umap"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	845 <has_h5_keys keys="layers/count"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	846 <has_h5_keys keys="layers/new_X"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	847 <has_h5_keys keys="obsp/connectivities"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	848 <has_h5_keys keys="obsp/distances"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	849 </assert_contents>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	850 </output>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	851 </test>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	852 <test expect_num_outputs="1">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	853 <!-- test 20 save_raw -->
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	854 <param name="input" value="tl.umap.h5ad"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	855 <conditional name="manipulate">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	856 <param name="function" value="save_raw"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	857 </conditional>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	858 <assert_stdout>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	859 <has_text_matching expression="adata.raw = adata"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	860 <has_text_matching expression="100 × 800"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	861 </assert_stdout>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	862 <output name="anndata" ftype="h5ad">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	863 <assert_contents>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	864 <has_h5_keys keys="obs/paul15_clusters"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	865 <has_h5_keys keys="uns/neighbors"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	866 <has_h5_keys keys="uns/iroot"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	867 <has_h5_keys keys="obsm/X_pca"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	868 <has_h5_keys keys="obsm/X_umap"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	869 <has_h5_keys keys="layers/count"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	870 <has_h5_keys keys="obsp/connectivities"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	871 <has_h5_keys keys="obsp/distances"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	872 </assert_contents>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	873 </output>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	874 </test>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	875 <test expect_num_outputs="1">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	876 <!-- test 21 rename_obs -->
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	877 <param name="input" value="krumsiek11.h5ad"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	878 <conditional name="manipulate">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	879 <param name="function" value="rename_obs"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	880 <param name="from_obs" value="cell_type"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	881 <param name="to_obs" value="new_cell_type"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	882 <param name="keep_original" value="false"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	883 </conditional>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	884 <assert_stdout>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	885 <has_text_matching expression="adata.obs\['new_cell_type'\] = adata.obs\['cell_type'\]"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	886 <has_text_matching expression="del adata.obs\['cell_type'\]"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	887 <has_text_matching expression="500 × 11"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	888 </assert_stdout>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	889 <output name="anndata" ftype="h5ad">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	890 <assert_contents>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	891 <has_h5_keys keys="obs/new_cell_type"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	892 <has_h5_keys keys="uns/highlights"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	893 <has_h5_keys keys="uns/iroot"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	894 </assert_contents>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	895 </output>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	896 </test>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	897 <test expect_num_outputs="1">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	898 <!-- test 22 rename_var -->
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	899 <param name="input" value="flag_new_key.h5ad"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	900 <conditional name="manipulate">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	901 <param name="function" value="rename_var"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	902 <param name="from_var" value="gene_ids"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	903 <param name="to_var" value="new_id"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	904 <param name="keep_original" value="false"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	905 </conditional>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	906 <assert_stdout>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	907 <has_text_matching expression="adata.var\['new_id'\] = adata.var\['gene_ids'\]"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	908 <has_text_matching expression="del adata.var\['gene_ids'\]"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	909 <has_text_matching expression="199 × 199"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	910 </assert_stdout>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	911 <output name="anndata" ftype="h5ad">
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	912 <assert_contents>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	913 <has_h5_keys keys="var/feature_types"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	914 <has_h5_keys keys="var/test"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	915 <has_h5_keys keys="var/new_id"/>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	916 </assert_contents>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	917 </output>
9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	918 </test>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	919 </tests>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	920 <help><![CDATA[
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	921 What it does
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	922
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	923 This tool takes an AnnData dataset, manipulates it and returns it.
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	924
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	925 The possible manipulations are:
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	926
10 4ebb4b3f1832 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d" iuc parents: 8 diff changeset	927 - Concatenate along the observations axis (`concatenate method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.concatenate.html>`__)
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	928
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	929 The `uns`, `varm` and `obsm` attributes are ignored.
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	930
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	931 If you use `join='outer'` this fills 0s for sparse data when variables are absent in a batch. Use this with care. Dense data is filled with `NaN`
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	932
10 4ebb4b3f1832 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d" iuc parents: 8 diff changeset	933 - Makes the obs index unique by appending '1', '2', etc (`obs_names_make_unique method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.obs_names_make_unique.html>`__)
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	934
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	935 The first occurrence of a non-unique value is ignored.
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	936
10 4ebb4b3f1832 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d" iuc parents: 8 diff changeset	937 - Makes the var index unique by appending '1', '2', etc (`var_names_make_unique method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.var_names_make_unique.html>`__)
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	938
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	939 The first occurrence of a non-unique value is ignored.
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	940
10 4ebb4b3f1832 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d" iuc parents: 8 diff changeset	941 - Rename categories of annotation `key` in `obs`, `var` and `uns` (`rename_categories method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.rename_categories.html>`__)
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	942
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	943 Besides calling `self.obs[key].cat.categories = categories` - similar for `var` - this also renames categories in unstructured annotation that uses the categorical annotation `key`
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	944
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	945 - Remove keys from obs or var annotations
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	946
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	947 Helps in cleaning up andata with many annotations. For example, helps in removing qc metrics calculated during the preprocesing or already existing cluster annotations.
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	948
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	949 - Flag genes start with a pattern
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	950
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	951 Useful for flagging the mitochondrial or ribosomal protein genes
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	952
10 4ebb4b3f1832 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d" iuc parents: 8 diff changeset	953 - Transform string annotations to categoricals (`strings_to_categoricals method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.strings_to_categoricals.html>`__)
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	954
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	955 Only affects string annotations that lead to less categories than the total number of observations.
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	956
10 4ebb4b3f1832 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d" iuc parents: 8 diff changeset	957 - Transpose the data matrix, leaving observations and variables interchanged (`transpose method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.transpose.html>`__)
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	958
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	959 Data matrix is transposed, observations and variables are interchanged.
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	960
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	961 - Add annotation for variables or
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	962
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	963 - Split the AnnData object into multiple AnnData objects based on the values of a given obs key
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	964
14 9402539a3aea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 4f6d044223f374ba44a4d46ad77559ca781e6db7 iuc parents: 13 diff changeset	965 For example, helps in splitting an anndata objects based on cluster annotation. This function generates a collection with a number of elements equal to the number of categories in the input obs key.
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	966
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	967 - Filter data variables or observations, by index or key
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	968
2 a28cc202e9f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 1 diff changeset	969 - Freeze the current state into the 'raw' attribute
a28cc202e9f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 1 diff changeset	970
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	971 @HELP@
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	972 ]]></help>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	973 <expand macro="citations"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	974 </tool>

Mercurial > repos > iuc > anndata_manipulate

annotate manipulate.xml @ 16:e0161aea7682 draft default tip