anndata_manipulate: manipulate.xml annotate

annotate manipulate.xml @ 13:3aa539e5b254 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit c1d84c1850c53deccc384de3960d2cec37bb2869

author	iuc
date	Fri, 08 Nov 2024 21:57:29 +0000
parents	461db9d6cf00
children	9402539a3aea

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='$manipulate.index_unique',
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	37 #else
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	38 index_unique=None,
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	39 #end if
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	40 batch_key='$manipulate.batch_key')
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	41
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	42 #else if $manipulate.function == 'var_names_make_unique'
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	43 adata.var_names_make_unique(join='$manipulate.join')
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	44
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	45 #else if $manipulate.function == 'obs_names_make_unique'
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	46 adata.obs_names_make_unique(join='$manipulate.join')
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	47
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	48 #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	49 #set $categories = [x.strip() for x in str($manipulate.categories).split(',')]
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	50 adata.rename_categories(
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	51 key='$manipulate.key',
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	52 categories=$categories)
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	53
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	54 #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	55 #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	56 #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	57 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	58 #end if
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	59
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	60 #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	61 #set $keys = [x.strip() for x in str($manipulate.var_keys).split(',')]
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	62 adata.var = adata.vars.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	63 #end if
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	64
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	65 #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	66 ## 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	67 #for $flag in $manipulate.gene_flags
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	68 k_cat = adata.var_names.str.startswith('${flag.startswith}')
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	69 if k_cat.sum() > 0:
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	70 adata.var['${flag.col_name}'] = k_cat
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	71 else:
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	72 print(f'No genes starting with {'${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	73 #end for
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	74
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	75 #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	76 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	77
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	78 #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	79 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	80
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	81 #else if $manipulate.function == 'add_annotation'
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	82 import pandas as pd
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	83 extra_annot_t = pd.read_csv('$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	84 #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	85 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	86 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	87 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	88 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	89 #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	90 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	91 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	92 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	93 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	94 #end if
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	95
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	96 #else if $manipulate.function == 'split_on_obs'
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	97 import os
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	98 res_dir = "output_split"
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	99 os.makedirs(res_dir, exist_ok=True)
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	100 for s,field_value in enumerate(adata.obs["${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	101 ad_s = adata[adata.obs.${manipulate.key} == field_value]
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	102 ad_s.write(f"{res_dir}/${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	103
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	104 #else if $manipulate.function == 'filter'
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	105 #if $manipulate.filter.filter == 'key'
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	106 #if $manipulate.var_obs == 'var'
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	107 filtered = adata.var['$manipulate.filter.key']
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	108 #else if $manipulate.var_obs == 'obs'
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	109 filtered = adata.obs['$manipulate.filter.key']
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	110 #end if
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	111
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	112 #if $manipulate.filter.filter_key.type == 'number'
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	113 #if $manipulate.filter.filter_key.filter == 'equal'
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	114 filtered = filtered == $manipulate.filter.filter_key.value
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	115 #else if $manipulate.filter.filter_key.filter == 'equal'
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	116 filtered = filtered != $manipulate.filter.filter_key.value
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	117 #else if $manipulate.filter.filter_key.filter == 'less'
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	118 filtered = filtered < $manipulate.filter.filter_key.value
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	119 #else if $manipulate.filter.filter_key.filter == 'less_or_equal'
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	120 filtered = filtered <= $manipulate.filter.filter_key.value
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	121 #else if $manipulate.filter.filter_key.filter == 'greater'
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	122 filtered = filtered > $manipulate.filter.filter_key.value
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.filter.filter_key.filter == 'greater_or_equal'
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	124 filtered = filtered >= $manipulate.filter.filter_key.value
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	125 #end if
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	126 #else if $manipulate.filter.filter_key.type == 'text'
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	127 #if $manipulate.filter.filter_key.filter == 'equal'
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	128 filtered = filtered == '$manipulate.filter.filter_key.value'
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	129 #else
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	130 filtered = filtered != '$manipulate.filter.filter_key.value'
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	131 #end if
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	132 #else if $manipulate.filter.filter_key.type == 'boolean'
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	133 filtered = filtered == $manipulate.filter.filter_key.value
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	134 #end if
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	135
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	136 #else if $manipulate.filter.filter == 'index'
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	137 #if str($manipulate.filter.index.format) == 'file'
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	138 with open('$manipulate.filter.index.file', 'r') as filter_f:
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	139 filters = [str(x.strip()) for x in filter_f.readlines()]
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	140 filtered = filters
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	141 #else
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	142 #set $filters = [str(x.strip()) for x in $manipulate.filter.index.text.split(',')]
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	143 filtered = $filters
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	144 #end if
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	145 #end if
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	146 print(filtered)
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	147
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	148 #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	149 adata = adata[:,filtered]
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	150 #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	151 adata = adata[filtered, :]
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	152 #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	153
a28cc202e9f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 1 diff changeset	154 #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	155 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	156
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	157 #end if
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	158
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	159 #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	160 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	161 print(adata)
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	162 #end if
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	163
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	164 ]]></configfile>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	165 </configfiles>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	166 <inputs>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	167 <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	168 <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	169 <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	170 <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	171 <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	172 <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	173 <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	174 <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	175 <option value="flag_genes">Flag genes start with a pattern</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	176 <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	177 <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	178 <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	179 <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-->
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	180 <option value="filter">Filter observations or variables</option>
2 a28cc202e9f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 1 diff changeset	181 <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	182 </param>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	183 <when value="concatenate">
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	184 <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	185 <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	186 <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	187 <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	188 </param>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	189 <param name="batch_key" type="text" value="batch" label="Key to add the batch annotation to obs"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	190 <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	191 <option value="-">-</option>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	192 <option value="_">_</option>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	193 <option value=" "> </option>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	194 <option value="/">/</option>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	195 </param>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	196 </when>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	197 <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	198 <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	199 </when>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	200 <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	201 <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	202 </when>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	203 <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	204 <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	205 <param name="categories" type="text" value="" label="Comma-separated list of new categories" help="It should be the same number as the old categories"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	206 </when>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	207 <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	208 <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	209 <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	210 </param>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	211 <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	212 <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	213 </param>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	214 </when>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	215 <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	216 <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	217 <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	218 <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	219 <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	220 <remove value="'" />
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	221 </valid>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	222 </sanitizer>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	223 </param>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	224 <param name="col_name" 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."/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	225 </repeat>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	226 </when>
7 1cd7d1a94481 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 033c2d20a0c73cd84c5c3aee73ae224183a9c1c2" iuc parents: 6 diff changeset	227 <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	228 <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	229 <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	230 <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	231 <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	232 <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	233 </param>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	234 <param name="new_annot" type="data" format="tabular" label="Table with new annotations"
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	235 help="The new table should have the same number of rows and same order than obs or var. The key names should be in the header (1st line)"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	236 </when>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	237 <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	238 <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	239 <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	240 <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	241 <remove value="'" />
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	242 </valid>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	243 </sanitizer>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	244 </param>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	245 </when>
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	246 <when value="filter">
2 a28cc202e9f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 1 diff changeset	247 <param name="var_obs" type="select" label="What to filter?">
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	248 <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	249 <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	250 </param>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	251 <conditional name="filter">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	252 <param name="filter" type="select" label="Type of filtering?">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	253 <option value="key">By key (column) values</option>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	254 <option value="index">By index (row)</option>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	255 </param>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	256 <when value="key">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	257 <param name="key" type="text" value="n_genes" label="Key to filter"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	258 <conditional name="filter_key">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	259 <param name="type" type="select" label="Type of value to filter">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	260 <option value="number">Number</option>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	261 <option value="text">Text</option>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	262 <option value="boolean">Boolean</option>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	263 </param>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	264 <when value="number">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	265 <param name="filter" type="select" label="Filter">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	266 <option value="equal">equal to</option>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	267 <option value="not_equal">not equal to</option>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	268 <option value="less">less than</option>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	269 <option value="less_or_equal">less than or equal to</option>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	270 <option value="greater">greater than</option>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	271 <option value="greater_or_equal">greater than or equal to</option>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	272 </param>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	273 <param name="value" type="float" value="2500" label="Value"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	274 </when>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	275 <when value="text">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	276 <param name="filter" type="select" label="Filter">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	277 <option value="equal">equal to</option>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	278 <option value="not_equal">not equal to</option></param>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	279 <param name="value" type="text" value="2500" label="Value"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	280 </when>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	281 <when value="boolean">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	282 <param name="value" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Value to keep"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	283 </when>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	284 </conditional>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	285 </when>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	286 <when value="index">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	287 <conditional name="index">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	288 <param name="format" type="select" label="Format for the filter by index">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	289 <option value="file">File</option>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	290 <option value="text" selected="true">Text</option>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	291 </param>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	292 <when value="text">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	293 <param name="text" type="text" value="" label="List of index to keep" help="Indexes separated by a comma"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	294 </when>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	295 <when value="file">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	296 <param name="file" type="data" format="txt" label="File with the list of index to keep" help="One index per line"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	297 </when>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	298 </conditional>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	299 </when>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	300 </conditional>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	301 </when>
7 1cd7d1a94481 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 033c2d20a0c73cd84c5c3aee73ae224183a9c1c2" iuc parents: 6 diff changeset	302 <when value="save_raw"></when>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	303 </conditional>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	304 </inputs>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	305 <outputs>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	306 <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${manipulate.function}) on ${on_string}">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	307 <filter>manipulate['function'] != 'split_on_obs'</filter>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	308 </data>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	309 <collection name="output_h5ad_split" type="list" label="${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	310 <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	311 <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	312 </collection>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	313 </outputs>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	314 <tests>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	315 <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	316 <!-- 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	317 <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	318 <conditional name="manipulate">
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	319 <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	320 <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	321 <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	322 <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	323 <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	324 </conditional>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	325 <assert_stdout>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	326 <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	327 <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	328 <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	329 <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	330 <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	331 <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	332 </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	333 <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	334 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	335 <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	336 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	337 </output>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	338 </test>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	339 <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	340 <!-- test 2 -->
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	341 <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	342 <conditional name="manipulate">
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	343 <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	344 <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	345 </conditional>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	346 <assert_stdout>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	347 <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	348 <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	349 </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	350 <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	351 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	352 <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	353 <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	354 <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	355 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	356 </output>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	357 </test>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	358 <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	359 <!-- test 3 -->
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	360 <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	361 <conditional name="manipulate">
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	362 <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	363 <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	364 </conditional>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	365 <assert_stdout>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	366 <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	367 <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	368 </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	369 <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	370 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	371 <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	372 <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	373 <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	374 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	375 </output>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	376 </test>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	377 <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	378 <!-- test 4 -->
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	379 <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	380 <conditional name="manipulate">
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	381 <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	382 <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	383 <param name="categories" value="ery, mk, mo, progenitor"/>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	384 </conditional>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	385 <assert_stdout>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	386 <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	387 <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	388 <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	389 <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	390 </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	391 <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	392 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	393 <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	394 <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	395 <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	396 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	397 </output>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	398 </test>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	399 <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	400 <!-- test 5 -->
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	401 <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	402 <conditional name="manipulate">
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	403 <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	404 </conditional>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	405 <assert_stdout>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	406 <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	407 <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	408 </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	409 <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	410 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	411 <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	412 <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	413 <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	414 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	415 </output>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	416 </test>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	417 <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	418 <!-- test 6 -->
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	419 <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	420 <conditional name="manipulate">
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	421 <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	422 </conditional>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	423 <assert_stdout>
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="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	425 <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	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="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	430 <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	431 <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	432 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	433 </output>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	434 </test>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	435 <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	436 <!-- test 7 -->
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	437 <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	438 <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	439 <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	440 <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	441 <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	442 </conditional>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	443 <assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	444 <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	445 </assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	446 <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	447 <assert_contents>
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="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	449 <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	450 <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	451 <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	452 <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	453 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	454 </output>
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	455 </test>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	456 <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	457 <!-- test 8 -->
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	458 <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	459 <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	460 <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	461 <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	462 <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	463 </conditional>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	464 <assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	465 <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	466 </assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	467 <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	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 <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	470 <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	471 <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	472 <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	473 <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	474 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	475 </output>
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	476 </test>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	477 <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	478 <!-- test 9 -->
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	479 <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	480 <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	481 <param name="function" value="filter"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	482 <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	483 <conditional name="filter">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	484 <param name="filter" value="index"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	485 <conditional name="index">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	486 <param name="format" value="text"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	487 <param name="text" value="Gata2,EKLF"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	488 </conditional>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	489 </conditional>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	490 </conditional>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	491 <assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	492 <has_text_matching expression="500 × 2"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	493 </assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	494 <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	495 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	496 <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	497 <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	498 <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	499 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	500 </output>
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	501 </test>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	502 <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	503 <!-- test 10 -->
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	504 <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	505 <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	506 <param name="function" value="filter"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	507 <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	508 <conditional name="filter">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	509 <param name="filter" value="key"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	510 <param name="key" value="cell_type"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	511 <conditional name="filter_key">
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	512 <param name="type" value="text"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	513 <param name="filter" value="equal"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	514 <param name="value" value="progenitor"/>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	515 </conditional>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	516 </conditional>
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	517 </conditional>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	518 <assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	519 <has_text_matching expression="260 × 11"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	520 </assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	521 <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	522 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	523 <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	524 <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	525 <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	526 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	527 </output>
1 1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	528 </test>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	529 <test expect_num_outputs="1">
2 a28cc202e9f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 1 diff changeset	530 <!-- test 11 -->
a28cc202e9f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 1 diff changeset	531 <param name="input" value="krumsiek11.h5ad"/>
a28cc202e9f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 1 diff changeset	532 <conditional name="manipulate">
a28cc202e9f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 1 diff changeset	533 <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	534 </conditional>
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	535 <assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	536 <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	537 </assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	538 <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	539 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	540 <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	541 <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	542 <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	543 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	544 </output>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	545 </test>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	546 <test expect_num_outputs="1">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	547 <!-- test 12 remove_keys -->
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	548 <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	549 <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	550 <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	551 <param name="obs_keys" 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	552 </conditional>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	553 <assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	554 <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	555 </assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	556 <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	557 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	558 <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	559 <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	560 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	561 </output>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	562 </test>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	563 <test expect_num_outputs="1">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	564 <!-- test 13 flag_genes -->
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	565 <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	566 <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	567 <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	568 <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	569 <param name="startswith" value="Gata"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	570 <param name="col_name" value="Gata_TF"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	571 </repeat>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	572 <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	573 <param name="startswith" value="Gf"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	574 <param name="col_name" value="GF"/>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	575 </repeat>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	576 </conditional>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	577 <assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	578 <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	579 </assert_stdout>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	580 <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	581 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	582 <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	583 <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	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 </output>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	586 </test>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	587 <test expect_num_outputs="1">
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	588 <!-- test 14 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	589 <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	590 <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	591 <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	592 <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	593 </conditional>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	594 <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	595 <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	596 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	597 <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	598 <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	599 <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	600 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	601 </element>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	602 <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	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="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	605 <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	606 <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	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 </element>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	609 <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	610 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	611 <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	612 <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	613 <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	614 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	615 </element>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	616 <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	617 <assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	618 <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	619 <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	620 <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	621 </assert_contents>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	622 </element>
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	623 </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	624 </test>
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	625 </tests>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	626 <help><![CDATA[
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	627 What it does
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	628
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	629 This tool takes a 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	630
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	631 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	632
10 4ebb4b3f1832 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d" iuc parents: 8 diff changeset	633 - 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	634
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	635 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	636
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	637 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	638
10 4ebb4b3f1832 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d" iuc parents: 8 diff changeset	639 - 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	640
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	641 The first occurance of a non-unique value is ignored.
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	642
10 4ebb4b3f1832 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d" iuc parents: 8 diff changeset	643 - 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	644
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	645 The first occurance of a non-unique value is ignored.
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	646
10 4ebb4b3f1832 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d" iuc parents: 8 diff changeset	647 - 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	648
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	649 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	650
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	651 - 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	652
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	653 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	654
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	655 - 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	656
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	657 Useful for flagging the mitochoncdrial or ribosomal protein genes
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	658
10 4ebb4b3f1832 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d" iuc parents: 8 diff changeset	659 - 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	660
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	661 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	662
10 4ebb4b3f1832 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d" iuc parents: 8 diff changeset	663 - 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	664
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	665 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	666
12 461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	667 - 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	668
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	669 - 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	670
461db9d6cf00 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa iuc parents: 11 diff changeset	671 For example, helps in splitting an anndata objects based on cluster annotation. This function generates a collection with 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	672
1a9848100b1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	673 - 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	674
2 a28cc202e9f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 1 diff changeset	675 - 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	676
0 c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	677 @HELP@
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	678 ]]></help>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	679 <expand macro="citations"/>
c2043062cbc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da iuc parents: diff changeset	680 </tool>

Mercurial > repos > iuc > anndata_manipulate

annotate manipulate.xml @ 13:3aa539e5b254 draft