spapros: selection.xml annotate

annotate selection.xml @ 0:c369fea6eab5 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0

author	iuc
date	Sun, 25 Aug 2024 13:35:59 +0000
parents
children

rev	line source
0 c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	1 <tool id="spapros" name="Selection" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	2 <description>of marker genes with spapros</description>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	3 <macros>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	4 <import>macros.xml</import>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	5 </macros>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	6 <expand macro="requirements">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	7 </expand>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	8 <expand macro="version_command"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	9 <command detect_errors="exit_code"><![CDATA[
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	10 @CMD@
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	11 ]]></command>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	12 <configfiles>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	13 <configfile name="script_file"><![CDATA[
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	14 @CMD_imports@
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	15 @CMD_read_inputs@
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	16
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	17 random.seed($seed)
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	18
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	19 mpl.rcParams['figure.dpi'] = $general_figure_options.dpi
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	20 plt.rcParams["font.size"] = $general_figure_options.fontsize
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	21
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	22 header_markerset='infer'
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	23 #if $cond_markerset.select_markerset == 'True' and $cond_markerset.header_markerset == 'not_included':
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	24 header_markerset=None
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	25 #end if
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	26
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	27 selector = sp.se.ProbesetSelector(
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	28 adata,
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	29 celltype_key='$celltype_key',
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	30 #if $genes_key != '':
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	31 genes_key='$genes_key',
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	32 #else:
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	33 genes_key=None,
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	34 #end if
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	35 #if $cond_n.select_n == 'True':
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	36 n=$cond_n.n,
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	37 #else:
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	38 n=None,
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	39 #end if
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	40 #if $preselected_genes != ''
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	41 preselected_genes = '$preselected_genes'.split(','),
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	42 #end if
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	43 #if $prior_genes != ''
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	44 prior_genes = '$prior_genes'.split(','),
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	45 #end if
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	46 #if $cond_n_pca_genes.select_n_pca_genes == 'True':
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	47 n_pca_genes=$cond_n_pca_genes.n_pca_genes,
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	48 #end if
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	49 #if $min_mean_difference != 0.0:
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	50 min_mean_difference=$min_mean_difference,
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	51 #end if
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	52 n_min_markers=$n_min_markers,
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	53 #if $celltypes != 'all':
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	54 celltypes='$celltypes'.split(','),
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	55 #else
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	56 celltypes='$celltypes',
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	57 #end if
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	58 #if $cond_markerset.select_markerset == 'True':
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	59 marker_list = {key: [v for v in list(value.values()) if pd.notna(v)] for key, value in pd.read_csv('$cond_markerset.markerset', sep='\t', index_col=0, header=header_markerset).to_dict(orient='index').items()},
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	60 #end if
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	61 n_list_markers=$n_list_markers,
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	62 marker_corr_th=$marker_corr_th,
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	63 #if $pca_penalties != ''
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	64 pca_penalties = '$pca_penalties'.split(','),
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	65 #end if
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	66 #if $DE_penalties != ''
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	67 DE_penalties = '$DE_penalties'.split(','),
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	68 #end if
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	69 #if $m_penalties_adata_celltypes != ''
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	70 m_penalties_adata_celltypes = '$m_penalties_adata_celltypes'.split(','),
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	71 #end if
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	72 #if $m_penalties_list_celltypes != ''
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	73 m_penalties_list_celltypes = '$m_penalties_list_celltypes'.split(','),
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	74 #end if
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	75 #if $advanced_options.cond_DE_selection_hparams.select_DE_selection_hparams == 'True':
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	76 DE_selection_hparams={"n": $advanced_options.cond_DE_selection_hparams.n_DE_selection_hparams, "per_group": $advanced_options.cond_DE_selection_hparams.per_group}
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	77 #end if
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	78 #if $advanced_options.cond_forest_hparams.select_forest_hparams == 'True':
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	79 forest_hparams={"n_trees": $advanced_options.cond_forest_hparams.n_trees, "subsample": $advanced_options.cond_forest_hparams.subsample, "test_subsample": $advanced_options.cond_forest_hparams.test_subsample},
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	80 #end if
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	81 #if $advanced_options.cond_forest_DE_baseline_hparams.select_forest_DE_baseline_hparams == 'True':
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	82 forest_DE_baseline_hparams={
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	83 "n_DE": $advanced_options.cond_forest_DE_baseline_hparams.n_DE,
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	84 "min_score": $advanced_options.cond_forest_DE_baseline_hparams.min_score,
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	85 "n_stds": $advanced_options.cond_forest_DE_baseline_hparams.n_stds,
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	86 "max_step": $advanced_options.cond_forest_DE_baseline_hparams.max_step,
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	87 "min_outlier_dif": $advanced_options.cond_forest_DE_baseline_hparams.min_outlier_dif,
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	88 "n_terminal_repeats": $advanced_options.cond_forest_DE_baseline_hparams.n_terminal_repeats,
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	89 },
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	90 #end if
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	91 #if $advanced_options.cond_add_forest_genes_hparams.select_add_forest_genes_hparams == 'True':
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	92 add_forest_genes_hparams={"n_max_per_it": $advanced_options.cond_add_forest_genes_hparams.n_max_per_it, "performance_th": $advanced_options.cond_add_forest_genes_hparams.performance_th, "importance_th": $advanced_options.cond_add_forest_genes_hparams.importance_th},
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	93 #end if
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	94 #if $advanced_options.cond_marker_selection_hparams.select_marker_selection_hparams == 'True':
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	95 marker_selection_hparams={"penalty_threshold": $advanced_options.cond_marker_selection_hparams.penalty_threshold},
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	96 #end if
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	97 verbosity=0,
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	98 seed=$seed,
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	99 n_jobs=int(os.environ.get('GALAXY_SLOTS', '4'))
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	100 )
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	101
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	102 selector.select_probeset()
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	103
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	104 sp.pl.masked_dotplot(
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	105 adata,
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	106 selector,
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	107 ct_key='$figure_options_masked_dotplot.ct_key',
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	108 imp_threshold=$figure_options_masked_dotplot.imp_threshold,
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	109 #if $figure_options_masked_dotplot.celltypes != '':
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	110 celltypes='$figure_options_masked_dotplot.celltypes',
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	111 #end if
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	112 #if $figure_options_masked_dotplot.n_genes != 0:
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	113 n_genes=$figure_options_masked_dotplot.n_genes,
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	114 #end if
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	115 #if $figure_options_masked_dotplot.comb_markers_only:
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	116 comb_markers_only=True,
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	117 #end if
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	118 #if $figure_options_masked_dotplot.markers_only:
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	119 markers_only=True,
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	120 #end if
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	121 cmap='$figure_options_masked_dotplot.cmap',
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	122 comb_marker_color='$figure_options_masked_dotplot.comb_marker_color',
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	123 marker_color='$figure_options_masked_dotplot.marker_color',
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	124 non_adata_celltypes_color='$figure_options_masked_dotplot.non_adata_celltypes_color',
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	125 use_raw=$figure_options_masked_dotplot.use_raw,
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	126 save='masked_dotplot.$format',
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	127 )
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	128
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	129 selector.plot_gene_overlap(
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	130 style='$figure_options_plot_gene_overlap.style',
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	131 save='gene_overlap.$format',
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	132 show=False
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	133 )
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	134
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	135 probe_genes = selector.probeset.index[selector.probeset.selection]
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	136 celltypes_DE_1vsall = list(selector.probeset[selector.probeset.selection]['celltypes_DE_1vsall'])
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	137 celltypes_DE_specific = list(selector.probeset[selector.probeset.selection]['celltypes_DE_specific'])
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	138 celltypes_DE = list(selector.probeset[selector.probeset.selection]['celltypes_DE'])
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	139 celltypes_marker = list(selector.probeset[selector.probeset.selection]['celltypes_marker'])
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	140
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	141 marker_dict = dict()
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	142
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	143 for i,g in enumerate(probe_genes):
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	144 recognized_celltypes = list(set(celltypes_DE_1vsall[i].split(',') + celltypes_DE_specific[i].split(',') + \
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	145 celltypes_DE[i].split(',') + celltypes_marker[i].split(',')))
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	146
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	147 if (len(recognized_celltypes) > 1 and '' in recognized_celltypes):
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	148 recognized_celltypes.remove('')
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	149
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	150 for c in recognized_celltypes:
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	151 if c == '':
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	152 c = 'Unkown'
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	153 if c not in marker_dict:
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	154 marker_dict[c] = [g]
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	155 else:
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	156 marker_dict[c] = marker_dict[c] + [g]
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	157
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	158 # Find the maximum length of lists
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	159 max_len = max(len(lst) for lst in marker_dict.values())
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	160 sorted_marker_dict_by_keys = {key: marker_dict[key] for key in sorted(marker_dict.keys())}
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	161 # Fill smaller lists with empty values
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	162 for key, value in sorted_marker_dict_by_keys.items():
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	163 sorted_marker_dict_by_keys[key] = value + [''] * (max_len - len(value))
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	164 df = pd.DataFrame(sorted_marker_dict_by_keys).T
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	165 df.to_csv('marker.tsv', sep='\t', index=True)
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	166
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	167 ]]></configfile>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	168 </configfiles>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	169 <inputs>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	170 <expand macro="inputs_anndata"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	171 <expand macro="param_plot_format"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	172 <param name="celltype_key" type="text" value="celltype" optional="false" label="Key in adata.obs with celltype annotations"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	173 <param name="genes_key" type="text" optional="true" label="Key in adata.var for preselected genes" help="This is typically highly_variable_genes. Leave empty to not subset genes."/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	174 <conditional name="cond_n">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	175 <param name="select_n" type="select" label="Do you want to set the number of finally selected genes?" help="Note that when `No` we automatically infer n as the minimal number of recommended genes.">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	176 <option value="False">No</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	177 <option value="True">Yes</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	178 </param>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	179 <when value="True">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	180 <param argument="n" type="integer" value="20" min="1" optional="false" label="Number of finally selected genes" help="Setting n might change the gene ranking since the final added list_markers are added based on the theoretically added genes without list_markers."/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	181 </when>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	182 <when value="False"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	183 </conditional>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	184 <param name="preselected_genes" type="text" optional="true" label="Pre selected genes (comma separated)" help="These will also have the highest ranking in the final list."/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	185 <param name="prior_genes" type="text" optional="true" label="Prioritized genes (comma separated)"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	186 <conditional name="cond_n_pca_genes">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	187 <param name="select_n_pca_genes" type="select" label="Do you want to set the number of preselected pca genes?" help="If not, then this step will be skipped.">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	188 <option value="True">Yes</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	189 <option value="False">No</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	190 </param>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	191 <when value="True">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	192 <param argument="n_pca_genes" type="integer" value="100" min="1" optional="false" label="Number of preselected pca genes"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	193 </when>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	194 <when value="False"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	195 </conditional>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	196 <param argument="min_mean_difference" type="float" value="0.0" optional="false" label="Minimal difference of mean expression between at least one celltype and the background" help="This minimal difference is applied as an additional binary penalty in pca_penalties, DE_penalties and m_penalties_adata_celltypes."/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	197 <param argument="n_min_markers" type="integer" value="2" min="1" optional="false" label="The minimal number of identified and added markers"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	198 <param name="celltypes" type="text" value="all" optional="false" label="Cell types for which trees are trained" help="If not `all` then seperate the cell type with a comma (e.g., Glia,Neuron)"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	199 <conditional name="cond_markerset">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	200 <param name="select_markerset" type="select" label="Do you want to provide a set of marker genes?">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	201 <option value="False">No</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	202 <option value="True">Yes</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	203 </param>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	204 <when value="True">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	205 <param name="markerset" type="data" format="tabular" label="Markerset tabular file with rows=conditions (e.g., celltypes) and column=features (e.g., genes)"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	206 <param name="header_markerset" type="select" optional="false" label="Header in the list of markers?">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	207 <option value="included">Header included</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	208 <option value="not_included">Header not included</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	209 </param>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	210 </when>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	211 <when value="False"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	212 </conditional>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	213 <param argument="n_list_markers" type="integer" value="2" min="1" optional="false" label="Minimal number of markers per celltype that are at least selected" help="Selected means either selecting genes from the marker list or having correlated genes in the already selected panel."/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	214 <param argument="marker_corr_th" type="float" value="0.5" optional="false" label="Minimal correlation to consider a gene as captured"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	215 <param name="pca_penalties" type="text" optional="true" label="List of keys for columns in adata.var containing penalty factors that are multiplied with the scores for PCA based gene selection" help="(comma separted)"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	216 <param name="DE_penalties" type="text" optional="true" label="List of keys for columns in adata.var containing penalty factors that are multiplied with the scores for DE based gene selection (comma separted)" help="(comma separted)"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	217 <param name="m_penalties_adata_celltypes" type="text" optional="true" label="List of keys for columns in adata.var containing penalty factors to filter out marker genes if a gene's penalty < threshold for celltypes in adata" help="(comma separted)"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	218 <param name="m_penalties_list_celltypes" type="text" optional="true" label="List of keys for columns in adata.var containing penalty factors to filter out marker genes if a gene's penalty < threshold for celltypes not in adata" help="(comma separted)"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	219 <param argument="seed" type="integer" value="123" min="0" optional="false" label="Random number seed"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	220
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	221 <section name="advanced_options" title="Advanced Options" expanded="false">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	222 <conditional name="cond_DE_selection_hparams">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	223 <param name="select_DE_selection_hparams" type="select" label="Do you want to tune hyperparameters for the DE based gene selection?">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	224 <option value="False">No</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	225 <option value="True">Yes</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	226 </param>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	227 <when value="True">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	228 <param argument="n_DE_selection_hparams" type="integer" value="3" optional="false" label="n"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	229 <param name="per_group" type="select" label="per_group">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	230 <option value="False">No</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	231 <option value="True">Yes</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	232 </param>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	233 </when>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	234 <when value="False"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	235 </conditional>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	236 <conditional name="cond_forest_hparams">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	237 <param name="select_forest_hparams" type="select" label="Do you want to tune hyperparameters for the forest based gene selection?">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	238 <option value="False">No</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	239 <option value="True">Yes</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	240 </param>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	241 <when value="True">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	242 <param argument="n_trees" type="integer" value="50" optional="false" label="n_trees"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	243 <param argument="subsample" type="integer" value="1000" optional="false" label="subsample"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	244 <param argument="test_subsample" type="integer" value="3000" optional="false" label="test_subsample"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	245 </when>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	246 <when value="False"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	247 </conditional>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	248 <conditional name="cond_forest_DE_baseline_hparams">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	249 <param name="select_forest_DE_baseline_hparams" type="select" label="Do you want to tune hyperparameters for the DE based gene selection?">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	250 <option value="False">No</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	251 <option value="True">Yes</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	252 </param>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	253 <when value="True">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	254 <param argument="n_DE" type="integer" value="1" optional="false" label="n_DE"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	255 <param argument="min_score" type="float" value="0.9" optional="false" label="min_score"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	256 <param argument="n_stds" type="float" value="1.0" optional="false" label="n_stds"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	257 <param argument="max_step" type="integer" value="3" optional="false" label="max_step"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	258 <param argument="min_outlier_dif" type="float" value="0.02" optional="false" label="min_outlier_dif"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	259 <param argument="n_terminal_repeats" type="integer" value="3" optional="false" label="n_terminal_repeats"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	260 </when>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	261 <when value="False"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	262 </conditional>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	263 <conditional name="cond_add_forest_genes_hparams">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	264 <param name="select_add_forest_genes_hparams" type="select" label="Do you want to tune hyperparameters for adding marker genes to decision trees?">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	265 <option value="False">No</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	266 <option value="True">Yes</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	267 </param>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	268 <when value="True">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	269 <param argument="n_max_per_it" type="integer" value="5" optional="false" label="n_max_per_it"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	270 <param argument="performance_th" type="float" value="0.02" optional="false" label="performance_th"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	271 <param argument="importance_th" type="integer" value="0" optional="false" label="importance_th"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	272 </when>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	273 <when value="False"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	274 </conditional>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	275 <conditional name="cond_marker_selection_hparams">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	276 <param name="select_marker_selection_hparams" type="select" label="Do you want to tune marker selection hyperparameters?">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	277 <option value="False">No</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	278 <option value="True">Yes</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	279 </param>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	280 <when value="True">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	281 <param argument="penalty_threshold" type="integer" value="1" optional="false" label="penalty_threshold"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	282 </when>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	283 <when value="False"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	284 </conditional>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	285 </section>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	286
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	287 <section name="general_figure_options" title="General Figure Output Options" expanded="false">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	288 <param argument="dpi" type="integer" value="300" min="1" label="Dpi of figures"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	289 <param argument="fontsize" type="integer" value="100" min="1" label="Font size of figures"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	290 </section>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	291
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	292 <section name="figure_options_masked_dotplot" title="Figure Output Options for masked_dotplot" expanded="false">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	293 <param name="ct_key" type="text" value="celltype" optional="false" label="Key in adata.var for preselected genes" help="Column of adata.obs with cell type annotation"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	294 <param argument="imp_threshold" type="float" value="0.05" min="0.0" optional="false" label="Annotate genes as Spapros marker only for those genes with importance > imp_threshold"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	295 <param name="celltypes" type="text" optional="true" label="Subset of celltypes (rows of dotplot)"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	296 <param argument="n_genes" type="integer" value="0" min="0" label="Plot top n_genes genes." help="If 0 then all."/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	297 <param name="comb_markers_only" type="boolean" value="false" label="Do you want to plot only genes that are Spapros markers for the plotted cell types?"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	298 <param name="markers_only" type="boolean" value="false" label="Do you want to plot only genes that are markers for the plotted cell types?"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	299 <param name="cmap" type="text" value="Reds" optional="false" label="Colormap of mean expressions"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	300 <param name="comb_marker_color" type="text" value="darkblue" optional="false" label="Color for Spapros markers"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	301 <param name="marker_color" type="text" value="blue" optional="false" label="Color for marker genes"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	302 <param name="non_adata_celltypes_color" type="text" value="grey" optional="false" label="Color for celltypes that don't occur in the data set."/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	303 <param name="use_raw" type="select" label="Do you want to use adata.raw for plotting?">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	304 <option value="False">No</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	305 <option value="True">Yes</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	306 </param>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	307 </section>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	308
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	309 <section name="figure_options_plot_gene_overlap" title="Figure Output Options for plot_gene_overlap" expanded="false">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	310 <param name="style" type="select" label="Plot type">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	311 <option value="upset">Upset plot</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	312 <option value="venn">Venn diagram</option>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	313 </param>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	314 </section>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	315
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	316 <expand macro="inputs_common_advanced"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	317 </inputs>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	318 <outputs>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	319 <data name="out_masked_dotplot_png" format="png" from_work_dir="*masked_dotplot.png" label="PNG masked_dotplot from ${tool.name} on ${on_string}">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	320 <filter>format == 'png'</filter>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	321 </data>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	322 <data name="out_masked_dotplot_pdf" format="pdf" from_work_dir="*masked_dotplot.pdf" label="PDF masked_dotplot from ${tool.name} on ${on_string}">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	323 <filter>format == 'pdf'</filter>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	324 </data>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	325 <data name="out_masked_dotplot_svg" format="svg" from_work_dir="*masked_dotplot.svg" label="SVG masked_dotplot from ${tool.name} on ${on_string}">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	326 <filter>format == 'svg'</filter>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	327 </data>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	328 <data name="out_gene_overlap_png" format="png" from_work_dir="*gene_overlap.png" label="PNG gene_overlap from ${tool.name} on ${on_string}">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	329 <filter>format == 'png'</filter>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	330 </data>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	331 <data name="out_gene_overlap_pdf" format="pdf" from_work_dir="*gene_overlap.pdf" label="PDF gene_overlap from ${tool.name} on ${on_string}">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	332 <filter>format == 'pdf'</filter>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	333 </data>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	334 <data name="out_gene_overlap_svg" format="svg" from_work_dir="*gene_overlap.svg" label="SVG gene_overlap from ${tool.name} on ${on_string}">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	335 <filter>format == 'svg'</filter>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	336 </data>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	337 <data name="marker_out" format="tabular" from_work_dir="marker.tsv" label="${tool.name} on ${on_string}: Markers"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	338 <expand macro="hidden_outputs"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	339 </outputs>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	340 <tests>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	341 <test expect_num_outputs="4">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	342 <param name="adata" value="tl.rank_genes_groups.newton-cg.pbmc68k_reduced_240cells.h5ad"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	343 <param name="format" value="png"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	344 <param name="genes_key" value="highly_variable"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	345 <param name="show_log" value="true" />
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	346 <section name="general_figure_options">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	347 <param name="dpi" value="100"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	348 </section>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	349 <output name="hidden_output">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	350 <assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	351 <has_text_matching expression="celltype_key='celltype',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	352 <has_text_matching expression="genes_key='highly_variable',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	353 <has_text_matching expression="n_pca_genes=100,"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	354 <has_text_matching expression="seed=123,"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	355 <has_text_matching expression="cmap='Reds',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	356 <has_text_matching expression="save='masked_dotplot.png',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	357 <has_text_matching expression="style='upset',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	358 <has_text_matching expression="save='gene_overlap.png',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	359 </assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	360 </output>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	361 <output name="out_masked_dotplot_png">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	362 <assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	363 <has_image_width width="4055" delta="2"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	364 <has_image_height height="1108" delta="2"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	365 </assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	366 </output>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	367 <output name="out_gene_overlap_png">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	368 <assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	369 <has_image_width width="1189" delta="2"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	370 <has_image_height height="600" delta="2"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	371 </assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	372 </output>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	373 <output name="marker_out" file="marker_out_test1.tsv" ftype="tabular"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	374 </test>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	375 <test expect_num_outputs="4">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	376 <param name="adata" value="tl.rank_genes_groups.newton-cg.pbmc68k_reduced_240cells.h5ad"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	377 <param name="format" value="png"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	378 <param name="genes_key" value="highly_variable"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	379 <param name="select_n" value="True"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	380 <param name="n" value="10"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	381 <section name="general_figure_options">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	382 <param name="dpi" value="100"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	383 </section>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	384 <param name="show_log" value="true" />
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	385 <output name="hidden_output">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	386 <assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	387 <has_text_matching expression="celltype_key='celltype',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	388 <has_text_matching expression="genes_key='highly_variable',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	389 <has_text_matching expression="n_pca_genes=100,"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	390 <has_text_matching expression="n=10,"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	391 <has_text_matching expression="seed=123,"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	392 <has_text_matching expression="cmap='Reds',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	393 <has_text_matching expression="save='masked_dotplot.png',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	394 <has_text_matching expression="style='upset',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	395 <has_text_matching expression="save='gene_overlap.png',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	396 </assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	397 </output>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	398 <output name="out_masked_dotplot_png">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	399 <assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	400 <has_image_width width="2914" delta="2"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	401 <has_image_height height="882" delta="2"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	402 </assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	403 </output>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	404 <output name="out_gene_overlap_png">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	405 <assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	406 <has_image_width width="1032" delta="2"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	407 <has_image_height height="600" delta="2"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	408 </assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	409 </output>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	410 <output name="marker_out" file="marker_out_test2.tsv" ftype="tabular"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	411 </test>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	412 <test expect_num_outputs="4">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	413 <param name="adata" value="tl.rank_genes_groups.newton-cg.pbmc68k_reduced_240cells.h5ad"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	414 <param name="format" value="png"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	415 <param name="genes_key" value="highly_variable"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	416 <param name="celltypes" value="CD34+,CD56+ NK"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	417 <section name="general_figure_options">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	418 <param name="dpi" value="100"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	419 </section>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	420 <param name="show_log" value="true" />
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	421 <output name="hidden_output">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	422 <assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	423 <has_text_matching expression="celltype_key='celltype',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	424 <has_text_matching expression="genes_key='highly_variable',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	425 <has_text_matching expression="n_pca_genes=100,"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	426 <has_text_matching expression="seed=123,"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	427 <has_text_matching expression="cmap='Reds',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	428 <has_text_matching expression="save='masked_dotplot.png',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	429 <has_text_matching expression="style='upset',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	430 <has_text_matching expression="save='gene_overlap.png',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	431 </assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	432 </output>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	433 <output name="out_masked_dotplot_png">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	434 <assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	435 <has_image_width width="2776" delta="2"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	436 <has_image_height height="882" delta="2"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	437 </assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	438 </output>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	439 <output name="out_gene_overlap_png">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	440 <assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	441 <has_image_width width="929" delta="2"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	442 <has_image_height height="565" delta="2"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	443 </assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	444 </output>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	445 <output name="marker_out" file="marker_out_test3.tsv" ftype="tabular"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	446 </test>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	447 <test expect_num_outputs="4">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	448 <param name="adata" value="tl.rank_genes_groups.newton-cg.pbmc68k_reduced_240cells.h5ad"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	449 <param name="format" value="png"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	450 <param name="genes_key" value="highly_variable"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	451 <param name="select_markerset" value="True"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	452 <param name="markerset" value="marker.tsv"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	453 <param name="header_markerset" value="not_included"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	454 <section name="general_figure_options">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	455 <param name="dpi" value="100"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	456 </section>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	457 <param name="show_log" value="true"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	458 <output name="hidden_output">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	459 <assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	460 <has_text_matching expression="celltype_key='celltype',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	461 <has_text_matching expression="genes_key='highly_variable',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	462 <has_text_matching expression="n_pca_genes=100,"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	463 <has_text_matching expression="seed=123,"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	464 <has_text_matching expression="cmap='Reds',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	465 <has_text_matching expression="save='masked_dotplot.png',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	466 <has_text_matching expression="style='upset',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	467 <has_text_matching expression="save='gene_overlap.png',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	468 </assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	469 </output>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	470 <output name="out_masked_dotplot_png">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	471 <assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	472 <has_image_width width="4055" delta="2"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	473 <has_image_height height="1108" delta="2"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	474 </assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	475 </output>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	476 <output name="out_gene_overlap_png">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	477 <assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	478 <has_image_width width="1154" delta="2"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	479 <has_image_height height="600" delta="2"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	480 </assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	481 </output>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	482 <output name="marker_out" file="marker_out_test4.tsv" ftype="tabular"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	483 </test>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	484 <test expect_num_outputs="4">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	485 <param name="adata" value="tl.rank_genes_groups.newton-cg.pbmc68k_reduced_240cells.h5ad"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	486 <param name="format" value="png"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	487 <param name="genes_key" value="highly_variable"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	488 <section name="advanced_options">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	489 <param name="select_DE_selection_hparams" value="True"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	490 <param name="select_forest_hparams" value="True"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	491 <param name="select_forest_DE_baseline_hparams" value="True"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	492 <param name="select_add_forest_genes_hparams" value="True"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	493 <param name="select_marker_selection_hparams" value="True"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	494 </section>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	495 <section name="general_figure_options">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	496 <param name="dpi" value="100"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	497 </section>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	498 <param name="show_log" value="true"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	499 <output name="hidden_output">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	500 <assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	501 <has_text_matching expression="celltype_key='celltype',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	502 <has_text_matching expression="genes_key='highly_variable',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	503 <has_text_matching expression="n_pca_genes=100,"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	504 <has_text_matching expression="seed=123,"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	505 <has_text_matching expression="cmap='Reds',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	506 <has_text_matching expression="save='masked_dotplot.png',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	507 <has_text_matching expression="style='upset',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	508 <has_text_matching expression="save='gene_overlap.png',"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	509 </assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	510 </output>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	511 <output name="out_masked_dotplot_png">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	512 <assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	513 <has_image_width width="4055" delta="2"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	514 <has_image_height height="1108" delta="2"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	515 </assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	516 </output>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	517 <output name="out_gene_overlap_png">
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	518 <assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	519 <has_image_width width="1189" delta="2"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	520 <has_image_height height="600" delta="2"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	521 </assert_contents>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	522 </output>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	523 <output name="marker_out" file="marker_out_test5.tsv" ftype="tabular"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	524 </test>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	525 </tests>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	526 <help><![CDATA[
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	527 Probe set selection for single-cell sequencing data using spapros.
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	528 ============================================================================================================
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	529
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	530 Spapros is a python package that provides a pipeline for probe set selection and evaluation for targeted spatial transcriptomics data.
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	531
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	532 Key Features:
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	533 Select probe sets for spatial transcriptomics which identify cell types of interest, capture general transcriptomic variation, and incorporate prior knowledge
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	534
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	535 Evaluate probe sets with an extensive pipeline
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	536
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	537 Further documentation can be found here: https://spapros.readthedocs.io/en/latest/index.html.
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	538
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	539 ]]></help>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	540 <expand macro="citations"/>
c369fea6eab5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit a773446d7e104d987bfd01ccdcc1d80066c504f0 iuc parents: diff changeset	541 </tool>

Mercurial > repos > iuc > spapros

annotate selection.xml @ 0:c369fea6eab5 draft default tip