snapatac2_network: network.xml annotate

author	iuc
date	Tue, 25 Nov 2025 16:39:58 +0000
parents
children

rev	line source
0 2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	1 <tool id="snapatac2_network" name="SnapATAC2 network" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	2 <description>analysis</description>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	3 <macros>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	4 <import>macros.xml</import>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	5 </macros>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	6 <expand macro="xrefs"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	7 <requirements>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	8 <expand macro="requirements"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	9 </requirements>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	10 <command detect_errors="exit_code"><![CDATA[
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	11 gunzip -c '$motifs.fields.path' > 'input.meme' &&
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	12 #if $gff_file_condi.gffSource == 'cached':
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	13 ln -s '$gff_file_condi.gff_pre_installed.fields.path' anno.gff &&
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	14 #else:
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	15 ln -s '$gff_file_condi.gff_history' anno.gff &&
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	16 #end if
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	17 #if $fasta_file_condi.fastaSource == 'indexed':
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	18 zcat '$fasta_file_condi.fasta_pre_installed.fields.path' > fasta.fa &&
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	19 #else:
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	20 zcat '$fasta_file_condi.fasta_history' > fasta.fa &&
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	21 #end if
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	22 mkdir -p network_dir &&
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	23 cp '$adata_rna' 'anndata_rna.h5ad' &&
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	24 cp '$adata_atac' 'anndata_atac.h5ad' &&
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	25 @CMD@
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	26 ]]></command>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	27 <configfiles>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	28 <configfile name="script_file"><![CDATA[
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	29 @CONF_IMPORTS@
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	30 ## import motifs
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	31 from snapatac2._snapatac2 import read_motifs, PyDNAMotif
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	32 #if $motifs == 'cisbp':
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	33 @CONF_IMPORT_MEME@
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	34 #end if
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	35 rna = snap.read('anndata_rna.h5ad', backed = None)
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	36 atac = snap.read('anndata_atac.h5ad', backed = None)
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	37
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	38 marker_peaks = snap.tl.marker_regions(
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	39 atac,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	40 groupby = '$groupby',
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	41 pvalue = $pvalue_marker
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	42 )
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	43
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	44
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	45 for cluster_id, peaks_index in marker_peaks.items():
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	46 print(f"Processing cluster {cluster_id} with {len(peaks_index)} peaks...")
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	47
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	48 # Convert pandas Index to list of strings
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	49 regions_list = peaks_index.tolist()
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	50
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	51 # Create network for this cluster
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	52 network = snap.tl.init_network_from_annotation(
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	53 regions = regions_list,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	54 anno_file = 'anno.gff',
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	55 upstream = $upstream,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	56 downstream = $downstream,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	57 id_type = '$id_type',
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	58 coding_gene_only = $coding_gene_only
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	59 )
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	60
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	61 # add cor scores
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	62 snap.tl.add_cor_scores(
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	63 network,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	64 gene_mat=rna,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	65 peak_mat=atac,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	66 select=None, # Will get available if requested by users
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	67 overwrite=False
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	68 )
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	69 # add regr scores
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	70
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	71 snap.tl.add_regr_scores(
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	72 network,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	73 gene_mat=rna,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	74 peak_mat=atac,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	75 select=None, # Will get available if requested by users
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	76 method = '$method',
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	77 scale_X = $scale_X,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	78 scale_Y = $scale_Y,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	79 alpha = $alpha,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	80 l1_ratio = $l1_ratio,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	81 overwrite=False
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	82 )
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	83
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	84 # add tf binding
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	85 snap.tl.add_tf_binding(
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	86 network,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	87 motifs = motifs,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	88 genome_fasta = 'fasta.fa',
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	89 pvalue = $pvalue_tf
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	90 )
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	91
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	92 ## No good documentation, will get updated in next version if a tutorial is available for it
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	93 ## # link TF to gene
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	94 ## genetic_network = snap.tl.link_tf_to_gene(
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	95 ## network
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	96 ## )
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	97
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	98 # Create plot for this cluster
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	99 snap.pl.network_edge_stat(
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	100 network = network,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	101 width = $width,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	102 height = $height,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	103 show = False,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	104 interactive = False,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	105 out_file = f'network_dir/plot_network_cluster_{cluster_id}.png',
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	106 )
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	107
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	108 ## No good documentation, will get updated in next version if a tutorial is available for it
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	109 ## snap.pl.network_edge_stat(
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	110 ## network = genetic_network,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	111 ## width = $width,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	112 ## height = $height,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	113 ## show = False,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	114 ## interactive = False,
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	115 ## out_file = f'network_dir/plot_genetic_network_cluster_{cluster_id}.png',
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	116 ## )
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	117 print(f"Completed cluster {cluster_id}")
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	118
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	119 print("All clusters processed!")
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	120 ]]></configfile>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	121 </configfiles>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	122 <inputs>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	123 <param name="adata_rna" type="data" format="h5ad" label="Annotated data matrix containing RNA data"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	124 <param name="adata_atac" type="data" format="h5ad" label="Annotated data matrix containing ATAC data"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	125 <expand macro="param_groupby"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	126 <param argument="pvalue_marker" type="float" value="0.01" label="P-value threshold to detect marker regions"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	127 <expand macro="param_gene_anno"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	128 <expand macro="param_genome_fasta"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	129 <param name="upstream" type="integer" value="250000" min="0" label="Upstream extension to the transcription start site"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	130 <param name="downstream" type="integer" value="250000" min="0" label="Downstream extension to the transcription start site"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	131 <param name="id_type" type="select" label="ID type of the gene in the annotation file">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	132 <option value="gene_name">Gene name</option>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	133 <option value="gene_id">Gene ID</option>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	134 <option value="transcript_id">Transcript ID</option>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	135 </param>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	136 <param name="coding_gene_only" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Retain only coding genes in the network"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	137 <param name="method" type="select" label="Regresson model">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	138 <!-- <option value="elastic_net">elastic_net</option> has problem with sparse matrix-->
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	139 <option value="gb_tree">gb_tree</option>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	140 </param>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	141 <param name="scale_X" type="boolean" checked="false" truevalue="True" falsevalue="False" label="Whether to scale the features"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	142 <param name="scale_Y" type="boolean" checked="false" truevalue="True" falsevalue="False" label="Whether to scale the response variable"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	143 <param name="alpha" type="float" value="1.5" label="Constant that multiplies the penalty terms in ‘elastic_net’"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	144 <param name="l1_ratio" type="float" min="0" max="1" value="0.5" label="L1 penalty ratio" help="If set to 0, L2 penalty is used, if set to 1, L1 penalty is used, and if set between 0 and 1, a combination of both penalties is used."/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	145 <expand macro="param_meme_table"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	146 <param argument="pvalue_tf" type="float" value="0.01" label="P-value threshold to detect TF binding"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	147 <expand macro="param_render_plot"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	148 <expand macro="param_common_advanced"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	149 </inputs>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	150 <outputs>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	151 <data name="hidden_output" format="txt" label="Log file" >
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	152 <filter>advanced_common['show_log']</filter>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	153 </data>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	154 <collection name="out_network" type="list" label="${tool.name} (${method}) on ${on_string} - Network">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	155 <discover_datasets pattern="__name_and_ext__" directory="network_dir/"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	156 <filter>out_file != 'svg' and out_file != 'html'</filter>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	157 </collection>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	158 <collection name="out_network_svg" type="list" label="${tool.name} (${method}) on ${on_string} - Network - svg">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	159 <discover_datasets pattern="__name_and_ext__" directory="network_dir/"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	160 <filter>out_file == 'svg'</filter>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	161 </collection>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	162 <collection name="out_network_html" type="list" label="${tool.name} (${method}) on ${on_string} - Network - html">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	163 <discover_datasets pattern="__name_and_ext__" directory="network_dir/"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	164 <filter>out_file == 'html'</filter>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	165 </collection>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	166 </outputs>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	167 <tests>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	168 <!-- metrics.frag_size_distr cached -->
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	169 <test expect_num_outputs="2">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	170 <param name="adata_rna" location="https://zenodo.org/records/17512085/files/snap_datasets_pbmc10k_multiome_RNA.h5ad.gz"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	171 <param name="adata_atac" location="https://zenodo.org/records/17512085/files/snap_datasets_pbmc10k_multiome_ATAC.h5ad.gz"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	172 <param name="groupby" value="cell_type"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	173 <param name="pvalue_marker" value="0.1"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	174 <conditional name="gff_file_condi">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	175 <param name="gffSource" value="cached"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	176 <param name="gff_pre_installed" value="hg38"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	177 </conditional>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	178 <conditional name="fasta_file_condi">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	179 <param name="fastaSource" value="indexed"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	180 <param name="fasta_pre_installed" value="hg38"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	181 </conditional>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	182 <param name="out_file" value="png"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	183 <expand macro="test_param_render_plot"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	184 <section name="advanced_common">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	185 <param name="show_log" value="true" />
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	186 </section>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	187 <output name="hidden_output">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	188 <assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	189 <has_text_matching expression="snap.tl.marker_regions"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	190 <has_text_matching expression="snap.tl.init_network_from_annotation"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	191 <has_text_matching expression="snap.tl.add_cor_scores"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	192 <has_text_matching expression="snap.tl.add_regr_scores"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	193 <has_text_matching expression="add_tf_binding"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	194 <!-- <has_text_matching expression="snap.tl.link_tf_to_gene"/> -->
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	195 <has_text_matching expression="snap.pl.network_edge_stat"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	196 <has_text_matching expression="groupby = 'cell_type'"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	197 <expand macro="test_render_plot_matching_text"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	198 </assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	199 </output>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	200 <output_collection name="out_network" type="list" count="8">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	201 <element name="plot_network_cluster_CD14 Mono">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	202 <assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	203 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	204 <has_image_channels channels="4"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	205 <has_image_height height="450" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	206 <has_image_width width="650" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	207 </assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	208 </element>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	209 <element name="plot_network_cluster_CD16 Mono">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	210 <assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	211 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	212 <has_image_channels channels="4"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	213 <has_image_height height="450" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	214 <has_image_width width="650" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	215 </assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	216 </element>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	217 <element name="plot_network_cluster_CD4 Naive">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	218 <assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	219 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	220 <has_image_channels channels="4"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	221 <has_image_height height="450" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	222 <has_image_width width="650" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	223 </assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	224 </element>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	225 <element name="plot_network_cluster_CD4 TCM">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	226 <assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	227 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	228 <has_image_channels channels="4"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	229 <has_image_height height="450" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	230 <has_image_width width="650" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	231 </assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	232 </element>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	233 <element name="plot_network_cluster_CD8 Naive">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	234 <assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	235 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	236 <has_image_channels channels="4"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	237 <has_image_height height="450" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	238 <has_image_width width="650" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	239 </assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	240 </element>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	241 <element name="plot_network_cluster_NK">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	242 <assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	243 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	244 <has_image_channels channels="4"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	245 <has_image_height height="450" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	246 <has_image_width width="650" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	247 </assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	248 </element>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	249 <element name="plot_network_cluster_Treg">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	250 <assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	251 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	252 <has_image_channels channels="4"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	253 <has_image_height height="450" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	254 <has_image_width width="650" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	255 </assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	256 </element>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	257 <element name="plot_network_cluster_cDC">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	258 <assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	259 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	260 <has_image_channels channels="4"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	261 <has_image_height height="450" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	262 <has_image_width width="650" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	263 </assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	264 </element>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	265 </output_collection>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	266 </test>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	267 <!-- metrics.frag_size_distr history -->
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	268 <test expect_num_outputs="2">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	269 <param name="adata_rna" location="https://zenodo.org/records/17512085/files/snap_datasets_pbmc10k_multiome_RNA.h5ad.gz"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	270 <param name="adata_atac" location="https://zenodo.org/records/17512085/files/snap_datasets_pbmc10k_multiome_ATAC.h5ad.gz"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	271 <param name="groupby" value="cell_type"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	272 <param name="pvalue_marker" value="0.1"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	273 <conditional name="gff_file_condi">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	274 <param name="gffSource" value="history"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	275 <param name="gff_history" location="https://zenodo.org/records/17512085/files/chr21.gff3.gz"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	276 </conditional>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	277 <conditional name="fasta_file_condi">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	278 <param name="fastaSource" value="history"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	279 <param name="fasta_history" location="https://zenodo.org/records/17512085/files/chr21.fasta.gz"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	280 </conditional>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	281 <param name="out_file" value="png"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	282 <expand macro="test_param_render_plot"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	283 <section name="advanced_common">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	284 <param name="show_log" value="true" />
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	285 </section>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	286 <output name="hidden_output">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	287 <assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	288 <has_text_matching expression="snap.tl.marker_regions"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	289 <has_text_matching expression="snap.tl.init_network_from_annotation"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	290 <has_text_matching expression="snap.tl.add_cor_scores"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	291 <has_text_matching expression="snap.tl.add_regr_scores"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	292 <has_text_matching expression="add_tf_binding"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	293 <!-- <has_text_matching expression="snap.tl.link_tf_to_gene"/> -->
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	294 <has_text_matching expression="snap.pl.network_edge_stat"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	295 <has_text_matching expression="groupby = 'cell_type'"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	296 <expand macro="test_render_plot_matching_text"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	297 </assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	298 </output>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	299 <output_collection name="out_network" type="list" count="8">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	300 <element name="plot_network_cluster_CD14 Mono">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	301 <assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	302 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	303 <has_image_channels channels="4"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	304 <has_image_height height="450" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	305 <has_image_width width="650" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	306 </assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	307 </element>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	308 <element name="plot_network_cluster_CD16 Mono">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	309 <assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	310 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	311 <has_image_channels channels="4"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	312 <has_image_height height="450" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	313 <has_image_width width="650" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	314 </assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	315 </element>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	316 <element name="plot_network_cluster_CD4 Naive">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	317 <assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	318 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	319 <has_image_channels channels="4"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	320 <has_image_height height="450" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	321 <has_image_width width="650" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	322 </assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	323 </element>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	324 <element name="plot_network_cluster_CD4 TCM">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	325 <assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	326 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	327 <has_image_channels channels="4"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	328 <has_image_height height="450" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	329 <has_image_width width="650" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	330 </assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	331 </element>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	332 <element name="plot_network_cluster_CD8 Naive">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	333 <assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	334 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	335 <has_image_channels channels="4"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	336 <has_image_height height="450" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	337 <has_image_width width="650" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	338 </assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	339 </element>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	340 <element name="plot_network_cluster_NK">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	341 <assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	342 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	343 <has_image_channels channels="4"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	344 <has_image_height height="450" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	345 <has_image_width width="650" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	346 </assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	347 </element>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	348 <element name="plot_network_cluster_Treg">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	349 <assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	350 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	351 <has_image_channels channels="4"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	352 <has_image_height height="450" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	353 <has_image_width width="650" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	354 </assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	355 </element>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	356 <element name="plot_network_cluster_cDC">
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	357 <assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	358 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	359 <has_image_channels channels="4"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	360 <has_image_height height="450" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	361 <has_image_width width="650" delta="20"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	362 </assert_contents>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	363 </element>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	364 </output_collection>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	365 </test>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	366 </tests>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	367 <help><![CDATA[
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	368 Build CRE-gene network from gene annotations, using `SnapATAC2`
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	369 ===============================================================
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	370
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	371 Link CREs to genes if they are close to genes’ promoter regions.
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	372
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	373 More details on the `SnapATAC2 documentation
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	374 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.tl.init_network_from_annotation.html>`__
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	375
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	376
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	377 Compute correlation scores for any two connected nodes in the network.
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	378
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	379 More details on the `SnapATAC2 documentation
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	380 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.tl.add_cor_scores.html>`__
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	381
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	382
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	383 Perform regression analysis for nodes and their parents in the network.
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	384
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	385 More details on the `SnapATAC2 documentation
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	386 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.tl.add_regr_scores.html>`__
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	387
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	388
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	389 Add TF motif binding information.
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	390
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	391 More details on the `SnapATAC2 documentation
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	392 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.tl.add_tf_binding.html>`__
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	393
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	394 ]]></help>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	395 <expand macro="citations"/>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	396 </tool>
2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d iuc parents: diff changeset	397

0

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

parents:

diff changeset

1 <tool id="snapatac2_network" name="SnapATAC2 network" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

2 <description>analysis</description>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

parents:

diff changeset

3 <macros>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

4 <import>macros.xml</import>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

5 </macros>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

parents:

diff changeset

6 <expand macro="xrefs"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

7 <requirements>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

parents:

diff changeset

8 <expand macro="requirements"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

9 </requirements>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

10 <command detect_errors="exit_code"><![CDATA[

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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11 gunzip -c '$motifs.fields.path' > 'input.meme' &&

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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12 #if $gff_file_condi.gffSource == 'cached':

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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13 ln -s '$gff_file_condi.gff_pre_installed.fields.path' anno.gff &&

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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14 #else:

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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15 ln -s '$gff_file_condi.gff_history' anno.gff &&

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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16 #end if

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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17 #if $fasta_file_condi.fastaSource == 'indexed':

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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18 zcat '$fasta_file_condi.fasta_pre_installed.fields.path' > fasta.fa &&

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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19 #else:

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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20 zcat '$fasta_file_condi.fasta_history' > fasta.fa &&

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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21 #end if

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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22 mkdir -p network_dir &&

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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23 cp '$adata_rna' 'anndata_rna.h5ad' &&

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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24 cp '$adata_atac' 'anndata_atac.h5ad' &&

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

25 @CMD@

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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26 ]]></command>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

27 <configfiles>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

28 <configfile name="script_file"><![CDATA[

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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29 @CONF_IMPORTS@

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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30 ## import motifs

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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31 from snapatac2._snapatac2 import read_motifs, PyDNAMotif

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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32 #if $motifs == 'cisbp':

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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diff changeset

33 @CONF_IMPORT_MEME@

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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34 #end if

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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diff changeset

35 rna = snap.read('anndata_rna.h5ad', backed = None)

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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diff changeset

36 atac = snap.read('anndata_atac.h5ad', backed = None)

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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diff changeset

37

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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diff changeset

38 marker_peaks = snap.tl.marker_regions(

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

39 atac,

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

40 groupby = '$groupby',

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

41 pvalue = $pvalue_marker

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

parents:

diff changeset

42 )

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

43

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

44

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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45 for cluster_id, peaks_index in marker_peaks.items():

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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diff changeset

46 print(f"Processing cluster {cluster_id} with {len(peaks_index)} peaks...")

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

47

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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diff changeset

48 # Convert pandas Index to list of strings

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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diff changeset

49 regions_list = peaks_index.tolist()

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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diff changeset

50

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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diff changeset

51 # Create network for this cluster

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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52 network = snap.tl.init_network_from_annotation(

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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diff changeset

53 regions = regions_list,

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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diff changeset

54 anno_file = 'anno.gff',

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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55 upstream = $upstream,

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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56 downstream = $downstream,

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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diff changeset

57 id_type = '$id_type',

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58 coding_gene_only = $coding_gene_only

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59 )

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60

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61 # add cor scores

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62 snap.tl.add_cor_scores(

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63 network,

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64 gene_mat=rna,

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65 peak_mat=atac,

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66 select=None, # Will get available if requested by users

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67 overwrite=False

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68 )

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69 # add regr scores

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70

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71 snap.tl.add_regr_scores(

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72 network,

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73 gene_mat=rna,

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74 peak_mat=atac,

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75 select=None, # Will get available if requested by users

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76 method = '$method',

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77 scale_X = $scale_X,

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78 scale_Y = $scale_Y,

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79 alpha = $alpha,

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80 l1_ratio = $l1_ratio,

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81 overwrite=False

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82 )

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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83

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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84 # add tf binding

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85 snap.tl.add_tf_binding(

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86 network,

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87 motifs = motifs,

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88 genome_fasta = 'fasta.fa',

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89 pvalue = $pvalue_tf

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90 )

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91

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92 ## No good documentation, will get updated in next version if a tutorial is available for it

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93 ## # link TF to gene

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94 ## genetic_network = snap.tl.link_tf_to_gene(

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95 ## network

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96 ## )

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97

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98 # Create plot for this cluster

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99 snap.pl.network_edge_stat(

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100 network = network,

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101 width = $width,

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102 height = $height,

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103 show = False,

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104 interactive = False,

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105 out_file = f'network_dir/plot_network_cluster_{cluster_id}.png',

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106 )

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107

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108 ## No good documentation, will get updated in next version if a tutorial is available for it

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109 ## snap.pl.network_edge_stat(

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110 ## network = genetic_network,

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111 ## width = $width,

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112 ## height = $height,

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113 ## show = False,

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114 ## interactive = False,

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115 ## out_file = f'network_dir/plot_genetic_network_cluster_{cluster_id}.png',

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116 ## )

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117 print(f"Completed cluster {cluster_id}")

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118

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119 print("All clusters processed!")

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120 ]]></configfile>

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121 </configfiles>

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122 <inputs>

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123 <param name="adata_rna" type="data" format="h5ad" label="Annotated data matrix containing RNA data"/>

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124 <param name="adata_atac" type="data" format="h5ad" label="Annotated data matrix containing ATAC data"/>

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125 <expand macro="param_groupby"/>

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126 <param argument="pvalue_marker" type="float" value="0.01" label="P-value threshold to detect marker regions"/>

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127 <expand macro="param_gene_anno"/>

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128 <expand macro="param_genome_fasta"/>

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129 <param name="upstream" type="integer" value="250000" min="0" label="Upstream extension to the transcription start site"/>

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130 <param name="downstream" type="integer" value="250000" min="0" label="Downstream extension to the transcription start site"/>

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131 <param name="id_type" type="select" label="ID type of the gene in the annotation file">

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132 <option value="gene_name">Gene name</option>

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133 <option value="gene_id">Gene ID</option>

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134 <option value="transcript_id">Transcript ID</option>

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135 </param>

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136 <param name="coding_gene_only" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Retain only coding genes in the network"/>

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137 <param name="method" type="select" label="Regresson model">

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138

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139 <option value="gb_tree">gb_tree</option>

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140 </param>

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141 <param name="scale_X" type="boolean" checked="false" truevalue="True" falsevalue="False" label="Whether to scale the features"/>

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142 <param name="scale_Y" type="boolean" checked="false" truevalue="True" falsevalue="False" label="Whether to scale the response variable"/>

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143 <param name="alpha" type="float" value="1.5" label="Constant that multiplies the penalty terms in ‘elastic_net’"/>

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144 <param name="l1_ratio" type="float" min="0" max="1" value="0.5" label="L1 penalty ratio" help="If set to 0, L2 penalty is used, if set to 1, L1 penalty is used, and if set between 0 and 1, a combination of both penalties is used."/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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145 <expand macro="param_meme_table"/>

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146 <param argument="pvalue_tf" type="float" value="0.01" label="P-value threshold to detect TF binding"/>

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147 <expand macro="param_render_plot"/>

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148 <expand macro="param_common_advanced"/>

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149 </inputs>

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150 <outputs>

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151 <data name="hidden_output" format="txt" label="Log file" >

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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152 <filter>advanced_common['show_log']</filter>

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153 </data>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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154 <collection name="out_network" type="list" label="${tool.name} (${method}) on ${on_string} - Network">

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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155 <discover_datasets pattern="__name_and_ext__" directory="network_dir/"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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156 <filter>out_file != 'svg' and out_file != 'html'</filter>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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157 </collection>

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158 <collection name="out_network_svg" type="list" label="${tool.name} (${method}) on ${on_string} - Network - svg">

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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159 <discover_datasets pattern="__name_and_ext__" directory="network_dir/"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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160 <filter>out_file == 'svg'</filter>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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161 </collection>

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162 <collection name="out_network_html" type="list" label="${tool.name} (${method}) on ${on_string} - Network - html">

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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163 <discover_datasets pattern="__name_and_ext__" directory="network_dir/"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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164 <filter>out_file == 'html'</filter>

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165 </collection>

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166 </outputs>

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167 <tests>

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168

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169 <test expect_num_outputs="2">

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170 <param name="adata_rna" location="https://zenodo.org/records/17512085/files/snap_datasets_pbmc10k_multiome_RNA.h5ad.gz"/>

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171 <param name="adata_atac" location="https://zenodo.org/records/17512085/files/snap_datasets_pbmc10k_multiome_ATAC.h5ad.gz"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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172 <param name="groupby" value="cell_type"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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173 <param name="pvalue_marker" value="0.1"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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174 <conditional name="gff_file_condi">

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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175 <param name="gffSource" value="cached"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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176 <param name="gff_pre_installed" value="hg38"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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177 </conditional>

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178 <conditional name="fasta_file_condi">

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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179 <param name="fastaSource" value="indexed"/>

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180 <param name="fasta_pre_installed" value="hg38"/>

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181 </conditional>

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182 <param name="out_file" value="png"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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183 <expand macro="test_param_render_plot"/>

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184 <section name="advanced_common">

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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185 <param name="show_log" value="true" />

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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186 </section>

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187 <output name="hidden_output">

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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188 <assert_contents>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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189 <has_text_matching expression="snap.tl.marker_regions"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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190 <has_text_matching expression="snap.tl.init_network_from_annotation"/>

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191 <has_text_matching expression="snap.tl.add_cor_scores"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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192 <has_text_matching expression="snap.tl.add_regr_scores"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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193 <has_text_matching expression="add_tf_binding"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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194

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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195 <has_text_matching expression="snap.pl.network_edge_stat"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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196 <has_text_matching expression="groupby = 'cell_type'"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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197 <expand macro="test_render_plot_matching_text"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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198 </assert_contents>

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199 </output>

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200 <output_collection name="out_network" type="list" count="8">

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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201 <element name="plot_network_cluster_CD14 Mono">

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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202 <assert_contents>

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203 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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204 <has_image_channels channels="4"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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205 <has_image_height height="450" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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206 <has_image_width width="650" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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207 </assert_contents>

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208 </element>

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209 <element name="plot_network_cluster_CD16 Mono">

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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210 <assert_contents>

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211 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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212 <has_image_channels channels="4"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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213 <has_image_height height="450" delta="20"/>

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214 <has_image_width width="650" delta="20"/>

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215 </assert_contents>

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216 </element>

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217 <element name="plot_network_cluster_CD4 Naive">

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218 <assert_contents>

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219 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>

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220 <has_image_channels channels="4"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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221 <has_image_height height="450" delta="20"/>

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222 <has_image_width width="650" delta="20"/>

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223 </assert_contents>

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224 </element>

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225 <element name="plot_network_cluster_CD4 TCM">

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226 <assert_contents>

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227 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>

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228 <has_image_channels channels="4"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

229 <has_image_height height="450" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

230 <has_image_width width="650" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

231 </assert_contents>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

232 </element>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

233 <element name="plot_network_cluster_CD8 Naive">

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

234 <assert_contents>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

235 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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236 <has_image_channels channels="4"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

237 <has_image_height height="450" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

238 <has_image_width width="650" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

239 </assert_contents>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

240 </element>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

241 <element name="plot_network_cluster_NK">

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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242 <assert_contents>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

243 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

244 <has_image_channels channels="4"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

245 <has_image_height height="450" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

246 <has_image_width width="650" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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247 </assert_contents>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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248 </element>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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249 <element name="plot_network_cluster_Treg">

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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250 <assert_contents>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

251 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

252 <has_image_channels channels="4"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

253 <has_image_height height="450" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

254 <has_image_width width="650" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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255 </assert_contents>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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256 </element>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

257 <element name="plot_network_cluster_cDC">

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

258 <assert_contents>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

259 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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260 <has_image_channels channels="4"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

261 <has_image_height height="450" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

262 <has_image_width width="650" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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263 </assert_contents>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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diff changeset

264 </element>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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265 </output_collection>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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266 </test>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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267

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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268 <test expect_num_outputs="2">

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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269 <param name="adata_rna" location="https://zenodo.org/records/17512085/files/snap_datasets_pbmc10k_multiome_RNA.h5ad.gz"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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270 <param name="adata_atac" location="https://zenodo.org/records/17512085/files/snap_datasets_pbmc10k_multiome_ATAC.h5ad.gz"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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271 <param name="groupby" value="cell_type"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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diff changeset

272 <param name="pvalue_marker" value="0.1"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

273 <conditional name="gff_file_condi">

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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274 <param name="gffSource" value="history"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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275 <param name="gff_history" location="https://zenodo.org/records/17512085/files/chr21.gff3.gz"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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276 </conditional>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

277 <conditional name="fasta_file_condi">

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

278 <param name="fastaSource" value="history"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

279 <param name="fasta_history" location="https://zenodo.org/records/17512085/files/chr21.fasta.gz"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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280 </conditional>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

281 <param name="out_file" value="png"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

parents:

diff changeset

282 <expand macro="test_param_render_plot"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

283 <section name="advanced_common">

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

284 <param name="show_log" value="true" />

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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285 </section>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

286 <output name="hidden_output">

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

287 <assert_contents>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

288 <has_text_matching expression="snap.tl.marker_regions"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

289 <has_text_matching expression="snap.tl.init_network_from_annotation"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

290 <has_text_matching expression="snap.tl.add_cor_scores"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

291 <has_text_matching expression="snap.tl.add_regr_scores"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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292 <has_text_matching expression="add_tf_binding"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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293

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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294 <has_text_matching expression="snap.pl.network_edge_stat"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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diff changeset

295 <has_text_matching expression="groupby = 'cell_type'"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

296 <expand macro="test_render_plot_matching_text"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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297 </assert_contents>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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diff changeset

298 </output>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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diff changeset

299 <output_collection name="out_network" type="list" count="8">

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

300 <element name="plot_network_cluster_CD14 Mono">

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

301 <assert_contents>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

302 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

parents:

diff changeset

303 <has_image_channels channels="4"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

parents:

diff changeset

304 <has_image_height height="450" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

parents:

diff changeset

305 <has_image_width width="650" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

306 </assert_contents>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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diff changeset

307 </element>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

308 <element name="plot_network_cluster_CD16 Mono">

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

309 <assert_contents>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

310 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

parents:

diff changeset

311 <has_image_channels channels="4"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

312 <has_image_height height="450" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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313 <has_image_width width="650" delta="20"/>

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314 </assert_contents>

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315 </element>

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iuc

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316 <element name="plot_network_cluster_CD4 Naive">

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iuc

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317 <assert_contents>

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318 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>

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319 <has_image_channels channels="4"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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320 <has_image_height height="450" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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diff changeset

321 <has_image_width width="650" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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322 </assert_contents>

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iuc

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323 </element>

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iuc

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diff changeset

324 <element name="plot_network_cluster_CD4 TCM">

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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325 <assert_contents>

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iuc

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326 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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327 <has_image_channels channels="4"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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328 <has_image_height height="450" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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329 <has_image_width width="650" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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330 </assert_contents>

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331 </element>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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332 <element name="plot_network_cluster_CD8 Naive">

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iuc

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333 <assert_contents>

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iuc

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334 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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335 <has_image_channels channels="4"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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336 <has_image_height height="450" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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337 <has_image_width width="650" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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338 </assert_contents>

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339 </element>

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340 <element name="plot_network_cluster_NK">

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341 <assert_contents>

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iuc

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342 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>

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iuc

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343 <has_image_channels channels="4"/>

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iuc

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344 <has_image_height height="450" delta="20"/>

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iuc

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345 <has_image_width width="650" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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346 </assert_contents>

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347 </element>

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iuc

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348 <element name="plot_network_cluster_Treg">

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iuc

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349 <assert_contents>

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iuc

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350 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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351 <has_image_channels channels="4"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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352 <has_image_height height="450" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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353 <has_image_width width="650" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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354 </assert_contents>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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355 </element>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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356 <element name="plot_network_cluster_cDC">

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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357 <assert_contents>

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iuc

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358 <has_image_center_of_mass center_of_mass="325,225" eps="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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359 <has_image_channels channels="4"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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360 <has_image_height height="450" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

parents:

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361 <has_image_width width="650" delta="20"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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362 </assert_contents>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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363 </element>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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364 </output_collection>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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365 </test>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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366 </tests>

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iuc

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367 <help><![CDATA[

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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368 Build CRE-gene network from gene annotations, using `SnapATAC2`

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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369 ===============================================================

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370

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371 Link CREs to genes if they are close to genes’ promoter regions.

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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372

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373 More details on the `SnapATAC2 documentation

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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374 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.tl.init_network_from_annotation.html>`__

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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375

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376

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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377 Compute correlation scores for any two connected nodes in the network.

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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378

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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379 More details on the `SnapATAC2 documentation

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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380 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.tl.add_cor_scores.html>`__

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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381

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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382

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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383 Perform regression analysis for nodes and their parents in the network.

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384

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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385 More details on the `SnapATAC2 documentation

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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386 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.tl.add_regr_scores.html>`__

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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387

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388

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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389 Add TF motif binding information.

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390

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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391 More details on the `SnapATAC2 documentation

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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392 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.tl.add_tf_binding.html>`__

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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393

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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394 ]]></help>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

iuc

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395 <expand macro="citations"/>

2c289e3b566a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d

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396 </tool>

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397

Mercurial > repos > iuc > snapatac2_network

annotate network.xml @ 0:2c289e3b566a draft default tip