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comparison diffbind.xml @ 17:2605cbdaa7d8 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
author iuc
date Fri, 15 Dec 2023 19:39:14 +0000
parents 163688bb8f73
children
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16:163688bb8f73 17:2605cbdaa7d8
1 <tool id="diffbind" name="DiffBind" version="2.10.0+galaxy0"> 1 <tool id="diffbind" name="DiffBind" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description> differential binding analysis of ChIP-Seq peak data</description> 2 <description> differential binding analysis of ChIP-Seq peak data</description>
3 <macros>
4 <token name="@TOOL_VERSION@">2.10.0</token>
5 <token name="@VERSION_SUFFIX@">1</token>
6 <token name="@PROFILE@">22.05</token>
7 </macros>
8 <xrefs>
9 <xref type="bio.tools">diffbind</xref>
10 <xref type="bioconductor">diffbind</xref>
11 </xrefs>
3 <requirements> 12 <requirements>
4 <requirement type="package" version="2.10.0">bioconductor-diffbind</requirement> 13 <requirement type="package" version="@TOOL_VERSION@">bioconductor-diffbind</requirement>
5 <requirement type="package" version="3.5.1">r-base</requirement> 14 <requirement type="package" version="3.5.1">r-base</requirement>
6 <requirement type="package" version="1.20.3">r-getopt</requirement> 15 <requirement type="package" version="1.20.3">r-getopt</requirement>
7 <requirement type="package" version="0.2.20">r-rjson</requirement> 16 <requirement type="package" version="0.2.20">r-rjson</requirement>
8 </requirements> 17 </requirements>
9 <stdio> 18 <stdio>
31 #set $temp_factor_names = list() 40 #set $temp_factor_names = list()
32 #set $temp_factor = list() 41 #set $temp_factor = list()
33 42
34 #for $g in $rep_group: 43 #for $g in $rep_group:
35 44
36 #set $peak_files = list() 45 #set $peak_files = dict()
37 #set $bam_files = list() 46 #set $bam_files = dict()
38 #set $bam_controls = list() 47 #set $bam_controls = dict()
39 48
40 #for $file in $g.peaks: 49 #for $file in $g.peaks:
41 #set $file_name = str($g.groupName) + "-" + re.sub('[^\w\-]', '_', str($file.element_identifier)) + "-peaks.bed" 50 #set $file_name = str($g.groupName) + "-" + re.sub('[^\w\-]', '_', str($file.element_identifier)) + "-peaks.bed"
42 ln -s '${file}' '${file_name}' && 51 ln -s '${file}' '${file_name}' &&
43 $peak_files.append($file_name) 52 #set $peak_files[str($file.element_identifier)] = str($file_name)
44 #end for 53 #end for
45 54
46 #for $bam in $g.bamreads: 55 #for $bam in $g.bamreads:
47 #set $bam_name = re.sub('[^\w\-]', '_', str($bam.element_identifier)) 56 #set $bam_name = re.sub('[^\w\-]', '_', str($bam.element_identifier))
48 #set $bam_file = $bam_name + "-bamreads.bam" 57 #set $bam_file = $bam_name + "-bamreads.bam"
49 #set $bam_index = $bam_name + "-bamreads.bai" 58 #set $bam_index = $bam_name + "-bamreads.bai"
50 ln -s '${bam}' '${bam_file}' && 59 ln -s '${bam}' '${bam_file}' &&
51 ln -s '${bam.metadata.bam_index}' '${bam_index}' && 60 ln -s '${bam.metadata.bam_index}' '${bam_index}' &&
52 $bam_files.append($bam_file) 61 #set $bam_files[str($bam.element_identifier)] = str($bam_file)
53 #end for 62 #end for
54 63
55 $temp_factor.append( {str($g.groupName): $peak_files} ) 64 #if len($peak_files.keys()) != len($bam_files.keys())
56 $temp_factor.append( {str($g.groupName): $bam_files} ) 65 >&2 echo "Group $g.groupName: same number of Peak and Bam files needs to be given" && exit 1 &&
66 #end if
67 $temp_factor.append( {str($g.groupName): [f[1] for f in sorted($peak_files.items())]} )
68 $temp_factor.append( {str($g.groupName): [f[1] for f in sorted($bam_files.items())]} )
57 69
58 #if str( $g.bamcontrol ) != 'None': 70 #if str( $g.bamcontrol ) != 'None':
59 #for $ctrl in $g.bamcontrol: 71 #for $ctrl in $g.bamcontrol:
60 #set $ctrl_name = re.sub('[^\w\-]', '_', str($ctrl.element_identifier)) 72 #set $ctrl_name = re.sub('[^\w\-]', '_', str($ctrl.element_identifier))
61 #set $ctrl_file = $ctrl_name + "-bamcontrol.bam" 73 #set $ctrl_file = $ctrl_name + "-bamcontrol.bam"
62 #set ctrl_index = $ctrl_name + "-bamcontrol.bai" 74 #set ctrl_index = $ctrl_name + "-bamcontrol.bai"
63 #if $ctrl_file not in json.dumps($temp_factor): 75 #if $ctrl_file not in json.dumps($temp_factor):
64 ln -s '${ctrl}' '${ctrl_file}' && 76 ln -s '${ctrl}' '${ctrl_file}' &&
65 ln -s '${ctrl.metadata.bam_index}' '${ctrl_index}' && 77 ln -s '${ctrl.metadata.bam_index}' '${ctrl_index}' &&
66 #end if 78 #end if
67 $bam_controls.append($ctrl_file) 79 #set $bam_controls[str($ctrl.element_identifier)] = str($ctrl_file)
68 #end for 80 #end for
69 $temp_factor.append( {str($g.groupName): $bam_controls} ) 81 #if len($peak_files.keys()) != len($bam_files.keys())
82 >&2 echo "Group $g.groupName: same number of Peak and Bam control files needs to be given" && exit 1 &&
83 #end if
84 $temp_factor.append( {str($g.groupName): [f[1] for f in sorted($bam_controls.items())]} )
70 #end if 85 #end if
71 86
72 #end for 87 #end for
73 88
74 $temp_factor.reverse() 89 $temp_factor.reverse()
303 Associated with each peakset are metadata relating to the experiment from which the peakset 318 Associated with each peakset are metadata relating to the experiment from which the peakset
304 was derived. Additionally, files containing mapped sequencing reads (BAM files) need to 319 was derived. Additionally, files containing mapped sequencing reads (BAM files) need to
305 be associated with each peakset (one for the ChIP data, and optionally another representing 320 be associated with each peakset (one for the ChIP data, and optionally another representing
306 a control sample) 321 a control sample)
307 322
323 Inputs for a group will be sorted by identifier before processing. For each group the corresponding
324 sets of peak and BAM files need to be provided. Ideally this is accomplished by providing the data in
325 collections.
326
327
308 **Groups** 328 **Groups**
309 329
310 You have to specify the name of the Group and the peak and BAM files for the two Groups you want to compare (e.g Resistant and Responsive) in the tool form above. 330 You have to specify the name of the Group and the peak and BAM files for the two Groups you want to compare (e.g Resistant and Responsive) in the tool form above.
311 331
312 Example: 332 Example: