Mercurial > repos > bgruening > diffbind
comparison diffbind.xml @ 17:2605cbdaa7d8 draft
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 | f907216064f6 |
comparison
equal
deleted
inserted
replaced
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: |