Mercurial > repos > bgruening > diffbind
comparison diffbind.xml @ 3:d6dcb3dd5f8f draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
author | bgruening |
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date | Tue, 08 Mar 2016 08:13:00 -0500 |
parents | 492d5ac7b2e2 |
children | 69138bfd8644 |
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2:492d5ac7b2e2 | 3:d6dcb3dd5f8f |
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1 <tool id="diffbind" name="DiffBind" version="2.0.2"> | 1 <tool id="diffbind" name="DiffBind" version="2.1.0"> |
2 <description> differential binding analysis of ChIP-Seq peak data</description> | 2 <description> differential binding analysis of ChIP-Seq peak data</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="binary">Rscript</requirement> | 4 <requirement type="binary">Rscript</requirement> |
5 <requirement type="R-module">DESeq2</requirement> | 5 <requirement type="R-module">DESeq2</requirement> |
6 <requirement type="package" version="3.0.3">R</requirement> | 6 <requirement type="package" version="3.0.3">R</requirement> |
7 <requirement type="package" version="1.2.10">deseq2</requirement> | 7 <requirement type="package" version="1.2.10">deseq2</requirement> |
8 <requirement type="package" version="1.8.3">diffbind</requirement> | 8 <requirement type="package" version="1.8.3">diffbind</requirement> |
9 </requirements> | 9 </requirements> |
10 <command> | |
11 <![CDATA[ | |
12 ## seems that diffbind also needs file extensions to work properly | |
13 #set $counter = 1 | |
14 #for $sample in $samples: | |
15 ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# && | |
16 ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# && | |
17 ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# && | |
18 ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# && | |
19 #set $counter = $counter + 1 | |
20 #end for | |
21 | |
22 Rscript $__tool_directory__/diffbind.R | |
23 -i $infile | |
24 -o $outfile | |
25 -p $plots | |
26 -f $format | |
27 ]]> | |
28 </command> | |
29 <stdio> | 10 <stdio> |
30 <regex match="Execution halted" | 11 <regex match="Execution halted" |
31 source="both" | 12 source="both" |
32 level="fatal" | 13 level="fatal" |
33 description="Execution halted." /> | 14 description="Execution halted." /> |
38 <regex match="Error in" | 19 <regex match="Error in" |
39 source="both" | 20 source="both" |
40 level="fatal" | 21 level="fatal" |
41 description="An undefined error occured, please check your intput carefully and contact your administrator." /> | 22 description="An undefined error occured, please check your intput carefully and contact your administrator." /> |
42 </stdio> | 23 </stdio> |
24 <command> | |
25 <![CDATA[ | |
26 ## seems that diffbind also needs file extensions to work properly | |
27 #set $counter = 1 | |
28 #for $sample in $samples: | |
29 ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# && | |
30 ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# && | |
31 #if str( $sample.bamcontrol ) != 'None': | |
32 ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# && | |
33 ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# && | |
34 #end if | |
35 #set $counter = $counter + 1 | |
36 #end for | |
37 | |
38 Rscript $__tool_directory__/diffbind.R | |
39 -i $infile | |
40 -o $outfile | |
41 -p $plots | |
42 -f $format | |
43 ]]> | |
44 </command> | |
45 <configfiles> | |
46 <configfile name="infile"> | |
47 #set $counter = 1 | |
48 #for $sample in $samples: | |
49 #if str( $sample.bamcontrol ) != 'None' and $counter == 1: | |
50 SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks | |
51 #elif $counter == 1: | |
52 SampleID,Tissue,Factor,Condition,Replicate,bamReads,Peaks | |
53 #end if | |
54 #if str( $sample.bamcontrol ) != 'None': | |
55 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + '_bamreads.bam'#,#echo str($counter) + '_bamcontrol.bam'#,$sample.peaks | |
56 #else: | |
57 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + '_bamreads.bam'#,$sample.peaks | |
58 #end if | |
59 #set $counter = $counter + 1 | |
60 #end for | |
61 </configfile> | |
62 </configfiles> | |
43 <inputs> | 63 <inputs> |
44 <repeat name="samples" title="Samples" min="2"> | 64 <repeat name="samples" title="Samples" min="2"> |
45 <param name="sample_id" type="text" value="Sample ID" label="Specify a sample id" help="e.g. BT474.1-" /> | 65 <param name="sample_id" type="text" value="Sample ID" label="Specify a sample id" help="e.g. BT474.1-" /> |
46 <param name="tissue" type="text" value="Tissue" label="Specify the tissue" help="e.g. BT474" /> | 66 <param name="tissue" type="text" value="Tissue" label="Specify the tissue" help="e.g. BT474" /> |
47 <param name="factor" type="text" value="Factor Name" label="Specify a factor name" help="e.g. ER" /> | 67 <param name="factor" type="text" value="Factor Name" label="Specify a factor name" help="e.g. ER" /> |
48 <param name="condition" type="text" value="Condition" label="Specify the condition" help="e.g. Resistent" /> | 68 <param name="condition" type="text" value="Condition" label="Specify the condition" help="e.g. Resistent" /> |
49 <param name="replicate" type="integer" value="1" label="Specify the replicate number" help="e.g. 1" /> | 69 <param name="replicate" type="integer" value="1" label="Specify the replicate number" help="e.g. 1" /> |
50 <param format="bam" name="bamreads" type="data" label="Read BAM file" help="Specify the Read BAM file, used for Peak calling."/> | 70 <param format="bam" name="bamreads" type="data" label="Read BAM file" help="Specify the Read BAM file, used for Peak calling."/> |
51 <param format="bam" name="bamcontrol" type="data" label="Control BAM file" help="Specify the Control BAM file, used for Peak calling."/> | 71 <param format="bam" name="bamcontrol" type="data" optional="True" label="Control BAM file" help="If specifying a control BAM file for this sample, then all samples are required to specify one."/> |
52 <param format="bed" name="peaks" type="data" label="Peak file" help="Result of your Peak calling experiment."/> | 72 <param format="bed" name="peaks" type="data" label="Peak file" help="Result of your Peak calling experiment."/> |
53 </repeat> | 73 </repeat> |
54 <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true" | 74 <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true" |
55 label="Visualising the analysis results" | 75 label="Visualising the analysis results" |
56 help="output an additional PDF files" /> | 76 help="output an additional PDF files" /> |
58 <option value="bed">BED</option> | 78 <option value="bed">BED</option> |
59 <option value="gff">GFF</option> | 79 <option value="gff">GFF</option> |
60 <option value="wig">WIG</option> | 80 <option value="wig">WIG</option> |
61 </param> | 81 </param> |
62 </inputs> | 82 </inputs> |
63 <configfiles> | |
64 <configfile name="infile"> | |
65 SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks | |
66 #set $counter = 1 | |
67 #for $sample in $samples: | |
68 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + '_bamreads.bam'#,#echo str($counter) + '_bamcontrol.bam'#,$sample.peaks | |
69 #set $counter = $counter + 1 | |
70 #end for | |
71 </configfile> | |
72 </configfiles> | |
73 <outputs> | 83 <outputs> |
74 <data format="bed" name="outfile" label="Differential binding sites on ${on_string}"> | 84 <data format="bed" name="outfile" label="Differential binding sites on ${on_string}"> |
75 <change_format> | 85 <change_format> |
76 <when input="format" value="wig" format="wig" /> | 86 <when input="format" value="wig" format="wig" /> |
77 <when input="format" value="gff" format="gff" /> | 87 <when input="format" value="gff" format="gff" /> |
79 </data> | 89 </data> |
80 <data format="pdf" name="plots" label="Differential binding sites on ${on_string}"> | 90 <data format="pdf" name="plots" label="Differential binding sites on ${on_string}"> |
81 <filter>pdf == True</filter> | 91 <filter>pdf == True</filter> |
82 </data> | 92 </data> |
83 </outputs> | 93 </outputs> |
84 | |
85 <help> | 94 <help> |
86 <![CDATA[ | 95 <![CDATA[ |
87 | 96 |
97 What it does | |
98 ************ | |
88 | 99 |
89 **What it does** | 100 Diffbind provides functions for processing ChIP-Seq data enriched for genomic loci where specific protein/DNA binding occurs, including peak sets identified by ChIP-Seq peak callers and aligned sequence read datasets. |
90 | 101 |
91 Diffbind provides functions for processing ChIP-Seq data enriched for genomic loci where specific protein/DNA binding occurs, including peak sets identified by ChIP-Seq peak callers and aligned sequence read datasets. | 102 Input |
103 ***** | |
92 | 104 |
93 **Input** | 105 * You have to specify your samples. Here is one example:: |
94 | 106 |
95 - You have to specify your samples. Here is one example: | 107 ID Tissue Factor Condition Treatment Replicate Caller Intervals |
108 BT4741 BT474 ER Resistant Full-Media 1 raw 1084 | |
96 | 109 |
97 ID Tissue Factor Condition Treatment Replicate Caller Intervals | 110 * BAM file which contains the mapped sequencing reads can be associated with each peakset |
98 BT4741 BT474 ER Resistant Full-Media 1 raw 1084 | 111 * Control BAM file represents a control dataset and are optional, but have to specified for all when used. |
112 * Peak file: Result of your Peak calling experiment | |
99 | 113 |
100 - BAM file which contains the mapped sequencing reads can be associated with each | 114 Output |
101 peakset | 115 ****** |
102 | |
103 - Control BAM file represents a control dataset | |
104 | |
105 - Peak file: Result of your Peak calling experiment | |
106 | |
107 | |
108 **Output** | |
109 | 116 |
110 As output format you can choose BED, GFF, WIG. | 117 As output format you can choose BED, GFF, WIG. |
111 | 118 |
112 | 119 References |
113 **References** | 120 ********** |
114 | 121 |
115 DiffBind_ Authors: Rory Stark, Gordon Brown (2011) | 122 DiffBind_ Authors: Rory Stark, Gordon Brown (2011) |
116 | 123 |
117 .. _DiffBind: http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html | 124 .. _DiffBind: http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html |
118 | 125 |
119 Wrapper authors: Bjoern Gruening, Pavankumar Videm | 126 Wrapper authors: Bjoern Gruening, Pavankumar Videm |
120 | 127 |
121 ]]> | 128 ]]> |
122 </help> | 129 </help> |
130 <citations> | |
131 <citation type="doi">doi:10.1038/nature10730</citation> | |
132 </citations> | |
123 </tool> | 133 </tool> |