Mercurial > repos > messersc > jamm
comparison jamm.xml @ 1:243f75d0ed6e draft default tip
Uploaded.
Includes new release 1.0.7 with fixed optional controls.
author | messersc |
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date | Thu, 19 Feb 2015 05:39:45 -0500 |
parents | d42f4d78c85e |
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0:d42f4d78c85e | 1:243f75d0ed6e |
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1 <tool id="jamm1.0.6rev2" name="JAMM" version="1.0.6.2"> | 1 <tool id="jamm" name="JAMM" version="1.0.7"> |
2 <description>Calls peaks on NGS data</description> | 2 <description>Calls peaks on NGS data</description> |
3 <requirements> | 3 <requirements> |
4 <!-- | 4 <requirement>R</requirement> |
5 <requirement type="package" version="2.5">b2g4pipe</requirement> | 5 <requirement>perl</requirement> |
6 --> | |
7 </requirements> | 6 </requirements> |
8 <command interpreter="python"> | 7 <command interpreter="python"> |
9 jammwrapper.py -i | 8 <![CDATA[ |
10 #for $x in $replicate | 9 jammwrapper.py -i |
11 ${x.input.file_name} | 10 #for $x in $input |
12 #end for | 11 ${x.replicate.file_name} #end for |
13 -g ${genomeSizeFile} | 12 |
14 -z $output | 13 #for $x in $control |
14 -c ${x.controlreplicate.file_name} #end for | |
15 | |
16 -g ${genomeSizeFile} | |
17 -o $output | |
18 -of $outputfiltered | |
15 -m $mode | 19 -m $mode |
16 -r $resolution | 20 -r $resolution |
17 -p $processes | 21 -p $processes |
22 -t $type | |
23 -f $fraglen | |
24 -b $binsize | |
25 ]]> | |
18 </command> | 26 </command> |
19 | 27 |
20 <stdio> | 28 <stdio> |
21 <!-- Wrapper ensures anything other than zero is an error --> | 29 <!-- Wrapper ensures anything other than zero is an error --> |
22 <exit_code range="1:" /> | 30 <exit_code range="1:" /> |
23 <exit_code range=":-1" /> | 31 <exit_code range=":-1" /> |
24 </stdio> | 32 </stdio> |
25 | 33 |
26 <inputs> | 34 <inputs> |
27 <repeat name="replicate" title="Replicate"> | 35 <repeat name="input" title="Sample Replicates"> |
28 <param name="input" type="data" format="bed"> | 36 <param name="replicate" type="data" format="bed"></param> |
29 </param> | 37 </repeat> |
30 </repeat> | 38 |
31 <param name="genomeSizeFile" type="data" label="File indicating chromosome sizes" description="Chromosome size"> | 39 <repeat name="control" title="Negative Control Replicates (e.g. input) - optional"> |
32 </param> | 40 <param name="controlreplicate" type="data" format="bed"></param> |
41 </repeat> | |
42 | |
43 <param name="genomeSizeFile" type="data" label="File indicating chromosome sizes" description="Chromosome size"></param> | |
33 <param name="mode" type="select" label="Mode (normal or narrow)"> | 44 <param name="mode" type="select" label="Mode (normal or narrow)"> |
34 <option value="normal">normal</option> | 45 <option value="normal">normal</option> |
35 <option value="narrow">narrow</option> | 46 <option value="narrow">narrow</option> |
36 </param> | 47 </param> |
37 <param name="resolution" type="select" label="Resolution (peak or region)"> | 48 <param name="resolution" type="select" label="Resolution (peak or region)"> |
38 <option value="peak">peak</option> | 49 <option value="peak">peak</option> |
39 <option value="region">region</option> | 50 <option value="region">region</option> |
51 <option value="window">window</option> | |
40 </param> | 52 </param> |
41 | 53 <param name="type" type="select" label="Type of data (Single or paired. Paired requires BEDPE datasets)"> |
42 <param name="processes" type="text" value="4" optional="true" help="Number of threads used by R" /> | 54 <option value="single" selected="true">single</option> |
55 <option value="paired">paired</option> | |
56 </param> | |
57 <param name="fraglen" type="text" value="ns" label="Fragment length. Estimated by default (ns)" /> | |
58 <param name="binsize" type="text" value="ns" label="Bin size. Estimated by default (ns)" /> | |
59 <param name="processes" type="text" value="4" label="Number of threads used by R" help="Depending on your Galaxy configuration, 1 should be safe and up to 4 should be fine." /> | |
60 | |
43 </inputs> | 61 </inputs> |
44 | 62 |
45 <outputs> | 63 <outputs> |
46 <data name="output" format="tabular" label="Narrowpeak tabular" /> | 64 <data name="output" format="tabular" label="Narrowpeak tabular" /> |
65 <data name="outputfiltered" format="tabular" label="Narrowpeak tabular filtered" /> | |
47 </outputs> | 66 </outputs> |
48 | 67 |
49 <tests> | 68 <tests> |
50 <test> | 69 <test> |
51 <param name="input" value="test1.bed" ftype="bed"/> | 70 <param name="replicate" value="test1.bed" ftype="bed"/> |
52 <param name="input" value="test2.bed" ftype="bed"/> | 71 <param name="replicate" value="test2.bed" ftype="bed"/> |
53 <param name="genomeSizeFile" value="chrSizes21.csize"/> | 72 <param name="genomeSizeFile" value="chrSizes21.csize"/> |
73 <output name="output" ftype="tabular"> | |
74 <assert_contents> | |
75 <has_text text="chr21" /> | |
76 </assert_contents> | |
77 </output> | |
78 </test> | |
79 <test> | |
80 <param name="replicate" value="test1.bed" ftype="bed"/> | |
81 <param name="replicate" value="test2.bed" ftype="bed"/> | |
82 <param name="controlreplicate" value="control.bed" /> | |
83 <param name="genomeSizeFile" value="chrSizes21.csize"/> | |
84 <param name="resolution" value="region" /> | |
54 <output name="output" ftype="tabular"> | 85 <output name="output" ftype="tabular"> |
55 <assert_contents> | 86 <assert_contents> |
56 <has_text text="chr21" /> | 87 <has_text text="chr21" /> |
57 </assert_contents> | 88 </assert_contents> |
58 </output> | 89 </output> |
62 <citations> | 93 <citations> |
63 <!-- Example of annotating a citation using a DOI. --> | 94 <!-- Example of annotating a citation using a DOI. --> |
64 <citation type="doi">10.1093/bioinformatics/btu568</citation> | 95 <citation type="doi">10.1093/bioinformatics/btu568</citation> |
65 </citations> | 96 </citations> |
66 <help> | 97 <help> |
67 .. class:: infomark | 98 **What it does** |
99 JAMM calls peaks on NGS data, i.e. for finding binding sites. | |
100 | |
101 .. class:: warningmark | |
68 | 102 |
69 This tool requires files in *bed* format. | 103 This tool requires files in *bed* format. |
70 | 104 |
71 ---- | 105 .. class:: infomark |
72 | 106 |
73 **What it does** | 107 If you are just starting out, you can find some sensible parameter choices here: |
74 JAMM calls peaks on NGS data, i.e. for finding binding sites. | 108 |
109 http://code.google.com/p/jamm-peak-finder/wiki/Usage#Examples | |
110 | |
111 * ChIP-Seq TF: everything default | |
112 * ChIP-Seq HM: Binsize=200 | |
113 * ChIP-Seq Broad HM: Binsize=200 Resolution=region | |
114 * ChIP-Seq Very Broad HM: Binsize=10000 Resolution=window | |
115 * DNase-seq: Fragment length=1 | |
75 </help> | 116 </help> |
76 </tool> | 117 </tool> |