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The arguments of the command line application have the following meaning: | The arguments of the command line application have the following meaning: | ||
<table border=0 cellpadding=10 align="center"> | |||
<tr> | |||
<td>name</td> | |||
<td>comment</td> | |||
<td>type</td> | |||
</tr> | |||
<tr><td colspan=3><hr></td></tr> | |||
<tr> | |||
<td><font color="green">home</font></td> | |||
<td>Home directory (The path to the directory containing the input file. Output files are written to this directory as well., default = ./)</td> | |||
<td>String</td> | |||
</tr> | |||
<tr> | |||
<td><font color="green">data</font></td> | |||
<td>Input file (The file name of the file containing the input sequences in annotated FastA format (see readme))</td> | |||
<td>String</td> | |||
</tr> | |||
<tr> | |||
<td><font color="green">infix</font></td> | |||
<td>Infix (a infix to be used for all output files (model, sequence logos, predicted binding sites))</td> | |||
<td>String</td> | |||
</tr> | |||
<tr> | |||
<td><font color="green">motifLength</font></td> | |||
<td>Position tag (The tag for the position information in the FastA-annotation of the input file)</td> | |||
<td>String</td> | |||
</tr> | |||
<tr> | |||
<td><font color="green">starts</font></td> | |||
<td>Value tag (The tag for the value information in the FastA-annotation of the input file)</td> | |||
<td>String</td> | |||
</tr> | |||
<tr> | |||
<td><font color="green">motifOrder</font></td> | |||
<td>Weighting factor (The value for weighting the data; either a value between 0 and 1, or a description relative to the standard deviation (e.g. +4sd), default = 0.2)</td> | |||
<td>Double</td> | |||
</tr> | |||
<tr> | |||
<td><font color="green">bgOrder</font></td> | |||
<td>Starts (The number of pre-optimization runs., valid range = [1, 100], default = 20)</td> | |||
<td>Integer</td> | |||
</tr> | |||
<tr> | |||
<td><font color="green">position</font></td> | |||
<td>Initial motif width (The motif width that is used initially, may be adjusted during optimization., valid range = [1, 50], default = 15)</td> | |||
<td>Integer</td> | |||
</tr> | |||
<tr> | |||
<td><font color="green">value</font></td> | |||
<td>Markov order of motif model (The Markov order of the model for the motif., valid range = [0, 3], default = 0)</td> | |||
<td>Integer</td> | |||
</tr> | |||
<tr> | |||
<td><font color="green">weightingFactor</font></td> | |||
<td>Markov order of background model (The Markov order of the model for the background sequence and the background sequence, -1 defines uniform distribution., valid range = [-1, 5], default = -1)</td> | |||
<td>Integer</td> | |||
</tr> | |||
<tr> | |||
<td><font color="green">ess</font></td> | |||
<td>Equivalent sample size (Reflects the strength of the prior on the model parameters., valid range = [0.0, Infinity], default = 4.0)</td> | |||
<td>Double</td> | |||
</tr> | |||
<tr> | |||
<td><font color="green">delete</font></td> | |||
<td>Delete BSs from profile (A switch for deleting binding site positions of discovered motifs from the profile before searching for futher motifs., default = true)</td> | |||
<td>Boolean</td> | |||
</tr> | |||
<tr> | |||
<td><font color="green">threads</font></td> | |||
<td>Compute threads (The number of threads that are use to evaluate the objective function and its gradient., valid range = [1, 128], OPTIONAL)</td> | |||
<td>Integer</td> | |||
</tr> | |||
</table> | |||
Revision as of 11:23, 5 January 2013
by Jan Grau, Stefan Posch, Ivo Grosse, and Jens Keilwagen
ChIPper is a universal tool for de-novo motif discovery. ChIPper has successfully been applied to ChIP-seq, ChIP-exo and protein-binding microarray (PBM) data.
We provide ChIPper as a public web-server, a web-application that can be installed in a local Galaxy server, and as a command line program.
ChIPper web-server
ChIPper is available as a public web-server at galaxy.informatik.uni-halle.de.
Download
ChIPper is implemented in Java using Jstacs. You can download the command line application as a Jar. In addition, we provide the Jar of the Galaxy web-application for installing it in your local Galaxy server.
ChIPper will be part of the next public release of the Jstacs library.
Running the command line application
For running the command line application, Java v1.6 or later is required.
The arguments of the command line application have the following meaning:
| name | comment | type |
| home | Home directory (The path to the directory containing the input file. Output files are written to this directory as well., default = ./) | String |
| data | Input file (The file name of the file containing the input sequences in annotated FastA format (see readme)) | String |
| infix | Infix (a infix to be used for all output files (model, sequence logos, predicted binding sites)) | String |
| motifLength | Position tag (The tag for the position information in the FastA-annotation of the input file) | String |
| starts | Value tag (The tag for the value information in the FastA-annotation of the input file) | String |
| motifOrder | Weighting factor (The value for weighting the data; either a value between 0 and 1, or a description relative to the standard deviation (e.g. +4sd), default = 0.2) | Double |
| bgOrder | Starts (The number of pre-optimization runs., valid range = [1, 100], default = 20) | Integer |
| position | Initial motif width (The motif width that is used initially, may be adjusted during optimization., valid range = [1, 50], default = 15) | Integer |
| value | Markov order of motif model (The Markov order of the model for the motif., valid range = [0, 3], default = 0) | Integer |
| weightingFactor | Markov order of background model (The Markov order of the model for the background sequence and the background sequence, -1 defines uniform distribution., valid range = [-1, 5], default = -1) | Integer |
| ess | Equivalent sample size (Reflects the strength of the prior on the model parameters., valid range = [0.0, Infinity], default = 4.0) | Double |
| delete | Delete BSs from profile (A switch for deleting binding site positions of discovered motifs from the profile before searching for futher motifs., default = true) | Boolean |
| threads | Compute threads (The number of threads that are use to evaluate the objective function and its gradient., valid range = [1, 128], OPTIONAL) | Integer |
Installing the web-application
The command-line program behind the web-application is a Jar as well, so Java is required on the server running Galaxy.
To install this command line program in Galaxy, copy it to the desired destination in the Galaxy tools directory.
The command line application writes its Galaxy tool definition file itself. If you are in the directory containing the command-line program for Galaxy, you can create the tool definition file by calling
java -jar ChIPperWeb.jar --create ChIPperWeb.xml
Afterwards, this directory contains the tool definition file ChIPperWeb.xml. Now you can register ChIPper in the Galaxy tool_conf.xml file. For details, see the Galaxy tutorial for adding new tools.
