comparison interproscan.xml @ 1:1685d3bea8d8 draft

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0:81eb6e8be5c2

    </command>
        <inputs>
            <param name="input" type="data" format="fasta" label="Protein Fasta File"/>

            <param name="appl" type="select" format="text" help="Select your programm.">
                <label>Applications to run ...</label>
                <option value="blastprodom+coils+gene3d+hamap+hmmpanther+hmmpir+hmmpfam+hmmsmart+hmmtigr+fprintscan+patternscan+profilescan+superfamily+seg+signalp+tmhmm" selected="true">all</option>
                <option value="seg">seg</option>
                <option value="signalp">signalp</option>
                <option value="tmhmm">tmhmm</option>
                <option value="fprintscan">fprintscan</option>

                <option value="hmmpanther">hmmpanther</option>
                <option value="hamap">hamap</option>
                <option value="gene3d">gene3d</option>
                <option value="coils">coils</option>
                <option value="blastprodom">blastprodom</option>
            </param> 

            <param name="oformat" type="select" label="Output format" help="Please select a output format.">
                <option value="gff" selected="true">gff</option>
                <option value="raw">raw</option>
                <option value="txt">txt</option>
                <option value="html">html</option>
                <option value="xml">xml</option>
                <option value="ebixml">EBI header on top of xml</option>
            </param>

 (SignalP v3) and TM helices (TMHMM v2) are supported (See the FAQs file
 for details).

**GENE3D**::

 Gene3D is supplementary to the CATH database. This protein sequence database
 contains proteins from complete genomes which have been clustered into protein
 families and annotated with CATH domains, Pfam domains and functional
 information from KEGG, GO, COG, Affymetrix and STRINGS.
 hmmpfam from the HMM2.3.2 package (by Sean Eddy,
 [e-mail], http://hmmer.wustl.edu).

**PANTHER**::

 The PANTHER (Protein ANalysis THrough Evolutionary Relationships)
 Classification System was designed to classify proteins (and their genes)
 in order to facilitate high-throughput analysis.
 hmmsearch from the HMM2.3.2 package (by Sean Eddy,
 [e-mail], http://hmmer.wustl.edu).
 and blastall from the Blast package (Altschul S.F. et al., 1997).

----------
References
----------

InterPro: the integrative protein signature database.
Nucleic Acids Research 37 (Database Issue), D224-228.
http://dx.doi.org/10.1093/nar/gkn785


Galaxy Wrapper Author:

*  Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
*  Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter

    </help>
</tool>

1:1685d3bea8d8

    </command>
        <inputs>
            <param name="input" type="data" format="fasta" label="Protein Fasta File"/>

            <param name="appl" type="select" format="text" label="Applications to run" help="Select your programm.">
                <option value="blastprodom+coils+gene3d+hamap+hmmpanther+hmmpir+hmmpfam+hmmsmart+hmmtigr+fprintscan+patternscan+profilescan+superfamily+seg+signalp+tmhmm" selected="true">all</option>
                <option value="seg">seg</option>
                <option value="signalp">signalp</option>
                <option value="tmhmm">tmhmm</option>
                <option value="fprintscan">fprintscan</option>

                <option value="hmmpanther">hmmpanther</option>
                <option value="hamap">hamap</option>
                <option value="gene3d">gene3d</option>
                <option value="coils">coils</option>
                <option value="blastprodom">blastprodom</option>
            </param>

            <param name="oformat" type="select" label="Output format" help="Please select a output format.">
                <option value="gff">gff</option>
                <option value="raw" selected="true">raw</option>
                <option value="txt">txt</option>
                <option value="html">html</option>
                <option value="xml">xml</option>
                <option value="ebixml">EBI header on top of xml</option>
            </param>

 (SignalP v3) and TM helices (TMHMM v2) are supported (See the FAQs file
 for details).

**GENE3D**::

  Gene3D is supplementary to the CATH database. This protein sequence database
  contains proteins from complete genomes which have been clustered into protein
  families and annotated with CATH domains, Pfam domains and functional
  information from KEGG, GO, COG, Affymetrix and STRINGS.
  hmmpfam from the HMM2.3.2 package (by Sean Eddy,
  [e-mail], http://hmmer.wustl.edu).

**PANTHER**::

  The PANTHER (Protein ANalysis THrough Evolutionary Relationships)
  Classification System was designed to classify proteins (and their genes)
  in order to facilitate high-throughput analysis.
  hmmsearch from the HMM2.3.2 package (by Sean Eddy,
  [e-mail], http://hmmer.wustl.edu).
  and blastall from the Blast package (Altschul S.F. et al., 1997).

----------
References
----------

InterPro: the integrative protein signature database.
Nucleic Acids Research 37 (Database Issue), D224-228.
http://dx.doi.org/10.1093/nar/gkn785


**Galaxy Wrapper Author**::

    *  Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
    *  Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter

    </help>
</tool>