Mercurial > repos > bgruening > iprscan

changeset 1:1685d3bea8d8 draft

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Uploaded
author bgruening
date Sun, 23 Jun 2013 07:39:13 -0400
parents 81eb6e8be5c2
children 32ae2da3a3e4
files interproscan.xml
diffstat 1 files changed, 19 insertions(+), 20 deletions(-) [+]
line wrap: on
line diff
--- a/interproscan.xml	Sun Jun 23 07:19:14 2013 -0400
+++ b/interproscan.xml	Sun Jun 23 07:39:13 2013 -0400
@@ -26,8 +26,7 @@
         <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>
+            <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>
@@ -45,11 +44,11 @@
                 <option value="gene3d">gene3d</option>
                 <option value="coils">coils</option>
                 <option value="blastprodom">blastprodom</option>
-            </param> 
+            </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="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>
@@ -207,21 +206,21 @@
 
 **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,
- eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
+  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,
+  eddy@genetics.wustl.edu, 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,
- eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
- and blastall from the Blast package (Altschul S.F. et al., 1997).
+  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,
+  eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
+  and blastall from the Blast package (Altschul S.F. et al., 1997).
 
 ----------
 References
@@ -243,10 +242,10 @@
 http://dx.doi.org/10.1093/nar/gkn785
 
 
-Galaxy Wrapper Author:
+**Galaxy Wrapper Author**::
 
-*  Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
-*  Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
+    *  Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
+    *  Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
 
     </help>
 </tool>