diff interpro/paso4.xml @ 0:c342ebb50f0b draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/interpro/paso4.xml	Thu May 22 05:09:07 2014 -0400
@@ -0,0 +1,68 @@
+<tool id="DLaGiFer_3" name="Common attributes selection" version="1.0.0">
+    <description>Extraction of common sequences attributes</description>
+    <command interpreter="perl">
+    paso4.pl "$infile" "$outfile"
+    </command>
+
+         <inputs>
+            <param name="infile" type="data" format="gff" label="Sequence in Fasta File"/>
+
+          
+           </inputs>
+	<outputs><data format="txt" name="outfile"/>
+	</outputs>
+
+<stdio><exit_code range="1:" level="fatal" description="Error" /></stdio>
+    <help>
+
+
+**What it does**
+
+This tool obtains certain common attributes of the sequences contained in a gff3 format file.  
+
+
+**Dependencies**
+
+Perl is required for running this tool.
+
+
+
+#####
+Input
+#####
+
+A gff3 file with protein attributes is required.  
+
+Generic Feature Format Version 3 (GFF3)
+
+The GFF3 format is a flat tab-delimited file, which is much richer then the TSV output format. It allows you to trace back from matches to predicted proteins and to nucleic acid sequences. It also contains a FASTA format representation of the predicted protein sequences and their matches. You will find a documentation of all the columns and attributes used on [http://www.sequenceontology.org/gff3.shtml].
+
+
+######
+Output
+######
+
+
+A text file is generated by this tool.
+
+Example Output
+--------------
+
+The common atributes of the sequences Q0KIY3 P02185 P02178 Q0KIY5 Q0KIY1 are:
+
+For Name atribute: SSF46458 PF00042 PR00613 G3DSA:1.10.490.10 PS01033
+
+For Ontology_term atribute: "GO:0005506" "GO:0020037" "GO:0015671" "GO:0019825"
+
+For Dbxref atribute: "InterPro:IPR009050" "InterPro:IPR000971" "InterPro:IPR002335" "InterPro:IPR012292"  
+
+
+
+**Galaxy Wrapper Authors**::
+
+    * Laura Entrambasaguas
+    * Ginés Almagro
+    * Fernando Pérez
+
+    </help>
+</tool>