# HG changeset patch
# User eduardo
# Date 1491745422 14400
# Node ID 8d0c12c9241d8ecc088a233cd3b1947fd2a5febe
# Parent  79d6bb2e6a5d0e50450b40b66fd0e85d2ef686d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mergegffs commit c9b4085466b82054831df7bb14a8ebe1fdc3e164-dirty

diff -r 79d6bb2e6a5d -r 8d0c12c9241d mergegffs.py
--- a/mergegffs.py	Sat Apr 08 18:17:27 2017 -0400
+++ b/mergegffs.py	Sun Apr 09 09:43:42 2017 -0400
@@ -23,18 +23,18 @@
 
 
         db = gffutils.create_db(args.peptides, dbfn=args.database, force=True, keep_order=True,merge_strategy='merge', sort_attribute_values=True)
-        if args.blastp == True:
-            os.system("blast2genomegff.py -b "+args.blastp+" -g  -d "+args.peptides+" -p blastp -t protein_match -T  -x > blastp.gff")
-            db=db.update(args.blastp)
-        if args.blastp == True:
-            os.system("convert2gff.py -i "+args.signalP+" -g "+args.peptides+" -T -t signalP > signalp.gff")
-            db=db.update(args.blastp)
-        if args.blastp == True:
-            os.system("convert2gff.py -i "+args.tmhmm+" -g "+args.peptides+" -T -t tmhmm > tmhmm.gff")
-            db=db.update(args.blastp)
-        if args.blastp == True:
+        if args.blastp is not None:
+            os.system("convert2gff.py -i "+args.blastp+" -g  "+args.peptides+" -p blastp -t protein_match -T  -x > blastp.gff")
+            db=db.update("blastp.gff")
+        if args.signalP is not None:
+            os.system("convert2gff.py -i "+args.signalP+" -g "+args.peptides+" -T -p signalP -t signalpep > signalp.gff")
+            db=db.update("signalP.gff")
+        if args.tmhmm is not None:
+            os.system("convert2gff.py -i "+args.tmhmm+" -g "+args.peptides+" -T -p tmhmm -t trans_helix > tmhmm.gff")
+            db=db.update("tmhmm.gff")
+        if args.pfam is not None:
             os.system("pfam2gff.py -i "+args.pfam+" -g "+args.peptides+" -T > PFAM.gff")
-            db=db.update(args.blastp)
+            db=db.update("PFAM.gff")
 
         with open(args.output, 'w') as fout:
             for f in db.all_features():
diff -r 79d6bb2e6a5d -r 8d0c12c9241d mergegffs.xml
--- a/mergegffs.xml	Sat Apr 08 18:17:27 2017 -0400
+++ b/mergegffs.xml	Sun Apr 09 09:43:42 2017 -0400
@@ -68,7 +68,7 @@
     <outputs>
         <data name="output" format="tabular" label="Merged gff" >
         </data>
-        <data name="sqlitedb" format="sqlite" from_work_dir="Trinotate.sqlite" label="Trinotate sqlite database" >
+        <data name="sqlitedb" format="sqlite"  label="Gffutils sqlite database" >
             <filter>keep_sqlite</filter>
         </data>
     </outputs>
diff -r 79d6bb2e6a5d -r 8d0c12c9241d tool_dependencies.xml
--- a/tool_dependencies.xml	Sat Apr 08 18:17:27 2017 -0400
+++ b/tool_dependencies.xml	Sun Apr 09 09:43:42 2017 -0400
@@ -4,7 +4,7 @@
     <repository changeset_revision="72c3d12f78a7" name="package_python_2_7_gffutils_0_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="genomegtftools" version="1.0">
-    <repository changeset_revision="3ba40e33a4f3" name="package_genomegtftools_1_0" owner="eduardo" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="4494aad6d1f3" name="package_genomegtftools_1_0" owner="eduardo" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="biopython" version="1.66">
     <repository changeset_revision="d86f7eb34488" name="package_biopython_1_66" owner="biopython" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />