# HG changeset patch
# User jjohnson
# Date 1523375524 14400
# Node ID af5f22779a8ece40f67ce5ea30083dbee21e598a
# Parent  a96b2754171c60833660d65aa239114defc15833
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit d65efea03eb2db8a43e64599a4f899ead1a252ba-dirty

diff -r a96b2754171c -r af5f22779a8e mzsqlite_psm_align.py
--- a/mzsqlite_psm_align.py	Tue Apr 10 10:55:22 2018 -0400
+++ b/mzsqlite_psm_align.py	Tue Apr 10 11:52:04 2018 -0400
@@ -409,7 +409,7 @@
         '-r', '--reads_bam', default=None,
         help='reads alignment bam path')
     parser.add_argument(
-        '-g', '--gffutils_file', default=None,
+        '-g', '--gffutils_sqlite', default=None,
         help='gffutils GTF sqlite DB')
     parser.add_argument(
         '-B', '--probed', default=None,
@@ -443,9 +443,9 @@
 
     probed = open(args.probed,'w') if args.probed else sys.stdout
     
-    gff_cursor = get_connection(args.gffutils_file).cursor() if args.gffutils_file else None
+    gff_cursor = get_connection(args.gffutils_sqlite).cursor() if args.gffutils_sqlite else None
     map_cursor = get_connection(args.genomic_mapping_sqlite).cursor()
-    mz_cursor = get_connection(args.mzsqlite_file).cursor()
+    mz_cursor = get_connection(args.mzsqlite).cursor()
 
     unmapped_accs = set()
     timings = dict()
@@ -656,7 +656,8 @@
                     add_time('GENOMIC_POS_QUERY',te - ts)
                 except:
                     unmapped_accs.add(acc)
-                    print('Unmapped: %s' % acc, file=sys.stderr)
+                    if args.debug:
+                        print('Unmapped: %s' % acc, file=sys.stderr)
             return len(locations)
         return -1
         
@@ -729,7 +730,8 @@
                     bases.append(list(set([c[i] for c in aa_codon_map[aa]])))
                 else:
                     bases.append([b for b, cnt in reversed(sorted(pileup[idx + i]['bases'].iteritems(), key=lambda (k,v): (v,k)))])
-                print('%s' % bases)
+                if args.debug:
+                    print('%s' % bases,file=sys.stderr)
             for b0 in bases[0]:
                 if b0 not in aa_na_map[aa]:
                     continue
@@ -812,7 +814,7 @@
     'XG' : 'A', #Peptide type
     'XU' : 'Z', #URI
     """
-    psm_cursor = get_connection(args.mzsqlite_file).cursor()
+    psm_cursor = get_connection(args.mzsqlite).cursor()
     ts = time()
     psms = psm_cursor.execute(PSM_QUERY)
     te = time()   
diff -r a96b2754171c -r af5f22779a8e mzsqlite_psm_align.xml
--- a/mzsqlite_psm_align.xml	Tue Apr 10 10:55:22 2018 -0400
+++ b/mzsqlite_psm_align.xml	Tue Apr 10 11:52:04 2018 -0400
@@ -7,6 +7,10 @@
         <requirement type="package">gffutils</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+        #if $readlignments:
+            ln -s -f '${$readlignments}' 'input.bam' &&
+            ln -s -f '${$readlignments.metadata.bam_index}' 'input.bam.bai' &&
+        #end if
         python '$__tool_directory__/mzsqlite_psm_align.py'  
             #if $ref.ref_source == 'cached':
                 --twobit='$ref.ref_loc.fields.path'
@@ -17,7 +21,7 @@
                 --gffutils_file '$gffutilsdb'
             #end if
             #if $readlignments:
-                --reads_bam '$readlignments'
+                --reads_bam 'input.bam'
             #end if
             #if 'probed' in str($output_formats).split(','):
                --probed '$probed'
@@ -62,13 +66,13 @@
         </param>
     </inputs>
     <outputs>
-        <data name="prosam" format="sam">
+        <data name="prosam" format="sam" label="pro.SAM on ${on_string}">
             <filter>'prosam' in output_formats</filter>
         </data>
-        <data name="probam" format="pro.bam">
+        <data name="probam" format="bam" label="pro.Bam on ${on_string}">
             <filter>'probam' in output_formats</filter>
         </data>
-        <data name="probed" format="pro.bed">
+        <data name="probed" format="bed" label="pro.Bed on ${on_string}">
             <filter>'probed' in output_formats</filter>
         </data>
     </outputs>