# HG changeset patch
# User greg
# Date 1509368358 14400
# Node ID bbfecb0ebe756347747c2c007f594be9b63688d8
# Parent  9f769f79ff1897f42d14f430399762bdde15e80e
Uploaded

diff -r 9f769f79ff18 -r bbfecb0ebe75 test-data/20.faa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/20.faa	Mon Oct 30 08:59:18 2017 -0400
@@ -0,0 +1,3 @@
+>contig_9
+XLRLKADEEAQCLNQMQRIIFDEIMEHVELEKGGFYFVYRPGGNGKTLWLAIISKLRSEGRIVLAVASSGIALLLVEGGR
+TAHSRFKIPIDVNEYNNCEIKQNIYLAELICHTNLVIWDEAPMTQYFVFEAVX
diff -r 9f769f79ff18 -r bbfecb0ebe75 test-data/20.fna
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/20.fna	Mon Oct 30 08:59:18 2017 -0400
@@ -0,0 +1,6 @@
+>contig_9
+NNACTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATTTTTGATGAAATTATGGAGCA
+TGTGGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGCCCTGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCT
+CAAAACTGAGAAGCGAGGGTAGAATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGA
+ACAGCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATTAAACAGAACATCTACCTCGC
+TGAACTTATATGTCACACCAATTTGGTCATTTGGGATGAGGCACCTATGACTCAATATTTTGTCTTTGAGGCGGTTGAN
diff -r 9f769f79ff18 -r bbfecb0ebe75 test-data/3494.faa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3494.faa	Mon Oct 30 08:59:18 2017 -0400
@@ -0,0 +1,3 @@
+>contig_10
+MAEENTTTMNLDLNLGPINNSSDDSEPSSRPYTDVAMNLEDWLDSPVRVREVVRHRNHRWRSLWRQIPIPPDTRNLALEL
+IGGNAP
diff -r 9f769f79ff18 -r bbfecb0ebe75 test-data/3494.fna
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3494.fna	Mon Oct 30 08:59:18 2017 -0400
@@ -0,0 +1,5 @@
+>contig_10
+ATGGCAGAAGAGAACACCACTACAATGAACCTCGATCTCAATTTGGGCCCCATCAATAACTCAAGCGACGATAGCGAACC
+TTCATCACGCCCTTATACTGATGTCGCAATGAACTTGGAAGATTGGTTAGATAGTCCCGTCCGAGTTCGTGAAGTCGTCC
+GCCACAGAAATCATAGGTGGCGCTCTTTGTGGCGCCAAATCCCAATTCCGCCTGATACGCGAAACCTCGCGCTCGAATTA
+ATCGGCGGCAATGCCCCN
diff -r 9f769f79ff18 -r bbfecb0ebe75 test-data/3722.faa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3722.faa	Mon Oct 30 08:59:18 2017 -0400
@@ -0,0 +1,3 @@
+>contig_7
+ENEWSGAEFLNEMAAMMTQNKSNENGTGTFEELQQLFDEMFQSDIESFNGCSSSSNETCSNSNKRNSIESSSANFRPENG
+NESGEISGKKNTRKGKGDX
diff -r 9f769f79ff18 -r bbfecb0ebe75 test-data/3722.fna
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3722.fna	Mon Oct 30 08:59:18 2017 -0400
@@ -0,0 +1,5 @@
+>contig_7
+GAGAATGAGTGGTCTGGGGCTGAGTTTTTGAATGAAATGGCGGCAATGATGACTCAAAATAAATCCAATGAAAACGGAAC
+CGGAACTTTTGAAGAACTGCAACAATTGTTCGATGAAATGTTTCAGAGCGACATCGAGTCCTTCAATGGTTGTTCTTCAT
+CATCCAATGAAACATGTAGCAACTCGAACAAGAGGAATTCCATTGAGTCGAGCTCGGCTAATTTCAGACCCGAAAATGGA
+AACGAAAGCGGCGAGATTAGCGGGAAGAAGAATACTAGGAAAGGTAAAGGTGACGNN
diff -r 9f769f79ff18 -r bbfecb0ebe75 test-data/38889.faa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/38889.faa	Mon Oct 30 08:59:18 2017 -0400
@@ -0,0 +1,4 @@
+>contig_2
+XLSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEK
+WVTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAAS
+QLLNYVRFDD
diff -r 9f769f79ff18 -r bbfecb0ebe75 test-data/38889.fna
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/38889.fna	Mon Oct 30 08:59:18 2017 -0400
@@ -0,0 +1,8 @@
+>contig_2
+NNCCTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCAGCAGACGA
+CTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACC
+TCATGTTGCTTGGAATGGGGCCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAA
+TGGGTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAACTCGGCTTC
+GGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGC
+CGGGTGAGACTCCTTTGCCTTGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCA
+CAACTGTTAAATTATGTGCGCTTTGATGAT
diff -r 9f769f79ff18 -r bbfecb0ebe75 test-data/39614.faa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/39614.faa	Mon Oct 30 08:59:18 2017 -0400
@@ -0,0 +1,3 @@
+>contig_3
+XVDEGVVVAGLSEQEKASVSEILTTARAHSETIENLKRDHSQQVSCIEQHTNDTFRQKYMDYEPTGSTPVRSEPDIPSKG
+TIESLRAMPIDALEEEFRENHSYESAVTGKELMPSVTTRAPFSQIN
diff -r 9f769f79ff18 -r bbfecb0ebe75 test-data/39614.fna
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/39614.fna	Mon Oct 30 08:59:18 2017 -0400
@@ -0,0 +1,6 @@
+>contig_3
+NNTGTGGATGAAGGAGTTGTTGTTGCTGGCTTGTCAGAGCAGGAGAAGGCATCTGTTTCTGAAATTCTGACAACTGCTAG
+AGCTCATTCAGAAACAATTGAGAACCTTAAGAGAGATCATTCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATA
+CTTTCAGGCAAAAATACATGGATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGATATTCCCAGCAAAGGC
+ACAATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAAGAATTTCGAGAAAACCATTCATACGAATCTGCTGT
+TACAGGAAAGGAACTAATGCCGTCTGTTACGACTCGTGCACCATTTTCACAGATCAAC
diff -r 9f769f79ff18 -r bbfecb0ebe75 test-data/5235.faa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/5235.faa	Mon Oct 30 08:59:18 2017 -0400
@@ -0,0 +1,3 @@
+>contig_1
+XKKLYGDKEDILVPDIFWDYTSGKVLTMEWVEGVKLNEQDAVESQGLSVLDLVNTGIQCSLRQLLEYGYFHADPHPGNLL
+ATPDGKLAFLDFGMMSETPEQARSAIIGHVVHMVNR
diff -r 9f769f79ff18 -r bbfecb0ebe75 test-data/5235.fna
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/5235.fna	Mon Oct 30 08:59:18 2017 -0400
@@ -0,0 +1,6 @@
+>contig_1
+NTTAAAAAATTATATGGAGACAAGGAAGATATCCTTGTCCCAGATATTTTCTGGGATTACACGAGTGGAAAGGTGCTAAC
+AATGGAGTGGGTTGAAGGTGTTAAATTAAATGAGCAAGATGCCGTTGAGAGTCAAGGGCTCAGTGTTCTGGATCTGGTGA
+ATACCGGCATACAGTGCAGTCTTCGACAGCTGCTTGAGTACGGCTATTTTCATGCAGATCCTCACCCAGGGAATCTCTTA
+GCTACACCTGACGGGAAGCTTGCTTTTCTTGATTTTGGAATGATGAGTGAGACTCCTGAACAAGCAAGATCGGCCATAAT
+TGGTCATGTTGTACACATGGTTAATCGN
diff -r 9f769f79ff18 -r bbfecb0ebe75 test-data/output.ptorthocs
--- a/test-data/output.ptorthocs	Wed Oct 25 11:30:06 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-<html><head><h3>Orthogroups and corresponding coding sequences files: 12 items</h3></head>
-<body><p/><table cellpadding="2">
-<tr><b>Datasets</th></b>
-<tr bgcolor="#D8D8D8"><td><a href="20.faa" type="text/plain">20.faa</a>
-</td></tr>
-<tr bgcolor="#FFFFFF"><td><a href="20.fna" type="text/plain">20.fna</a>
-</td></tr>
-<tr bgcolor="#D8D8D8"><td><a href="3494.faa" type="text/plain">3494.faa</a>
-</td></tr>
-<tr bgcolor="#FFFFFF"><td><a href="3494.fna" type="text/plain">3494.fna</a>
-</td></tr>
-<tr bgcolor="#D8D8D8"><td><a href="3722.faa" type="text/plain">3722.faa</a>
-</td></tr>
-<tr bgcolor="#FFFFFF"><td><a href="3722.fna" type="text/plain">3722.fna</a>
-</td></tr>
-<tr bgcolor="#D8D8D8"><td><a href="38889.faa" type="text/plain">38889.faa</a>
-</td></tr>
-<tr bgcolor="#FFFFFF"><td><a href="38889.fna" type="text/plain">38889.fna</a>
-</td></tr>
-<tr bgcolor="#D8D8D8"><td><a href="39614.faa" type="text/plain">39614.faa</a>
-</td></tr>
-<tr bgcolor="#FFFFFF"><td><a href="39614.fna" type="text/plain">39614.fna</a>
-</td></tr>
-<tr bgcolor="#D8D8D8"><td><a href="5235.faa" type="text/plain">5235.faa</a>
-</td></tr>
-<tr bgcolor="#FFFFFF"><td><a href="5235.fna" type="text/plain">5235.fna</a>
-</td></tr>
-</table></body></html>
diff -r 9f769f79ff18 -r bbfecb0ebe75 test-data/tool-data/plant_tribes/scaffolds/README.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tool-data/plant_tribes/scaffolds/README.txt	Mon Oct 30 08:59:18 2017 -0400
@@ -0,0 +1,3 @@
+For functional tests to work, this directory must contain symlinks to the scaffolds data
+installed into the Galaxy instance to which planemo points via the --galaxy_root parameter.
+This would typically be something like ~/galaxy/tool-data/plant_tribes/scaffolds/22Gv1.1.
diff -r 9f769f79ff18 -r bbfecb0ebe75 utils.py
--- a/utils.py	Wed Oct 25 11:30:06 2017 -0400
+++ b/utils.py	Mon Oct 30 08:59:18 2017 -0400
@@ -54,29 +54,3 @@
 
 def stop_err(msg):
     sys.exit(msg)
-
-
-def write_html_output(output, title, dir):
-    with open(output, 'w') as fh:
-        dir_items = sorted(os.listdir(dir))
-        # Directories can only contain either files or directories,
-        # but not both.
-        if len(dir_items) > 0:
-            item_path = os.path.join(dir, dir_items[0])
-            if os.path.isdir(item_path):
-                header = 'Directories'
-            else:
-                header = 'Datasets'
-        else:
-            header = ''
-        fh.write('<html><head><h3>%s: %d items</h3></head>\n' % (title, len(dir_items)))
-        fh.write('<body><p/><table cellpadding="2">\n')
-        fh.write('<tr><b>%s</th></b>\n' % header)
-        for index, fname in enumerate(dir_items):
-            if index % 2 == 0:
-                bgcolor = '#D8D8D8'
-            else:
-                bgcolor = '#FFFFFF'
-            link = '<a href="%s" type="text/plain">%s</a>\n' % (fname, fname)
-            fh.write('<tr bgcolor="%s"><td>%s</td></tr>\n' % (bgcolor, link))
-        fh.write('</table></body></html>\n')