changeset 10:b8c05adb68da draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
author iuc
date Wed, 23 Aug 2017 20:57:09 -0400
parents 794b2859c286
children 7a5164f99316
files fimo_wrapper.py macros.xml meme.xml test-data/meme_psp_gen_reports_output.tabular test-data/meme_psp_protein_input.fasta test-data/output.memepsp
diffstat 6 files changed, 46 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/fimo_wrapper.py	Thu Jun 29 20:39:45 2017 -0400
+++ b/fimo_wrapper.py	Wed Aug 23 20:57:09 2017 -0400
@@ -112,8 +112,8 @@
     if returncode != 0:
         stderr = get_stderr(tmp_stderr)
         stop_err(stderr)
-except Exception, e:
-    stop_err('Error running FIMO:\n%s' % str(e))
+except Exception as e:
+    stop_err('Error running FIMO:\n%s' % e)
 
 shutil.move(os.path.join(args.output_path, 'fimo.txt'), args.txt_output)
 
--- a/macros.xml	Thu Jun 29 20:39:45 2017 -0400
+++ b/macros.xml	Wed Aug 23 20:57:09 2017 -0400
@@ -1,5 +1,6 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <macros>
+    <token name="@WRAPPER_VERSION@">4.11.2</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="1.3.23">graphicsmagick</requirement>
--- a/meme.xml	Thu Jun 29 20:39:45 2017 -0400
+++ b/meme.xml	Wed Aug 23 20:57:09 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="meme_meme" name="MEME" version="4.11.2.0">
+<tool id="meme_meme" name="MEME" version="@WRAPPER_VERSION@.0">
     <description>- Multiple Em for Motif Elicitation</description>
     <macros>
         <import>macros.xml</import>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/meme_psp_gen_reports_output.tabular	Wed Aug 23 20:57:09 2017 -0400
@@ -0,0 +1,19 @@
+540 bases or amino acids
+0.5	0.5	4	4
+0.5	0.5	6	6
+0.5	0.5	7	7
+0.5	0.5	8	8
+0.5	0.5	9	9
+0.5	0.5	10	10
+0.5	0.5	11	11
+0.5	0.5	12	12
+0.5	0.5	13	13
+0.5	0.5	14	14
+0.5	0.5	15	15
+0.5	0.5	16	16
+0.5	0.5	17	17
+0.5	0.5	18	18
+0.5	0.5	19	19
+0.5	0.5	20	20
+
+score 0.9 occurred 483 times
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/meme_psp_protein_input.fasta	Wed Aug 23 20:57:09 2017 -0400
@@ -0,0 +1,17 @@
+>ICYA_MANSE 
+GDIFYPGYCPDVKPVNDFDLSAFAGAWHEIAKLPLENENQGKCTIAEYKY
+DGKKASVYNSFVSNGVKEYMEGDLEIAPDAKYTKQGKYVMTFKFGQRVVN
+LVPWVLATDYKNYAINYNCDYHPDKKAHSIHAWILSKSKVLEGNTKEVVD
+NVLKTFSHLIDASKFISNDFSEAACQYSTTYSLTGPDRH
+
+>LACB_BOVIN 
+MKCLLLALALTCGAQALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDA
+QSAPLRVYVEELKPTPEGDLEILLQKWENGECAQKKIIAEKTKIPAVFKI
+DALNENKVLVLDTDYKKYLLFCMENSAEPEQSLACQCLVRTPEVDDEALE
+KFDKALKALPMHIRLSFNPTQLEEQCHI
+
+>BBP_PIEBR 
+NVYHDGACPEVKPVDNFDWSNYHGKWWEVAKYPNSVEKYGKCGWAEYTPE
+GKSVKVSNYHVIHGKEYFIEGTAYPVGDSKIGKIYHKLTYGGVTKENVFN
+VLSTDNKNYIIGYYCKYDEDKKGHQDFVWVLSRSKVLTGEAKTAVENYLI
+GSPVVDSQKLVYSDFSEAACKVN
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.memepsp	Wed Aug 23 20:57:09 2017 -0400
@@ -0,0 +1,6 @@
+>BBP_PIEBR 20 scaledmin = 0.1 scaledmax = 0.9
+0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0.006488825 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+>ICYA_MANSE 20 scaledmin = 0.1 scaledmax = 0.9
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+>LACB_BOVIN 20 scaledmin = 0.1 scaledmax = 0.9
+0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0.006284916 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0