Mercurial > repos > iuc > meme_fimo

changeset 11:c470b36b592d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
author iuc
date Wed, 23 Aug 2017 20:57:21 -0400
parents 307b2f3559bf
children 02f6ad791bbf
files fimo.xml fimo_wrapper.py macros.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.xml	Thu Jun 29 20:39:58 2017 -0400
+++ b/fimo.xml	Wed Aug 23 20:57:21 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="meme_fimo" name="FIMO" version="4.11.2.0">
+<tool id="meme_fimo" name="FIMO" version="@WRAPPER_VERSION@.0">
     <description>- Scan a set of sequences for motifs.</description>
     <macros>
         <import>macros.xml</import>
--- a/fimo_wrapper.py	Thu Jun 29 20:39:58 2017 -0400
+++ b/fimo_wrapper.py	Wed Aug 23 20:57:21 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 20:39:58 2017 -0400
+++ b/macros.xml	Wed Aug 23 20:57:21 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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/meme_psp_gen_reports_output.tabular	Wed Aug 23 20:57:21 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 20:57:21 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 20:57:21 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
+0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0.005878511 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+>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