Mercurial > repos > abims-sbr > pairwise

diff pairwise.xml @ 11:ae65822c1fb7 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
author lecorguille
date Mon, 24 Sep 2018 03:56:40 -0400
parents 1e0c547d88fe
children
line wrap: on
line diff
--- a/pairwise.xml	Fri Jul 06 02:51:09 2018 -0400
+++ b/pairwise.xml	Mon Sep 24 03:56:40 2018 -0400
@@ -197,9 +197,19 @@
 
     - 'Pairwise' : the general output. It gives the information about what the tool has done for each pairwise.
 
-    - 'Pairwise_DNA' : the output which contains nucleic sequences (of the pairwise) that are homologous. The sequences are with nucleotides. It shows for both the query and match :
-        the name        
-        the sequence in nucleotides
+    - 'Pairwise_DNA' : the output which contains nucleic sequences (of the pairwise) that are homologous. The sequences are in nucleic format. There are one file per couple of species, and homologous pairs are written by sets of 4 lines : 
+
+Exemple for two homologous pairs for the output file for species X/Y :
+
+| >Gene_A_species_X_homologous_to_Gene_B_species_Y
+| Nucleic_sequence_from_filter_assemblies
+| >Gene_B_species_Y_homologous_to_Gene_A_species_X
+| Nucleic_sequence_from_filter_assemblies
+| >Gene_C_species_X_homologous_to_Gene_D_species_Y
+| Nucleic_sequence_from_filter_assemblies
+| >Gene_D_species_Y_homologous_to_Gene_C_species_X
+| Nucleic_sequence_from_filter_assemblies
+
 
 --------
 
@@ -230,6 +240,4 @@
     ]]>
     </help>
 
-    <expand macro="citations" />
-
 </tool>