# HG changeset patch
# User bitlab
# Date 1605614324 0
# Node ID 6377afdf6aa25518d09cf6f733f11ae8b50ec56a
# Parent  c0a83821df64dab07e333d8447172e7d26fcbf2d
Uploaded

diff -r c0a83821df64 -r 6377afdf6aa2 gecko/.gitignore
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/bin/matrix.mat
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/frags2align.xml
--- a/gecko/frags2align.xml	Tue Nov 17 11:56:38 2020 +0000
+++ b/gecko/frags2align.xml	Tue Nov 17 11:58:44 2020 +0000
@@ -1,9 +1,9 @@
 <tool id="frags2align" name="Frags to align">
   <description>Extract alignments from a binary Frags file</description>
   <inputs>
-    <param name="fragsFile" type="data" format="frags" label="Frags file" help="Binary Frags file" />
-    <param name="fastaX" type="data" format="fasta" label="x Genome" help="Single genome file in fasta format"/>    
-    <param name="fastaY" type="data" value="fasta" label="y Genome" help="Single genome file in fasta format" />
+    <param name="fragsFile" type="data" format="bin" label="Frags file" help="Binary Frags file" />
+    <param name="fastaX" type="data" format="fasta" label="Sequence X" help="Query sequence file in fasta format"/>    
+    <param name="fastaY" type="data" value="fasta" label="Sequence Y" help="Reference sequence file in fasta format" />
   </inputs>
   <command> make all -C ${__tool_directory__}/src/ ; ${__tool_directory__}/bin/frags2align.sh $fragsFile $fastaX $fastaY $alignments </command>
   <outputs>
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/gecko.xml
--- a/gecko/gecko.xml	Tue Nov 17 11:56:38 2020 +0000
+++ b/gecko/gecko.xml	Tue Nov 17 11:58:44 2020 +0000
@@ -5,14 +5,14 @@
 
   <inputs>
     <param name="genome1" type="data" format="fasta" label="Sequence X" help="Query sequence file in fasta format" />
-    <param name="genome2" type="data" format="fasta" label="Sequence Y" help="Query reference file in fasta format"/>    
+    <param name="genome2" type="data" format="fasta" label="Sequence Y" help="Reference sequence file in fasta format"/>    
     <param name="length" type="integer" value="20" label="Minimum length to report a frag" />
-    <param name="similarity" type="integer" value="20" label="Minimum similarity to report frag" />
+    <param name="similarity" type="integer" value="60" label="Minimum similarity to report frag" />
     <param name="wl" type="integer" value="16" label="Word length" />
   </inputs>
 
   <outputs>
-     <data name="frags_output0" type="data" format="frags" label="Frags comparison for ${genome1.name}_${genome2.name}"/>
+     <data name="frags_output0" type="data" format="bin" label="Frags comparison for ${genome1.name}_${genome2.name}"/>
      <data name="csv_output1" format="csv" label="Csv comparison for ${genome1.name}_${genome2.name}"/> 
   </outputs>
 
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/FragHits.c
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/Makefile
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/combineFrags.c
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/commonFunctions.c
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/commonFunctions.h
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/comparisonFunctions.c
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/comparisonFunctions.h
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/dictionaryFunctions.c
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/dictionaryFunctions.h
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/filterFrags.c
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/filterHits.c
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/fragStat.c
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/fragmentv2.c
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/fragmentv2.h
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/fragmentv3.c
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/fragmentv3.h
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/frags2text.c
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/getCSB.c
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/getInfoCSB.c
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/hdStat.c
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/hits.c
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/hitsStat.c
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/indexmaker.c
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/lista.c
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/lista.h
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/matrix.mat
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/quicksort.c
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/quicksort.h
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/reverseComplement.c
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/sortHits.c
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/sortWords.c
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/structs.h
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/w2hd.c
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/words.c
diff -r c0a83821df64 -r 6377afdf6aa2 gecko/src/wordsStat.c