# HG changeset patch
# User xuebing
# Date 1331926307 14400
# Node ID adb693f05135ecf71dadc053a2435d53d2ba9b42
# Parent  01843668f8dd6e4da74525d26c111d96cde6b72d
Uploaded

diff -r 01843668f8dd -r adb693f05135 match.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/match.xml	Fri Mar 16 15:31:47 2012 -0400
@@ -0,0 +1,54 @@
+<tool id="match" name="match">
+  <description>find short motif occurrences</description>
+  <command> match $motif $seq $output $nmismatch $rc $bed > $log</command>
+  <inputs>
+    
+    <param name="motif" type="data" format="fasta" label="Search occurances of the following motifs" help="one or multiple sequences, FASTA format"/>         
+    <param name="seq" type="data" format="fasta" label="in sequences" help="one or multiple sequences, FASTA format"/>   
+      <param name="nmismatch" size="10" type="integer" value="0" label="number of mismatches allowed"/>
+    <param name="rc" label="Do not score the reverse complement DNA strand. Both strands are scored by default" type="boolean" truevalue="norc" falsevalue="rc" checked="False"/>
+        <param name="bed" label="output BED format" help="Default is tabular file (see example below). Please only check this if your sequence identifier looks like: hg18_chr6_122208322_122209078_+ (true for galaxy tool extracted sequences)" type="boolean" truevalue="bed" falsevalue="nobed" checked="True"/>
+  </inputs>
+  <outputs>
+    <data format="log" name="log" label="${tool.name} on ${on_string} (log)"/>
+    <data format="bed" name="output" label="${tool.name} on ${on_string} (bed)"/>
+  </outputs>
+  <help>
+
+**What it does**
+
+This tool searches occurrences of a short nucleotide seuqences (allowing mismatches) in a set of longer sequences.
+
+Example motif file::
+
+    >motif1
+    CAGGTAAGT
+    >motif2
+    GTTTGGGGGCC
+    
+Example sequence file::
+
+    >hg18_chr6_122208322_122209078_+
+    CGTCGTAGCTACTAGCTACGTACGTACGTAGCTAGCATGCATGCTACGTA
+    CGTAGCTAGCTAAAAAAAAAAAAAAACTGCGGCTAGCTAGCTAGCTACGT
+    CGATCGTAGCTAC...
+    >hg18_chr6_1208322_122209023_+
+    CGATGCTAGCTAGCTAGCTACGTAGCTAGCTAGTCGATGCTAGCTAGCTA     
+    ATGCTAGCTAGC....
+    
+Output (bed)::
+
+    chr11	72790893	72790902	ACTTAACTG	1	-	antisense	5ss,G4T:CAGTTAAGT-rc	hg18_chr11_72790846_72791902_+	47
+    chr11	72791880	72791889	CAGGTAAGA	1	+	sense	5ss,T9A:CAGGTAAGA	hg18_chr11_72790846_72791902_+	1034
+
+
+Output (tab)::
+
+    Tmod4	802	5ss:CAGGTAAGT-rc	ACTTACCTG
+    Atp7b	77	5ss:CAGGTAAGT	CAGGTAAGT
+    Fnta	665	5ss:CAGGTAAGT	CAGGTAAGT
+
+
+
+  </help>
+</tool>