Mercurial > repos > xuebing > match

changeset 6:e3c56fd9eb72

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Deleted selected files
author xuebing
date Fri, 16 Mar 2012 15:59:16 -0400
parents 473f9f288d6a
children 2028a81a9575
files match.xml
diffstat 1 files changed, 0 insertions(+), 54 deletions(-) [+]
line wrap: on
line diff
--- a/match.xml	Fri Mar 16 15:39:27 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-<tool id="match" name="match">
-  <description>find short motif occurrences</description>
-  <command> match $motif $seq $output $nmismatch $rc $bed > $log</command>
-  <inputs>
-    
-    <param name="motif" type="data" format="fasta" label="Search occurances of the following motifs" help="one or multiple sequences, FASTA format"/>         
-    <param name="seq" type="data" format="fasta" label="in sequences" help="one or multiple sequences, FASTA format"/>   
-      <param name="nmismatch" size="10" type="integer" value="0" label="number of mismatches allowed"/>
-    <param name="rc" label="Do not score the reverse complement DNA strand. Both strands are scored by default" type="boolean" truevalue="norc" falsevalue="rc" checked="False"/>
-        <param name="bed" label="output BED format" help="Default is tabular file (see example below). Please only check this if your sequence identifier looks like: hg18_chr6_122208322_122209078_+ (true for galaxy tool extracted sequences)" type="boolean" truevalue="bed" falsevalue="nobed" checked="False"/>
-  </inputs>
-  <outputs>
-    <data format="txt" name="log" label="${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>