diff fimo2-old.xml @ 14:76e1b1b21cce default tip

Deleted selected files

--- a/fimo2-old.xml	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,63 +0,0 @@
-<tool id="fimo" name="motif search">
-  <description>using FIMO</description>
-  <command> fimo 
-    #if $background_select.bg_select == "fromfile":
-    -bgfile $bgfile
-    #end if
-    
-  $norc --output-pthresh $pth --verbosity 1 $motif $database 
-  &amp;&amp; mv fimo_out/fimo.html ${html_outfile}
-  
-  &amp;&amp; mv fimo_out/fimo.txt ${txt_outfile}
-  
-  &amp;&amp; rm -rf fimo_out
-  
-  </command>
-  <inputs>
-    <conditional name="motif_selection">   
-        <param name="motif_sel" type="select" label="Motif Source">
-            <option value="user" selected="true">Use motif file in Your History</option>
-            <option value="known" >Known motif</option>
-        </param>
-        ##<when value="known">
-        ##    <param name="motif" type="select" label="Select motif">
-        ##        <option value="/Users/xuebing/galaxy-dist/tool-data/motif-database/5primerSpliceSite" selected="true">mouse 5 primer splice site</option>
-        ##        <option value="/Users/xuebing/galaxy-dist/tool-data/motif-database/5primerSpliceSite">mouse 3 primer splice site</option>
-        ##        <option value="/Users/xuebing/galaxy-dist/tool-data/motif-database/TATA-Box.meme">TATA box</option>
-        ##    </param>
-        ##</when>
-        <when value="user">
-            <param name="motif" type="data" format="txt" label="Motif file" help="created using the tool create-motif-file, or import from Shared Data"/>
-        </when>
-    </conditional>     
-         
-    <param name="database" type="data" format="fasta" label="Sequence file (FASTA)"/>
-      
-    <conditional name="background_select">
-    	<param name="bg_select" type="select" label="Background model" >
-		  <option value="uniform" selected="true">uniform</option>
-		  <option value="fromfile">load from file</option>
-	    </param>
-	    <when value="fromfile">
-		    <param name="bgfile" type="data" format="txt" label="File for background model"/>
-	    </when>
-    </conditional>
-      
-      <param name="pth" size="10" type="float" value="0.01" label="p-value threshold"/>
-    <param name="norc" label="Do not score the reverse complement DNA strand. Both strands are scored by default" type="boolean" truevalue="-norc" falsevalue="" checked="False"/>
-  </inputs>
-  <outputs>
-    <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"/>
-    <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (txt)"/>
-  </outputs>
-  <help>
-
-**What it does**
-
-This tool uses FIMO to find matches of a motif in a fasta file. See more details:
-
-http://meme.sdsc.edu/meme/fimo-intro.html
- 
-
-  </help>
-</tool>