Mercurial > repos > xuebing > sharplabtool
diff fimo2-old.xml @ 14:76e1b1b21cce default tip
Deleted selected files
author | xuebing |
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date | Tue, 13 Mar 2012 19:05:10 -0400 |
parents | 292186c14b08 |
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--- 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 - && mv fimo_out/fimo.html ${html_outfile} - - && mv fimo_out/fimo.txt ${txt_outfile} - - && rm -rf fimo_out - - </command> - <inputs> - <conditional name="motif_selection"> - <param name="motif_sel" type="select" label="Motif Source"> - <option value="user" selected="true">Use motif file in Your History</option> - <option value="known" >Known motif</option> - </param> - ##<when value="known"> - ## <param name="motif" type="select" label="Select motif"> - ## <option value="/Users/xuebing/galaxy-dist/tool-data/motif-database/5primerSpliceSite" selected="true">mouse 5 primer splice site</option> - ## <option value="/Users/xuebing/galaxy-dist/tool-data/motif-database/5primerSpliceSite">mouse 3 primer splice site</option> - ## <option value="/Users/xuebing/galaxy-dist/tool-data/motif-database/TATA-Box.meme">TATA box</option> - ## </param> - ##</when> - <when value="user"> - <param name="motif" type="data" format="txt" label="Motif file" help="created using the tool create-motif-file, or import from Shared Data"/> - </when> - </conditional> - - <param name="database" type="data" format="fasta" label="Sequence file (FASTA)"/> - - <conditional name="background_select"> - <param name="bg_select" type="select" label="Background model" > - <option value="uniform" selected="true">uniform</option> - <option value="fromfile">load from file</option> - </param> - <when value="fromfile"> - <param name="bgfile" type="data" format="txt" label="File for background model"/> - </when> - </conditional> - - <param name="pth" size="10" type="float" value="0.01" label="p-value threshold"/> - <param name="norc" label="Do not score the reverse complement DNA strand. Both strands are scored by default" type="boolean" truevalue="-norc" falsevalue="" checked="False"/> - </inputs> - <outputs> - <data format="html" name="html_outfile" label="${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>