Mercurial > repos > yufei-luo > s_mart
diff SMART/galaxy/GetFlanking.xml @ 6:769e306b7933
Change the repository level.
| author | yufei-luo |
|---|---|
| date | Fri, 18 Jan 2013 04:54:14 -0500 |
| parents | |
| children | 440ceca58672 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SMART/galaxy/GetFlanking.xml Fri Jan 18 04:54:14 2013 -0500 @@ -0,0 +1,179 @@ +<tool id="GetFlanking" name="get flanking"> + <description>Get the flanking regions of a set of reference.</description> + <command interpreter="python"> + ../Java/Python/GetFlanking.py -i $formatType.inputFileName1 + #if $formatType.FormatInputFileName1 == 'bed': + -f bed + #elif $formatType.FormatInputFileName1 == 'gff': + -f gff + #elif $formatType.FormatInputFileName1 == 'gff2': + -f gff2 + #elif $formatType.FormatInputFileName1 == 'gff3': + -f gff3 + #elif $formatType.FormatInputFileName1 == 'sam': + -f sam + #elif $formatType.FormatInputFileName1 == 'gtf': + -f gtf + #end if + + -j $formatType2.inputFileName2 + #if $formatType2.FormatInputFileName2 == 'bed': + -g bed + #elif $formatType2.FormatInputFileName2 == 'gff': + -g gff + #elif $formatType2.FormatInputFileName2 == 'gff2': + -g gff2 + #elif $formatType2.FormatInputFileName2 == 'gff3': + -g gff3 + #elif $formatType2.FormatInputFileName2 == 'sam': + -g sam + #elif $formatType2.FormatInputFileName2 == 'gtf': + -g gtf + #end if + + #if $OptionUpDownStream.OptionUD == 'UpStream': + -5 + #elif $OptionUpDownStream.OptionUD == 'DownStream': + -3 + #end if + + + #if $OptionColinearOrAntiSens.OptionCA == 'Colinear': + -c + #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens': + -a + #end if + + #if $OptionMax.maximum == "Yes": + -D $OptionMax.max + #end if + #if $OptionMin.minimum == "Yes": + -d $OptionMin.min + #end if + + -o $outputFile + + + + </command> + + <inputs> + <conditional name="formatType"> + <param name="FormatInputFileName1" type="select" label="query File Format"> + <option value="bed">bed</option> + <option value="gff">gff</option> + <option value="gff2">gff2</option> + <option value="gff3">gff3</option> + <option value="sam">sam</option> + <option value="gtf">gtf</option> + </param> + <when value="bed"> + <param name="inputFileName1" format="bed" type="data" label="Input File 1"/> + </when> + <when value="gff"> + <param name="inputFileName1" format="gff" type="data" label="Input File 1"/> + </when> + <when value="gff2"> + <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/> + </when> + <when value="gff3"> + <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/> + </when> + <when value="sam"> + <param name="inputFileName1" format="sam" type="data" label="Input File 1"/> + </when> + <when value="gtf"> + <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/> + </when> + </conditional> + + <conditional name="formatType2"> + <param name="FormatInputFileName2" type="select" label="Refence File Format"> + <option value="bed">bed</option> + <option value="gff">gff</option> + <option value="gff2">gff2</option> + <option value="gff3">gff3</option> + <option value="sam">sam</option> + <option value="gtf">gtf</option> + </param> + <when value="bed"> + <param name="inputFileName2" format="bed" type="data" label="Input File 2"/> + </when> + <when value="gff"> + <param name="inputFileName2" format="gff" type="data" label="Input File 2"/> + </when> + <when value="gff2"> + <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/> + </when> + <when value="gff3"> + <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/> + </when> + <when value="sam"> + <param name="inputFileName2" format="sam" type="data" label="Input File 2"/> + </when> + <when value="gtf"> + <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/> + </when> + </conditional> + + <conditional name="OptionUpDownStream"> + <param name="OptionUD" type="select" label="UpStream or DownStream"> + <option value="UpStream">UpStream</option> + <option value="DownStream">DownStream</option> + <option value="NONE" selected="true">NONE</option> + </param> + <when value="UpStream"> + </when> + <when value="DownStream"> + </when> + <when value="NONE"> + </when> + </conditional> + + <conditional name="OptionColinearOrAntiSens"> + <param name="OptionCA" type="select" label="Colinear or anti-sens"> + <option value="Colinear">Colinear</option> + <option value="AntiSens">AntiSens</option> + <option value="NONE" selected="true">NONE</option> + </param> + <when value="Colinear"> + </when> + <when value="AntiSens"> + </when> + <when value="NONE"> + </when> + </conditional> + + <conditional name="OptionMax"> + <param name="maximum" type="select" label="maximum distance between 2 elements"> + <option value="Yes">Yes</option> + <option value="No" selected="true">No</option> + </param> + <when value="Yes"> + <param name="max" type="integer" value="0"/> + </when> + <when value="No"> + </when> + </conditional> + + <conditional name="OptionMin"> + <param name="minimum" type="select" label="minimum distance between 2 elements"> + <option value="Yes">Yes</option> + <option value="No" selected="true">No</option> + </param> + <when value="Yes"> + <param name="min" type="integer" value="0" /> + </when> + <when value="No"> + </when> + </conditional> + + </inputs> + + + <outputs> + <data format="gff3" name="outputFile" label="[GetFlanking] Output File"/> + </outputs> + + +</tool>