Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/galaxy/restrictFromSize.xml @ 1:30c5431d8ce4

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Uploaded
author yufei-luo
date Thu, 17 Jan 2013 11:01:51 -0500
parents e0f8dcca02ed
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 <tool id="restrictFromSize" name="restrict from size">
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2 <description>Select the elements of a list of sequences or transcripts with a given size.</description>
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3 <command interpreter="python">
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4 ../Java/Python/restrictFromSize.py -i $formatType.inputFileName
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5 #if $formatType.FormatInputFileName == 'bed':
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6 -f bed
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7 #elif $formatType.FormatInputFileName == 'gff':
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8 -f gff
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9 #elif $formatType.FormatInputFileName == 'gff2':
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10 -f gff2
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11 #elif $formatType.FormatInputFileName == 'gff3':
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12 -f gff3
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13 #elif $formatType.FormatInputFileName == 'sam':
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14 -f sam
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15 #elif $formatType.FormatInputFileName == 'gtf':
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16 -f gtf
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17 #end if
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18
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19 #if $OptionMax.maximum == "Yes":
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20 -M $OptionMax.max
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21 #end if
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22 #if $OptionMin.minimum == "Yes":
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23 -m $OptionMin.min
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24 #end if
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25
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26 -o $outputFileGff
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27 </command>
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28
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29 <inputs>
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30 <conditional name="formatType">
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31 <param name="FormatInputFileName" type="select" label="Input File Format">
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32 <option value="bed">bed</option>
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33 <option value="gff">gff</option>
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34 <option value="gff2">gff2</option>
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35 <option value="gff3">gff3</option>
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36 <option value="sam">sam</option>
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37 <option value="gtf">gtf</option>
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38 </param>
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39 <when value="bed">
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40 <param name="inputFileName" format="bed" type="data" label="Input File"/>
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41 </when>
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42 <when value="gff">
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43 <param name="inputFileName" format="gff" type="data" label="Input File"/>
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44 </when>
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45 <when value="gff2">
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46 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
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47 </when>
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48 <when value="gff3">
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49 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
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50 </when>
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51 <when value="sam">
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52 <param name="inputFileName" format="sam" type="data" label="Input File"/>
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53 </when>
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54 <when value="gtf">
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55 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
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56 </when>
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57 </conditional>
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58
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59 <conditional name="OptionMax">
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60 <param name="maximum" type="select" label="maximum number of np">
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61 <option value="Yes">Yes</option>
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62 <option value="No" selected="true">No</option>
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63 </param>
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64 <when value="Yes">
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65 <param name="max" type="integer" value="1" help="Be Careful! The value must be upper than 0"/>
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66 </when>
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67 <when value="No">
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68 </when>
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69 </conditional>
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70
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71 <conditional name="OptionMin">
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72 <param name="minimum" type="select" label="minimum number of np">
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73 <option value="Yes">Yes</option>
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74 <option value="No" selected="true">No</option>
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75 </param>
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76 <when value="Yes">
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77 <param name="min" type="integer" value="1" help="Be Careful! The value must be upper than 0"/>
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78 </when>
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79 <when value="No">
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80 </when>
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81 </conditional>
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82
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83 </inputs>
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84
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85 <outputs>
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86 <data name="outputFileGff" format="gff3" label="[restrictFromSize] Output File"/>
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87 </outputs>
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88
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89 <help>
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90 command example: restrictFromSize.py -i cis_e10_cluster20InSeed2515_nbEUp10.gff3 -f gff -o cis_e10_cluster20InSeed2515_nbEUp10_lgUp50 -m 50
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91 </help>
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92
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93 </tool>