Mercurial > repos > yufei-luo > s_mart

comparison SMART/galaxy/CompareOverlappingSmallQuery.xml @ 56:97aa2e42bfdf

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Uploaded
author m-zytnicki
date Wed, 05 Feb 2014 11:51:11 -0500
parents 2c0c0a89fad7
children 90f4b29d884f
comparison
equal deleted inserted replaced
55:2ac71607aa60 56:97aa2e42bfdf
13 -f gff2 13 -f gff2
14 #elif $formatType.FormatInputFileName1 == 'gff3': 14 #elif $formatType.FormatInputFileName1 == 'gff3':
15 -f gff3 15 -f gff3
16 #elif $formatType.FormatInputFileName1 == 'sam': 16 #elif $formatType.FormatInputFileName1 == 'sam':
17 -f sam 17 -f sam
18 #elif $formatType.FormatInputFileName1 == 'bam':
19 -f bam
18 #elif $formatType.FormatInputFileName1 == 'gtf': 20 #elif $formatType.FormatInputFileName1 == 'gtf':
19 -f gtf 21 -f gtf
20 #end if 22 #end if
21 -j $formatType2.inputFileName2 23 -j $formatType2.inputFileName2
22 #if $formatType2.FormatInputFileName2 == 'bed': 24 #if $formatType2.FormatInputFileName2 == 'bed':
27 -g gff2 29 -g gff2
28 #elif $formatType2.FormatInputFileName2 == 'gff3': 30 #elif $formatType2.FormatInputFileName2 == 'gff3':
29 -g gff3 31 -g gff3
30 #elif $formatType2.FormatInputFileName2 == 'sam': 32 #elif $formatType2.FormatInputFileName2 == 'sam':
31 -g sam 33 -g sam
34 #elif $formatType2.FormatInputFileName2 == 'bam':
35 -g bam
32 #elif $formatType2.FormatInputFileName2 == 'gtf': 36 #elif $formatType2.FormatInputFileName2 == 'gtf':
33 -g gtf 37 -g gtf
34 #end if 38 #end if
35 -o $outputFileGff 39 -o $outputFileGff
36 #if $OptionDistance.Dist == 'Yes': 40 #if $OptionDistance.Dist == 'Yes':
62 <option value="bed">bed</option> 66 <option value="bed">bed</option>
63 <option value="gff">gff</option> 67 <option value="gff">gff</option>
64 <option value="gff2">gff2</option> 68 <option value="gff2">gff2</option>
65 <option value="gff3">gff3</option> 69 <option value="gff3">gff3</option>
66 <option value="sam">sam</option> 70 <option value="sam">sam</option>
71 <option value="bam">bam</option>
67 <option value="gtf">gtf</option> 72 <option value="gtf">gtf</option>
68 </param> 73 </param>
69 <when value="bed"> 74 <when value="bed">
70 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/> 75 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
71 </when> 76 </when>
78 <when value="gff3"> 83 <when value="gff3">
79 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/> 84 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
80 </when> 85 </when>
81 <when value="sam"> 86 <when value="sam">
82 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/> 87 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
88 </when>
89 <when value="bam">
90 <param name="inputFileName1" format="bam" type="data" label="Input File 1"/>
83 </when> 91 </when>
84 <when value="gtf"> 92 <when value="gtf">
85 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/> 93 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
86 </when> 94 </when>
87 </conditional> 95 </conditional>
91 <option value="bed">bed</option> 99 <option value="bed">bed</option>
92 <option value="gff">gff</option> 100 <option value="gff">gff</option>
93 <option value="gff2">gff2</option> 101 <option value="gff2">gff2</option>
94 <option value="gff3">gff3</option> 102 <option value="gff3">gff3</option>
95 <option value="sam">sam</option> 103 <option value="sam">sam</option>
104 <option value="bam">bam</option>
96 <option value="gtf">gtf</option> 105 <option value="gtf">gtf</option>
97 </param> 106 </param>
98 <when value="bed"> 107 <when value="bed">
99 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/> 108 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
100 </when> 109 </when>
107 <when value="gff3"> 116 <when value="gff3">
108 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/> 117 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
109 </when> 118 </when>
110 <when value="sam"> 119 <when value="sam">
111 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/> 120 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
121 </when>
122 <when value="bam">
123 <param name="inputFileName2" format="bam" type="data" label="Input File 2"/>
112 </when> 124 </when>
113 <when value="gtf"> 125 <when value="gtf">
114 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/> 126 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
115 </when> 127 </when>
116 </conditional> 128 </conditional>