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comparison SMART/galaxy/CompareOverlappingSmallRef.xml @ 60:90f4b29d884f

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Uploaded
author m-zytnicki
date Fri, 21 Feb 2014 08:32:36 -0500
parents 97aa2e42bfdf
children 783e6ed4eb66
comparison
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59:2a4884ba3e5c 60:90f4b29d884f
1 <tool id="CompareOverlappingSmallRef" name="compare overlapping small reference"> 1 <tool id="CompareOverlappingSmallRef" name="compare overlapping small reference">
2 <description>Provide the queries that overlap with a reference, when the reference dataset is small.</description> 2 <description>Provide the queries that overlap with a reference, when the query data set is small.</description>
3 <requirements> 3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement> 4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python"> 6 <command interpreter="python">
7 ../Java/Python/CompareOverlappingSmallQuery.py -i $formatType.inputFileName1 7 ../Java/Python/CompareOverlappingSmallRef.py -i $formatType.inputFileName1 -f $formatType.FormatInputFileName1 -j $formatType2.inputFileName2 -g $formatType2.FormatInputFileName2 -o $outputFileGff $InvertMatch $NotOverlapping $OptionInclusionQuery $OptionInclusionRef -m $OptionMinOverlap
8 #if $formatType.FormatInputFileName1 == 'bed':
9 -f bed
10 #elif $formatType.FormatInputFileName1 == 'gff':
11 -f gff
12 #elif $formatType.FormatInputFileName1 == 'gff2':
13 -f gff2
14 #elif $formatType.FormatInputFileName1 == 'gff3':
15 -f gff3
16 #elif $formatType.FormatInputFileName1 == 'sam':
17 -f sam
18 #elif $formatType.FormatInputFileName1 == 'bam':
19 -f bam
20 #elif $formatType.FormatInputFileName1 == 'gtf':
21 -f gtf
22 #end if
23 -j $formatType2.inputFileName2
24 #if $formatType2.FormatInputFileName2 == 'bed':
25 -g bed
26 #elif $formatType2.FormatInputFileName2 == 'gff':
27 -g gff
28 #elif $formatType2.FormatInputFileName2 == 'gff2':
29 -g gff2
30 #elif $formatType2.FormatInputFileName2 == 'gff3':
31 -g gff3
32 #elif $formatType2.FormatInputFileName2 == 'sam':
33 -g sam
34 #elif $formatType2.FormatInputFileName2 == 'bam':
35 -g bam
36 #elif $formatType2.FormatInputFileName2 == 'gtf':
37 -g gtf
38 #end if
39 -o $outputFileGff
40 #if $OptionDistance.Dist == 'Yes': 8 #if $OptionDistance.Dist == 'Yes':
41 -d $OptionDistance.distance 9 -d $OptionDistance.distance
42 #end if
43 #if $OptionMinOverlap.present == 'Yes':
44 -m $OptionMinOverlap.minOverlap
45 #end if 10 #end if
46 #if $OptionPcOverlapQuery.present == 'Yes': 11 #if $OptionPcOverlapQuery.present == 'Yes':
47 -p $OptionPcOverlapQuery.minOverlap 12 -p $OptionPcOverlapQuery.minOverlap
48 #end if 13 #end if
49 #if $OptionPcOverlapRef.present == 'Yes': 14 #if $OptionPcOverlapRef.present == 'Yes':
50 -P $OptionPcOverlapRef.minOverlap 15 -P $OptionPcOverlapRef.minOverlap
51 #end if 16 #end if
52 #if $OptionCollinearOrAntiSens.OptionCA == 'Collinear': 17 #if $OptionCA == 'Collinear':
53 -c 18 -c
54 #elif $OptionCollinearOrAntiSens.OptionCA == 'AntiSens': 19 #elif $OptionCA == 'AntiSense':
55 -a 20 -a
56 #end if 21 #end if
57 $InvertMatch
58 $NotOverlapping
59 $OptionInclusionQuery
60 $OptionInclusionRef
61 </command> 22 </command>
62 23
63 <inputs> 24 <inputs>
64 <conditional name="formatType"> 25 <conditional name="formatType">
65 <param name="FormatInputFileName1" type="select" label="Input Query File Format"> 26 <param name="FormatInputFileName1" type="select" label="Input Query File Format">
89 <when value="bam"> 50 <when value="bam">
90 <param name="inputFileName1" format="bam" type="data" label="Input File 1"/> 51 <param name="inputFileName1" format="bam" type="data" label="Input File 1"/>
91 </when> 52 </when>
92 <when value="gtf"> 53 <when value="gtf">
93 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/> 54 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
94 </when> 55 </when>
95 </conditional> 56 </conditional>
96 57
97 <conditional name="formatType2"> 58 <conditional name="formatType2">
98 <param name="FormatInputFileName2" type="select" label="Input Reference File Format"> 59 <param name="FormatInputFileName2" type="select" label="Input Reference File Format">
99 <option value="bed">bed</option> 60 <option value="bed">bed</option>
135 <param name="distance" type="integer" value="0"/> 96 <param name="distance" type="integer" value="0"/>
136 </when> 97 </when>
137 <when value="No"> 98 <when value="No">
138 </when> 99 </when>
139 </conditional> 100 </conditional>
140 <conditional name="OptionMinOverlap"> 101 <param name="OptionMinOverlap" type="integer" value="1" label="Min. # of overlapping nt. to declare an overlap."/>
141 <param name="present" type="select" label="Minimum number of common nucleotides to declare an overlap">
142 <option value="Yes">Yes</option>
143 <option value="No" selected="true">No</option>
144 </param>
145 <when value="Yes">
146 <param name="minOverlap" type="integer" value="0"/>
147 </when>
148 <when value="No">
149 </when>
150 </conditional>
151 <conditional name="OptionPcOverlapQuery"> 102 <conditional name="OptionPcOverlapQuery">
152 <param name="present" type="select" label="N% of the query must overlap"> 103 <param name="present" type="select" label="N% of the query must overlap">
153 <option value="Yes">Yes</option> 104 <option value="Yes">Yes</option>
154 <option value="No" selected="true">No</option> 105 <option value="No" selected="true">No</option>
155 </param> 106 </param>
156 <when value="Yes"> 107 <when value="Yes">
157 <param name="minOverlap" type="integer" value="0"/> 108 <param name="minOverlap" type="integer" value="100"/>
158 </when> 109 </when>
159 <when value="No"> 110 <when value="No">
160 </when> 111 </when>
161 </conditional> 112 </conditional>
162 <conditional name="OptionPcOverlapRef"> 113 <conditional name="OptionPcOverlapRef">
163 <param name="present" type="select" label="N% of the reference must overlap"> 114 <param name="present" type="select" label="N% of the reference must overlap">
164 <option value="Yes">Yes</option> 115 <option value="Yes">Yes</option>
165 <option value="No" selected="true">No</option> 116 <option value="No" selected="true">No</option>
166 </param> 117 </param>
167 <when value="Yes"> 118 <when value="Yes">
168 <param name="minOverlap" type="integer" value="0"/> 119 <param name="minOverlap" type="integer" value="100"/>
169 </when> 120 </when>
170 <when value="No"> 121 <when value="No">
171 </when> 122 </when>
172 </conditional> 123 </conditional>
173 <param name="OptionInclusionQuery" type="boolean" truevalue="-k" falsevalue="" checked="false" label="The query must be nested in a query"/> 124 <param name="OptionInclusionQuery" type="boolean" truevalue="-k" falsevalue="" checked="false" label="The query must be nested in a reference"/>
174 <param name="OptionInclusionRef" type="boolean" truevalue="-K" falsevalue="" checked="false" label="The reference must be nested in a query"/> 125 <param name="OptionInclusionRef" type="boolean" truevalue="-K" falsevalue="" checked="false" label="The reference must be nested in a query"/>
175 <conditional name="OptionCollinearOrAntiSens"> 126 <param name="OptionCA" type="select" label="Collinear or anti-sense only">
176 <param name="OptionCA" type="select" label="Collinear or anti-sens"> 127 <option value="Collinear">Collinear</option>
177 <option value="Collinear">Collinear</option> 128 <option value="AntiSense">AntiSense</option>
178 <option value="AntiSens">AntiSens</option> 129 <option value="All" selected="true">All</option>
179 <option value="NONE" selected="true">NONE</option> 130 </param>
180 </param>
181 <when value="Collinear">
182 </when>
183 <when value="AntiSens">
184 </when>
185 <when value="NONE">
186 </when>
187 </conditional>
188 <param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match: the output file will contain all query elements which do NOT overlap"/> 131 <param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match: the output file will contain all query elements which do NOT overlap"/>
189 <param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="Also report the query data which do not overlap, with the nbOverlaps tag set to 0."/> 132 <param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="Also report the query data which do not overlap, with the nbOverlaps tag set to 0."/>
190 </inputs> 133 </inputs>
191 134
192 <outputs> 135 <outputs>