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comparison SMART/galaxy/getDifference.xml @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
1 <tool id="getDifference" name="get difference"> 1 <tool id="getDifference" name="get Difference">
2 <description>Gets all the regions of the genome, except the one given in an annotation file. Alternatively, it may also give all the elements from the first set which does not ovelap with the second set (at the nucleotide level).</description> 2 <description>Gets all the regions of the genome, except the one given or get all the elements from the first set which does not ovelap with the second set (at the nucleotide level).</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python"> 3 <command interpreter="python">
7 ../Java/Python/getDifference.py -i $formatType.inputFileName1 4 ../Java/Python/getDifference.py -i $formatType.inputFileName1
8 #if $formatType.FormatInputFileName1 == 'bed': 5 #if $formatType.FormatInputFileName1 == 'bed':
9 -f bed 6 -f bed
10 #elif $formatType.FormatInputFileName1 == 'gff': 7 #elif $formatType.FormatInputFileName1 == 'gff':
31 #elif $formatType2.FormatInputFileName2 == 'sam': 28 #elif $formatType2.FormatInputFileName2 == 'sam':
32 -g sam 29 -g sam
33 #elif $formatType2.FormatInputFileName2 == 'gtf': 30 #elif $formatType2.FormatInputFileName2 == 'gtf':
34 -g gtf 31 -g gtf
35 #end if 32 #end if
33
36 34
37 $split 35 $split
38 36
39 #if $OptionSequence.option == "Yes": 37 #if $OptionSequence.option == "Yes":
40 -s $OptionSequence.sequence 38 -s $OptionSequence.sequence
102 <when value="gtf"> 100 <when value="gtf">
103 <param name="inputFileName2" format="gtf" type="data" label="reference file"/> 101 <param name="inputFileName2" format="gtf" type="data" label="reference file"/>
104 </when> 102 </when>
105 </conditional> 103 </conditional>
106 104
107 <param name="split" type="boolean" truevalue="-p" falsevalue="" checked="false" label="When comparing to a set of genomic coordinates, do not join into exons."/> 105 <param name="split" type="boolean" truevalue="-p" falsevalue="" checked="false" label="split option" help="When comparing to a set of genomic coordinates, do not join."/>
106
108 107
109 <conditional name="OptionSequence"> 108 <conditional name="OptionSequence">
110 <param name="option" type="select" label="Compare with a reference fasta file."> 109 <param name="option" type="select" label="Compare with a reference fasta file.">
111 <option value="Yes">Yes</option> 110 <option value="Yes">Yes</option>
112 <option value="No" selected="true">No</option> 111 <option value="No" selected="true">No</option>
120 119
121 </inputs> 120 </inputs>
122 121
123 122
124 <outputs> 123 <outputs>
125 <data name="outputFileGff" format="gff3" label="[get difference] output file."/> 124 <data name="outputFileGff" format="gff3" label="[getDifference]output File."/>
126 </outputs> 125 </outputs>
127 126
128 <help>
129 This tools has two different (but similar) uses. When given two sets of transcripts, it trims the elements of the set so that they do not overlap with the second set.
130
131 When only one set of transcripts is given, together with a reference genome, it produces a list of transcripts which complements the first set.
132 </help>
133 </tool> 127 </tool>