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comparison SMART/galaxy/ConvertTranscriptFile.xml @ 15:440ceca58672

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Uploaded
author m-zytnicki
date Mon, 22 Apr 2013 11:08:07 -0400
parents 769e306b7933
children 94ab73e8a190
comparison
equal deleted inserted replaced
14:c79b9ae3f65f 15:440ceca58672
1 <tool id="ConvertTranscriptFile" name="Convert transcript file"> 1 <tool id="ConvertTranscriptFile" name="convert transcript file">
2 <description>Convert a file from a format to another.</description> 2 <description>Convert a file from a format to another.</description>
3 <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFormatType.inputFileName 3 <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFormatType.inputFileName
4 #if $inputFormatType.FormatInputFileName == 'gff3': 4 #if $inputFormatType.FormatInputFileName == 'gff3':
5 -f gff3 5 -f gff3
6 #elif $inputFormatType.FormatInputFileName == 'bed': 6 #elif $inputFormatType.FormatInputFileName == 'bed':
7 -f bed 7 -f bed
8 #elif $inputFormatType.FormatInputFileName == 'gff2':
9 -f gff2
10 #elif $inputFormatType.FormatInputFileName == 'bam': 8 #elif $inputFormatType.FormatInputFileName == 'bam':
11 -f blast 9 -f blast
12 #elif $inputFormatType.FormatInputFileName == 'sam': 10 #elif $inputFormatType.FormatInputFileName == 'sam':
13 -f sam 11 -f sam
14 #elif $inputFormatType.FormatInputFileName == 'gtf': 12 #elif $inputFormatType.FormatInputFileName == 'gtf':
15 -f gtf 13 -f gtf
16 #end if 14 #end if
17 15
18 -g $outputFormatType.outFormat 16 -g $outputFormatType.outFormat
19 #if $optionSequence.choose == 'Yes':
20 -s $optionSequence.value
21 #end if
22
23 17
24 -n $name 18 -n $name
25 $strand 19 $strand
26 -o $outputFile 20 -o $outputFile
27 21
29 <inputs> 23 <inputs>
30 <conditional name="inputFormatType"> 24 <conditional name="inputFormatType">
31 <param name="FormatInputFileName" type="select" label="Input File Format"> 25 <param name="FormatInputFileName" type="select" label="Input File Format">
32 <option value="gff3">GFF3</option> 26 <option value="gff3">GFF3</option>
33 <option value="bed">BED</option> 27 <option value="bed">BED</option>
34 <option value="gff2">GFF2</option>
35 <option value="bam">BAM</option> 28 <option value="bam">BAM</option>
36 <option value="sam">SAM</option> 29 <option value="sam">SAM</option>
37 <option value="gtf">GTF</option> 30 <option value="gtf">GTF</option>
38 </param> 31 </param>
39 <when value="gff3"> 32 <when value="gff3">
40 <param name="inputFileName" format="gff3" type="data" label="Input File"/> 33 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
41 </when> 34 </when>
42 <when value="bed"> 35 <when value="bed">
43 <param name="inputFileName" format="bed" type="data" label="Input File"/> 36 <param name="inputFileName" format="bed" type="data" label="Input File"/>
44 </when>
45 <when value="gff2">
46 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
47 </when> 37 </when>
48 <when value="bam"> 38 <when value="bam">
49 <param name="inputFileName" format="bam" type="data" label="Input File"/> 39 <param name="inputFileName" format="bam" type="data" label="Input File"/>
50 </when> 40 </when>
51 <when value="sam"> 41 <when value="sam">
59 49
60 <conditional name="outputFormatType"> 50 <conditional name="outputFormatType">
61 <param name="outFormat" type="select" label="Please choose the format that you want to convert to (corresponding to your input file format)."> 51 <param name="outFormat" type="select" label="Please choose the format that you want to convert to (corresponding to your input file format).">
62 <option value="gff3">GFF3</option> 52 <option value="gff3">GFF3</option>
63 <option value="bed">BED</option> 53 <option value="bed">BED</option>
64 <option value="gff2">GFF2</option>
65 <option value="wig">WIG</option> 54 <option value="wig">WIG</option>
66 <option value="sam">SAM</option> 55 <option value="sam">SAM</option>
67 <option value="csv">CSV</option> 56 <option value="csv">CSV</option>
68 <option value="gtf">GTF</option> 57 <option value="gtf">GTF</option>
69 </param> 58 </param>
70 <when value="gff3"> 59 <when value="gff3">
71 </when> 60 </when>
72 <when value="bed"> 61 <when value="bed">
73 </when>
74 <when value="gff2">
75 </when> 62 </when>
76 <when value="wig"> 63 <when value="wig">
77 </when> 64 </when>
78 <when value="sam"> 65 <when value="sam">
79 </when> 66 </when>
83 </when> 70 </when>
84 </conditional> 71 </conditional>
85 72
86 <param name="name" type="text" value="SMART" label="name for the transcripts"/> 73 <param name="name" type="text" value="SMART" label="name for the transcripts"/>
87 74
88 <conditional name="optionSequence">
89 <param name="choose" type="select" label="give the corresponding Multi-Fasta file (useful for EMBL format)">
90 <option value="Yes">Yes</option>
91 <option value="No" selected="true">No</option>
92 </param>
93 <when value="Yes">
94 <param name="value" type="data" format="mfa" />
95 </when>
96 <when value="No">
97 </when>
98 </conditional>
99
100 <param name="strand" type="boolean" truevalue="-t" falsevalue="" checked="false" label="consider the 2 strands as different (only useful for writing WIG files)"/> 75 <param name="strand" type="boolean" truevalue="-t" falsevalue="" checked="false" label="consider the 2 strands as different (only useful for writing WIG files)"/>
101 76
102 </inputs> 77 </inputs>
103 78
104 <outputs> 79 <outputs>
105 <data name="outputFile" format="gff3" label="$inputFormatType.FormatInputFileName to $outputFormatType.outFormat"> 80 <data name="outputFile" format="gff3" label="$inputFormatType.FormatInputFileName to $outputFormatType.outFormat">
106 <change_format> 81 <change_format>
107 <when input="outputFormatType.outFormat" value="bed" format="bed" /> 82 <when input="outputFormatType.outFormat" value="bed" format="bed" />
108 <when input="outputFormatType.outFormat" value="gff2" format="gff2" /> 83 <when input="outputFormatType.outFormat" value="gff" format="gff" />
109 <when input="outputFormatType.outFormat" value="wig" format="wig" /> 84 <when input="outputFormatType.outFormat" value="wig" format="wig" />
110 <when input="outputFormatType.outFormat" value="sam" format="sam" /> 85 <when input="outputFormatType.outFormat" value="sam" format="sam" />
111 <when input="outputFormatType.outFormat" value="csv" format="csv" /> 86 <when input="outputFormatType.outFormat" value="csv" format="csv" />
112 <when input="outputFormatType.outFormat" value="gtf" format="gtf" /> 87 <when input="outputFormatType.outFormat" value="gtf" format="gtf" />
113 </change_format> 88 </change_format>
114 </data> 89 </data>
115 </outputs> 90 </outputs>
116 91
117 <help> 92 <help>
93 Simple conversion tool.
118 </help> 94 </help>
119 </tool> 95 </tool>