Mercurial > repos > charles-bernard > alfa

comparison ALFA/alfa_wrapper.xml @ 29:c8acc8808b52 draft

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Uploaded
author charles-bernard
date Sat, 19 Nov 2016 04:25:42 -0500
parents c3f91012ac19
children
comparison
equal deleted inserted replaced
28:2496883e588b 29:c8acc8808b52
14 14
15 --project_name "${projectName}" 15 --project_name "${projectName}"
16 16
17 ##__INPUT 1__## 17 ##__INPUT 1__##
18 #if str ( $annotation.annotationSource['annotationSourceSelection'] ) == "index" 18 #if str ( $annotation.annotationSource['annotationSourceSelection'] ) == "index"
19 --index $annotation.annotationSource['strandedIndex'] $annotation.annotationSource['unstrandedIndex'] 19 --index "$annotation.annotationSource['strandedIndex']" "$annotation.annotationSource['unstrandedIndex']"
20 #else if str ( $annotation.annotationSource['annotationSourceSelection'] ) == "built_in_index" 20 #else if str ( $annotation.annotationSource['annotationSourceSelection'] ) == "built_in_index"
21 --bi_index $annotation.annotationSource.built_in_index_prefix.fields.prefix 21 --bi_index "$annotation.annotationSource.built_in_index_prefix.fields.prefix"
22 #else 22 #else
23 --annotation $annotation.annotationSource['annotationFile'] 23 --annotation "$annotation.annotationSource['annotationFile']"
24 #end if 24 #end if
25 25
26 ##__INPUT 2__## 26 ##__INPUT 2__##
27 --reads_format $reads.readsType['readsTypeSelection'] 27 --reads_format $reads.readsType['readsTypeSelection']
28 --reads 28 --reads
29 #for $i, $r in enumerate ( $reads.readsType['readsList'] ) 29 #for $i, $r in enumerate ( $reads.readsType['readsList'] )
30 __fname__$r.readsFile 30 "__fname__$r.readsFile"
31 __label__$r.readsLabel 31 "__label__$r.readsLabel"
32 #end for 32 #end for
33 --strandness $reads['strandness'] 33 --strandness $reads['strandness']
34 34
35 ##__OUTPUT FILES__## 35 ##__OUTPUT FILES__##
36 #if str ( $outputFiles['plot'] ) == "True" 36 #if str ( $outputFiles['plot'] ) == "True"
37 #if str ( $outputOptions['plotFormat'] ) == "pdf" 37 #if str ( $outputOptions['plotFormat'] ) == "pdf"
38 --output_pdf $outputPdf 38 --output_pdf "$outputPdf"
39 #else if str ( $outputOptions['plotFormat'] ) == "png" 39 #else if str ( $outputOptions['plotFormat'] ) == "png"
40 --output_png $outputCategoriesPng $outputBiotypesPng 40 --output_png "$outputCategoriesPng" "$outputBiotypesPng"
41 #else 41 #else
42 --output_svg $outputCategoriesSvg $outputBiotypesSvg 42 --output_svg "$outputCategoriesSvg" "$outputBiotypesSvg"
43 #end if 43 #end if
44 #end if 44 #end if
45 #if str ( $outputFiles['countFile'] ) == "True" 45 #if str ( $outputFiles['countFile'] ) == "True"
46 --output_count $outputCountFile 46 --output_count "$outputCountFile"
47 #end if 47 #end if
48 #if str ( $outputFiles['index'] ) == "True" 48 #if str ( $outputFiles['index'] ) == "True"
49 --output_index $outputStrandedIndex $outputUnstrandedIndex 49 --output_index "$outputStrandedIndex" "$outputUnstrandedIndex"
50 #end if 50 #end if
51 51
52 ##__OUTPUT OPTIONS__## 52 ##__OUTPUT OPTIONS__##
53 --categories_depth $outputOptions['categoriesDepth'] 53 --categories_depth $outputOptions['categoriesDepth']
54 #if str ( $outputFiles['plot'] ) == "True" 54 #if str ( $outputFiles['plot'] ) == "True"
56 #if str ( $outputOptions.plotThreshold['plotThresholdChoice'] ) == "True" 56 #if str ( $outputOptions.plotThreshold['plotThresholdChoice'] ) == "True"
57 --threshold $outputOptions.plotThreshold.yMin $outputOptions.plotThreshold.yMax 57 --threshold $outputOptions.plotThreshold.yMin $outputOptions.plotThreshold.yMax
58 #end if 58 #end if
59 #end if 59 #end if
60 60
61 --log_report $logReport 61 --log_report "$logReport"
62 --tool_dir $__tool_directory__ 62 --tool_dir "$__tool_directory__"
63 ]]> 63 ]]>
64 </command> 64 </command>
65 <inputs> 65 <inputs>
66 <param name="projectName" value="ALFA" type="text" size="20" label="Project Name"> 66 <param name="projectName" value="ALFA" type="text" size="20" label="Project Name">
67 <validator type="empty_field" message="Please, specify a name for your project."/> 67 <validator type="empty_field" message="Please, specify a name for your project."/>