Mercurial > repos > iuc > rgrnastar

annotate rg_rnaStar.xml @ 30:4014de1b6daf draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
author iuc
date Tue, 27 Aug 2024 14:11:16 +0000
parents 3e94726bfa9d
children
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a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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1 <tool id="rna_star" name="RNA STAR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
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2 <description>Gapped-read mapper for RNA-seq data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="edam"/>
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7 <xrefs>
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8 <xref type="bio.tools">star</xref>
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9 </xrefs>
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10 <expand macro="requirements"/>
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11 <expand macro="stdio" />
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12
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318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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13 <!--
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14 important quote (https://groups.google.com/forum/#!topic/rna-star/q4zGzlPgwXY):
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15 Hi Gary,
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17 if you generate the genome with GTF file, and do not specify the value for - -sjdbOverhang, it will be set to the default 100.
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18 If you want to be able to set arbitrary value of - -sjdbOverhang on the fly, you have to generate the genome without annotations (GTF) - then you supply both the - -sjdbOverhang and GTF file at the mapping step.
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20 Cheers
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21 Alex
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22 -->
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23 <command><![CDATA[
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24 @TEMPINDEX@
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25 STAR
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26 @REFGENOMEHANDLING@
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28 --readFilesIn
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29 #if str($singlePaired.sPaired) == 'paired_collection':
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30 '$singlePaired.input.forward' '$singlePaired.input.reverse'
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32 #if $singlePaired.input.forward.is_of_type('fastq.gz', 'fastqsanger.gz'):
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33 @FASTQ_GZ_OPTION@
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34 #end if
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35 #else
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36 '$singlePaired.input1'
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37 #if str($singlePaired.sPaired) == 'paired':
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38 '$singlePaired.input2'
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39 #end if
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41 #if $singlePaired.input1.is_of_type('fastq.gz', 'fastqsanger.gz'):
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42 @FASTQ_GZ_OPTION@
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43 #end if
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44 #end if
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45
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46 --outSAMtype BAM SortedByCoordinate
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47
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48 ## Two pass mode
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49 --twopassMode ${twopass.twopassMode} ${twopass.twopass_read_subset}
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50 #if str($twopass.sj_precalculated).strip():
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51 #for $sj_input in $twopass.sj_precalculated:
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52 '$sj_input'
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53 #end for
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54 #end if
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55 #if str($twopass.twopassMode) != 'None':
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56 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
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57 ## need to check first if its a cached index or from history
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58 ## if it's cached then the sjdbGTFfile and sjdbOverhang params are not provided
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59 #if str($refGenomeSource.geneSource) == 'history':
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60 #if not $refGenomeSource.GTFconditional.sjdbGTFfile:
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61 ## case of cached index without built-in gene model,
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62 ## when user does not supply the optional gtf, but
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63 ## specifies the splice junction overhang
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64 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
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65 #end if
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66 #end if
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67 #end if
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68 #end if
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69
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70 --quantMode ${refGenomeSource.GTFconditional.quantmode_output.quantMode}
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71 #if 'TranscriptomeSAM' in str($refGenomeSource.GTFconditional.quantmode_output.quantMode):
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72 --quantTranscriptomeBan ${refGenomeSource.GTFconditional.quantmode_output.quantTranscriptomeBan}
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73 #end if
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74
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75 ## Output format parameters
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77 ## Read tags
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78 #set read_tags = str($oformat.outSAMattributes).split(',')
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79 #if 'XS' in str($oformat.outSAMattributes):
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80 ## STAR writes XS tag when --outSAMstrandField intronMotif is used
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81 $read_tags.remove('XS')
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82 --outSAMstrandField intronMotif
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83 #end if
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84 #if 'HI' in str($oformat.outSAMattributes):
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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85 --outSAMattrIHstart ${oformat.HI_offset}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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86 #end if
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87 #set $tag_names = ' '.join($read_tags)
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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88 --outSAMattributes $tag_names
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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89
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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90 ## Read FLAG
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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91 --outSAMprimaryFlag ${oformat.outSAMprimaryFlag}
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92
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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93 ## Read MAPQ
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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94 --outSAMmapqUnique ${oformat.outSAMmapqUnique}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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95
28
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96 ## Transform diploid mode output to reference coordinates
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97 #if str($refGenomeSource.geneSource) == 'history':
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98 #if 'diploidconditional' in $refGenomeSource:
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99 #if str($refGenomeSource.diploidconditional.diploid) == 'Yes':
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100 '${refGenomeSource.diploidconditional.genomeTransformOutput}'
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101 #end if
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102 #end if
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103 #end if
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104
10
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105 ## Output filter parameters
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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106
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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107 ## Basic Filters
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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108 #if str($filter.basic_filters) != 'None':
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109 #set $filter_options = str($filter.basic_filters).split(',')
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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110 #else:
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111 #set filter_options = []
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112 #end if
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113 #if 'exclude_unmapped' in $filter_options:
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114 $filter_options.remove('exclude_unmapped')
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115 --outSAMunmapped None
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116 #else:
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117 --outSAMunmapped Within
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118 #end if
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119 #if '--outFilterIntronMotifs RemoveNoncanonical' in $filter_options:
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120 ## RemoveNoncanonical excludes a superset of the reads excluded
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121 ## with RemoveNoncanonicalUnannotated
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122 #if '--outFilterIntronMotifs RemoveNoncanonicalUnannotated' in $filter_options:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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123 $filter_options.remove('--outFilterIntronMotifs RemoveNoncanonicalUnannotated')
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124 #end if
10
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125 #end if
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126 #echo ' '.join($filter_options)
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127
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128 ## Other Filters
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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129 #if str( $filter.output_params2.output_select2 ) == 'yes':
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130 --outFilterType $filter.output_params2.outFilterType
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131 --outFilterMultimapScoreRange $filter.output_params2.outFilterMultimapScoreRange
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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132 --outFilterMultimapNmax $filter.output_params2.outFilterMultimapNmax
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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133 --outFilterMismatchNmax $filter.output_params2.outFilterMismatchNmax
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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134 --outFilterMismatchNoverLmax $filter.output_params2.outFilterMismatchNoverLmax
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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135 --outFilterMismatchNoverReadLmax $filter.output_params2.outFilterMismatchNoverReadLmax
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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136 --outFilterScoreMin $filter.output_params2.outFilterScoreMin
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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137 --outFilterScoreMinOverLread $filter.output_params2.outFilterScoreMinOverLread
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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138 --outFilterMatchNmin $filter.output_params2.outFilterMatchNmin
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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139 --outFilterMatchNminOverLread $filter.output_params2.outFilterMatchNminOverLread
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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140 --outSAMmultNmax $filter.output_params2.outSAMmultNmax
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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141 --outSAMtlen $filter.output_params2.outSAMtlen
2
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142 #end if
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143
3
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144 ## Other parameters
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145 #if str( $algo.params.settingsType ) == 'star_fusion':
3
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146 ## Preset parameters for STAR-Fusion
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147 --chimSegmentMin 12
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148 --chimJunctionOverhangMin 12
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149 --alignSJDBoverhangMin 10
10
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150 --alignMatesGapMax 100000
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151 --alignIntronMax 100000
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152 --chimSegmentReadGapMax 3
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153 --alignSJstitchMismatchNmax 5 -1 5 5
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154 --peOverlapNbasesMin 12
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155 --peOverlapMMp 0.1
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156 --chimMultimapScoreRange 10
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157 --chimMultimapNmax 10
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158 --chimNonchimScoreDropMin 10
22
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159
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160 #elif str( $algo.params.settingsType ) == 'arriba':
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161 ## Preset parameters for Arriba
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162 --peOverlapNbasesMin 10
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163 --alignSplicedMateMapLminOverLmate 0.5
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164 --alignSJstitchMismatchNmax 5 -1 5 5
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165 --chimSegmentMin 10
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166 --chimJunctionOverhangMin 10
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167 --chimScoreDropMax 30
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168 --chimScoreJunctionNonGTAG 0
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169 --chimScoreSeparation 1
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170 --chimSegmentReadGapMax 3
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171 --chimMultimapNmax 50
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172
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173 #elif str( $algo.params.settingsType ) == 'full':
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174 ## Extended parameter options
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175
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176 ## Seed parameter options
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177 --seedSearchStartLmax ${algo.params.seed.seedSearchStartLmax}
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178 --seedSearchStartLmaxOverLread ${algo.params.seed.seedSearchStartLmaxOverLread}
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179 --seedSearchLmax ${algo.params.seed.seedSearchLmax}
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180 --seedMultimapNmax ${algo.params.seed.seedMultimapNmax}
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181 --seedPerReadNmax ${algo.params.seed.seedPerReadNmax}
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182 --seedPerWindowNmax ${algo.params.seed.seedPerWindowNmax}
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183 --seedNoneLociPerWindow ${algo.params.seed.seedNoneLociPerWindow}
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184
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185 ## Alignment parameter options
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186 --alignIntronMin ${algo.params.align.alignIntronMin}
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187 --alignIntronMax ${algo.params.align.alignIntronMax}
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188 --alignMatesGapMax ${algo.params.align.alignMatesGapMax}
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189 --alignSJoverhangMin ${algo.params.align.alignSJoverhangMin}
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190 --alignSJstitchMismatchNmax ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax1} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax2} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax3} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax4}
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191 --alignSJDBoverhangMin ${algo.params.align.alignSJDBoverhangMin}
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192 --alignSplicedMateMapLmin ${algo.params.align.alignSplicedMateMapLmin}
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193 --alignSplicedMateMapLminOverLmate ${algo.params.align.alignSplicedMateMapLminOverLmate}
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194 --alignWindowsPerReadNmax ${algo.params.align.alignWindowsPerReadNmax}
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195 --alignTranscriptsPerWindowNmax ${algo.params.align.alignTranscriptsPerWindowNmax}
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196 --alignTranscriptsPerReadNmax ${algo.params.align.alignTranscriptsPerReadNmax}
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197 --alignEndsType ${algo.params.align.alignEndsType}
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198 --peOverlapNbasesMin ${algo.params.align.peOverlapNbasesMin}
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199 --peOverlapMMp ${algo.params.align.peOverlapMMp}
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200 ## Chimeric alignment parameter options
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201 #if str($chimOutType):
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202 --chimSegmentMin ${algo.params.chim_settings.chimSegmentMin}
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203 --chimScoreMin ${algo.params.chim_settings.chimScoreMin}
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204 --chimScoreDropMax $algo.params.chim_settings.chimScoreDropMax
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205 --chimScoreSeparation $algo.params.chim_settings.chimScoreSeparation
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206 --chimScoreJunctionNonGTAG $algo.params.chim_settings.chimScoreJunctionNonGTAG
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207 --chimSegmentReadGapMax $algo.params.chim_settings.chimSegmentReadGapMax
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208 --chimFilter $algo.params.chim_settings.chimFilter
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209 --chimJunctionOverhangMin $algo.params.chim_settings.chimJunctionOverhangMin
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210 --chimMainSegmentMultNmax $algo.params.chim_settings.chimMainSegmentMultNmax
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211 #if str($chimOutType) == 'Junctions':
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212 --chimMultimapNmax $algo.params.chim_settings.chimMultimapNmax
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213 #else:
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214 --chimMultimapNmax 0
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215 #end if
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216 --chimMultimapScoreRange $algo.params.chim_settings.chimMultimapScoreRange
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217 #end if
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218
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219 ## Limits
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220 @LIMITS@
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221 #else:
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222 ## Go with STAR's default algorithmic settings,
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223 ## but we need to provide a reasonable default
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224 ## (taken from STAR-Fusion)
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225 ## for --chimSegmentMin in case the user enabled chimeric
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226 ## alignments (the STAR default is 0, which disables chimeric
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227 ## alignments). For consistency, also set
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228 ## --chimMultimapNmax to 1 when chimeric alignments are reported
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229 ## in Junctions format only.
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230 #if str($chimOutType):
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231 --chimSegmentMin 12
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232 #if str($chimOutType) == 'Junctions':
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233 --chimMultimapNmax 1
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234 #end if
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235 #end if
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236 #end if
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237 --outBAMsortingThreadN \${GALAXY_SLOTS:-4}
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238 --outBAMsortingBinsN $perf.outBAMsortingBinsN
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239 --winAnchorMultimapNmax $perf.winAnchorMultimapNmax
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240 --limitBAMsortRAM \$((\${GALAXY_MEMORY_MB:-0}*1000000))
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241
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242 #if $oformat.wasp_conditional.waspOutputMode == "wasp_mode":
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243 --waspOutputMode SAMtag
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244 --varVCFfile '$oformat.wasp_conditional.varVCFfile'
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245 #end if
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246
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247 ## Handle chimeric options and output
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248 #if str($chimOutType):
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249 --chimOutType $chimOutType
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250 #if 'Junctions' in str($chimOutType):
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251 --chimOutJunctionFormat 1
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252 #end if
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253 #end if
23
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254
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255 ##outWig:
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256 @OUTWIG@
3
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257 &&
10
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258 ## recompress BAM output for smaller file size
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259 samtools view -b -o '$mapped_reads' Aligned.sortedByCoord.out.bam
23
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260 #if 'TranscriptomeSAM' in str($refGenomeSource.GTFconditional.quantmode_output.quantMode):
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261 ## same recompression for optional transcriptome BM
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262 &&
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263 samtools view -b -o '$transcriptome_mapped_reads' Aligned.toTranscriptome.out.bam
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264 #end if
23
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265 ##outWig:
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266 @OUTWIGOUTPUTS@
1
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267 ]]></command>
0
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268
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269 <inputs>
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270 <!-- FASTQ input(s) and options specifically for paired-end data. -->
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271 <conditional name="singlePaired">
2
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272 <param name="sPaired" type="select" label="Single-end or paired-end reads">
3
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273 <option value="single" selected="true">Single-end</option>
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274 <option value="paired">Paired-end (as individual datasets)</option>
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275 <option value="paired_collection">Paired-end (as collection)</option>
0
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276 </param>
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277 <when value="single">
3
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278 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file"/>
0
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279 </when>
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280 <when value="paired">
3
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281 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file, forward reads"/>
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282 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data" label="RNA-Seq FASTQ/FASTA file, reverse reads"/>
2
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283 </when>
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284 <when value="paired_collection">
3
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285 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input" type="data_collection" collection_type="paired" label="RNA-Seq FASTQ/FASTA paired reads"/>
0
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286 </when>
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287 </conditional>
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288
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289 <!-- Genome source. -->
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290 <conditional name="refGenomeSource">
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291 <param name="geneSource" type="select" label="Custom or built-in reference genome" help="Built-ins were indexed using default options">
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292 <option value="indexed" selected="true">Use a built-in index</option>
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293 <option value="history">Use reference genome from history and create temporary index</option>
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294 </param>
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295 <when value="indexed">
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296 <conditional name="GTFconditional">
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297 <param name="GTFselect" type="select"
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298 label="Reference genome with or without an annotation"
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299 help="Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions, and, optionally, provide your own splice-junction annonations.">
23
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300 <option value="without-gtf-with-gtf" selected='true'>use genome reference without builtin gene-model but provide a gtf</option>
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301 <option value="without-gtf">use genome reference without builtin gene-model and do not provide a gtf</option>
15
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302 <option value="with-gtf">use genome reference with builtin gene-model</option>
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303 </param>
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304 <when value="with-gtf">
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305 <expand macro="index_selection" with_gene_model="1" />
23
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306 <expand macro="quantMode" />
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307 </when>
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308 <when value="without-gtf-with-gtf">
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309 <expand macro="index_selection" with_gene_model="0" />
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310 <expand macro="SJDBOPTIONS"/>
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311 <expand macro="quantMode" />
15
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312 </when>
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313 <when value="without-gtf">
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314 <expand macro="index_selection" with_gene_model="0" />
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315 <expand macro="quantModeNoGTF" />
15
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316 </when>
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317 </conditional>
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318 </when>
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319 <when value="history">
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320 <expand macro="ref_selection" />
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321 <conditional name="GTFconditional">
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322 <param name="GTFselect" type="select"
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323 label="Build index with or without known splice junctions annotation"
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324 help="To build an index with known splice junctions annotated, you will have to provide a GTF or GFF3 dataset that describes the gene models (the location of genes, transcripts and exons) known for the reference genome.">
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325 <option value="without-gtf">build index without gene-model</option>
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326 <option value="with-gtf">build index with gene-model</option>
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327 </param>
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328 <when value="with-gtf">
23
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329 <expand macro="SJDBOPTIONS"/>
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330 <expand macro="quantMode" />
15
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331 </when>
23
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332 <when value="without-gtf">
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333 <expand macro="quantModeNoGTF" />
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334 </when>
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335 </conditional>
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336 <conditional name="diploidconditional">
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337 <param name="diploid" type="select" label="Diploid mode" help="Map RNA-seq reads to a diploid genome">
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338 <option value="No" selected="True">No</option>
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339 <option value="Yes">Yes</option>
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340 </param>
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341 <when value="Yes">
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342 <param argument="--genomeTransformVCF" type="data" format="vcf" label="VCF file with diploid SNVs and InDels" help="The homozygous and heterozygous alleles from this VCF will be inserted into the reference genome to create a transformed genome with two haplotypes"/>
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343 <param argument="--genomeTransformOutput" type="boolean" checked="false" truevalue="--genomeTransformOutput SAM SJ Quant" falsevalue="--genomeTransformOutput None" label="Transform alignments, spliced junctions and quantifications back to the reference coordinates" help="Use this if downstream processing relies on reference coordinates"/>
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344 </when>
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345 <when value="No">
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346 </when>
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347 </conditional>
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348 </when>
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349 </conditional>
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350
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351 <conditional name="twopass">
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352 <param argument="--twopassMode" type="select"
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353 label="Use 2-pass mapping for more sensitive novel splice junction discovery"
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354 help="For a study with multiple samples, multisample 2-pass mapping is the most sensitive approach. It involves two separate runs of STAR for each sample, where, in the second run of each sample, the splice junctions found in any sample in the first runs are treated as additional known junctions. If you plan to use the mapping results as input for STAR-Fusion it is recommended that you use at least single-sample 2-pass mapping of all reads.">
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355 <option value="None">No</option>
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356 <option value="Basic">Yes, perform single-sample 2-pass mapping of all reads</option>
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357 <option value="Basic --twopass1readsN">Yes, but base novel splice junction detection in the first pass on a subset of all reads (faster, but less sensitive than single-sample 2-pass mode)</option>
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358 <option value="None --sjdbFileChrStartEnd">Yes, I want to use multi-sample 2-pass mapping and I have obtained splice junctions datasets of all samples through previous 1-pass runs of STAR.</option>
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359 </param>
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360 <when value="None">
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361 <param name="twopass_read_subset" type="hidden" value="" />
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362 <param name="sj_precalculated" type="hidden" value="" />
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363 </when>
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364 <when value="Basic">
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365 <param name="twopass_read_subset" type="hidden" value="" />
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366 <param name="sj_precalculated" type="hidden" value="" />
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367 </when>
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368 <when value="Basic --twopass1readsN">
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369 <param name="sj_precalculated" type="hidden" value="" />
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370 <param argument="--twopass1readsN" name="twopass_read_subset" type="integer" min="1" value="50000" label="Number of reads to map in the first pass"/>
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371 </when>
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372 <when value="None --sjdbFileChrStartEnd">
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373 <param name="twopass_read_subset" type="hidden" value="" />
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374 <param name="sj_precalculated" type="data" multiple="true" format="interval"
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375 label="Pregenerated splice junctions datasets of your samples" />
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376 </when>
10
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377 </conditional>
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378 <param argument="--chimOutType" type="select"
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379 label="Report chimeric alignments?"
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380 help="Choose if and how chimeric alignments should be reported. STAR-Fusion users should select the 'Junctions' option and use the resulting tabular dataset as input to STAR-Fusion. Everyone else: note that selecting 'WithinBAM' or 'WithinBAM Junctions' disables the --chimMultimapNmax setting in the algorithmic parameters section below (the tool will only consider uniquely mapped reads in the search for chimeric alignments). If you disable the reporting of chimeric alignments here, then all chimeric alignment settings in the algorithmic parameters section below will be ignored.">
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381 <option value="">Don't report chimeric alignments</option>
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382 <option value="Junctions">As separate tabular "Junctions" output (Junctions)</option>
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383 <option value="WithinBAM">Within the BAM output (together with regular alignments; WithinBAM)</option>
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384 <option value="WithinBAM HardClip">Within the BAM output (together with regular alignments; WithinBAM HardClip) hard-clipping in the CIGAR for supplemental chimeric alignments</option>
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385 <option value="WithinBAM SoftClip">Within the BAM output (together with regular alignments; WithinBAM SoftClip) soft-clipping in the CIGAR for supplemental chimeric alignments</option>
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386 </param>
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387
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388 <section name="oformat" title="BAM output format specification" expanded="true">
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389 <param argument="--outSAMattributes" type="select" display="checkboxes" multiple="true" optional="true"
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390 label="Read alignment tags to include in the BAM output"
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391 help="Note on using the XS tag: If the XS tag is used, STAR will filter out alignments with undefined strand (i.e., those containing only non-canonical unannotated junctions). Using this tag is recommended if you plan to use the STAR results with STAR-Fusion. In addition, it is required for compatibility
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392 with Cufflinks if your sequences come from an unstranded library preparation.">
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393 <expand macro="common_SAM_attributes"/>
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394 <option value="MC">MC (CIGAR string for mate/next segment)</option>
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395 <option value="XS">XS (strand flag, see parameter help below) </option>
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396 <option value="ch" selected="true">ch (used to indicate chimeric alignments)</option> <!--This is not the default in STAR-->
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397 </param>
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398 <param argument="--outSAMattrIHstart" name="HI_offset" type="select" display="radio"
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399 label="HI tag values should be">
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400 <option value="1" selected="true">one-based</option>
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401 <option value="0">zero-based</option>
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402 </param>
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403 <!-- Using - -outSAMprimaryFlag AllBestScore would cause a
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404 violation of the SAM/BAM spec, which says:
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405 "For each read/contig in a SAM file, it is required that one and
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406 only one line associated with the read satisfies
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407 ‘FLAG & 0x900 == 0’.
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408 This line is called the primary line of the read."
2
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409
10
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410 Thus, this parameter has been removed from the tool interface:
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411 <param argument="- -outSAMprimaryFlag" type="boolean"
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412 truevalue="AllBestScore" falsevalue="OneBestScore" checked="false"
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413 label="Would you like all alignments with the best score labeled
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414 primary?"/> -->
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415 <param name="outSAMprimaryFlag" type="hidden" value="OneBestScore" />
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416 <expand macro="outSAMmapqUnique"/>
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417 <expand macro="wasp"/>
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418 </section>
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419 <section name="filter" title="Output filter criteria" expanded="true">
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420 <param name="basic_filters" type="select" display="checkboxes" multiple="true" optional="true"
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421 label="Exclude the following records from the BAM output">
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422 <option value="exclude_unmapped">Unmapped reads</option>
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423 <option value="--outFilterIntronStrands RemoveInconsistentStrands">Alignments that have junctions with inconsistent strands</option>
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424 <option value="--outFilterIntronMotifs RemoveNoncanonicalUnannotated">Alignments across unannotated non-canonical junctions</option>
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425 <option value="--outFilterIntronMotifs RemoveNoncanonical">All alignments across non-canonical junctions (recommended for compatibility with Cufflinks)</option>
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426 </param>
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427 <!-- Additional output parameter settings. -->
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428 <conditional name="output_params2">
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429 <param name="output_select2" type="select" label="Would you like to set additional output filters?">
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430 <option value="no" selected="true">No</option>
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431 <option value="yes">Yes</option>
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432 </param>
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433 <when value="yes">
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434 <param argument="--outFilterType" type="boolean" truevalue="BySJout" falsevalue="Normal" checked="false" label="Would you like to keep only reads that contain junctions that passed filtering?"/>
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435 <param argument="--outFilterMultimapScoreRange" type="integer" value="1" min="0" label="Score range below the maximum score for multimapping alignments"/>
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436 <param argument="--outFilterMultimapNmax" type="integer" value="10" min="1" label="Maximum number of alignments to output a read's alignment results, plus 1" help="Reads with at least this number of alignments will have no alignments output"/>
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437 <param argument="--outFilterMismatchNmax" type="integer" value="10" min="0" label="Maximum number of mismatches to output an alignment, plus 1" help="Alignments with at least this number of mismatches will not be output"/>
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438 <param argument="--outFilterMismatchNoverLmax" type="float" value="0.3" min="0" max="1" label="Maximum ratio of mismatches to mapped length" help="Alignments with a mismatch ratio of at least this value will not be output"/>
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439 <param argument="--outFilterMismatchNoverReadLmax" type="float" value="1" min="0" max="1" label="Maximum ratio of mismatches to read length" help="Alignments with a mismatch ratio of at least this value will not be output"/>
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440 <param argument="--outFilterScoreMin" type="integer" value="0" min="0" label="Minimum alignment score" help="Alignments must have scores higher than this value to be output"/>
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441 <param argument="--outFilterScoreMinOverLread" type="float" value="0.66" min="0" max="1" label="Minimum alignment score, normalized to read length" help="Alignments must have (normalized) scores higher than this value to be output"/>
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442 <param argument="--outFilterMatchNmin" type="integer" value="0" min="0" label="Minimum number of matched bases" help="Alignments must have the number of matched bases higher than this value to be output"/>
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443 <param argument="--outFilterMatchNminOverLread" type="float" value="0.66" min="0" max="1" label="Minimum number of matched bases, normalized to read length" help="Alignments must have the (normalized) number of matched bases higher than this value to be output"/>
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444 <param argument="--outSAMmultNmax" type="integer" value="-1" min="-1" label="Maximum number of multimapping alignments to output for a read" help="A value of -1 (the default) results in all alignments (up to --outFilterMultimapNmax) being output" />
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445 <param argument="--outSAMtlen" type="select" label="Calculation method for TLEN">
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446 <option value="1" selected="true">leftmost base of the (+)strand mate to rightmost base of the (-)mate. (+)sign for the (+)strand mate</option>
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447 <option value="2">leftmost base of any mate to rightmost base of any mate. (+)sign for the mate with the leftmost base. This is different from 1 for overlapping mates with protruding ends</option>
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448 </param>
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449 </when>
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450 <when value="no"/>
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451 </conditional>
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452 </section>
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453
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454 <!-- Algorithmic settings. -->
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455 <section name="algo" title="Algorithmic settings" expanded="true">
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456 <conditional name="params">
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457 <param name="settingsType" type="select" label="Configure seed, alignment and limits options">
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458 <option value="default" selected="true">Use Defaults</option>
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459 <option value="star_fusion">Use parameters suggested for STAR-Fusion</option>
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460 <option value="arriba">Use parameters suggested for Arriba</option>
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461 <option value="full">Extended parameter list</option>
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462 </param>
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463 <when value="default"/>
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464 <!-- Set STAR-fusion parameters in command section -->
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465 <when value="star_fusion"/>
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466 <when value="arriba"/>
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467
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468 <when value="full">
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469 <section name="seed" title="Seed parameters" expanded="false">
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470 <param argument="--seedSearchStartLmax" type="integer" min="1" value="50" label="Search start point through the read"/>
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471 <param argument="--seedSearchStartLmaxOverLread" type="float" min="0" value="1.0" label="Search start point through the read, normalized to read length"/>
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472 <param argument="--seedSearchLmax" type="integer" min="0" value="0" label="Maximum length of seeds" help="Default of 0 indicates no maximum length"/>
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473 <param argument="--seedMultimapNmax" type="integer" min="1" value="10000" label="Maximum number of mappings to use a piece in stitching"/>
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474 <param argument="--seedPerReadNmax" type="integer" min="1" value="1000" label="Maximum number of seeds per read"/>
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475 <param argument="--seedPerWindowNmax" type="integer" min="1" value="50" label="Maximum number of seeds per window"/>
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476 <param argument="--seedNoneLociPerWindow" type="integer" min="1" value="10" label="Maximum number of one seed loci per window"/>
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477 </section>
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478
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479 <section name="align" title="Alignment parameters" expanded="false">
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480 <param argument="--alignIntronMin" type="integer" min="0" value="21" label="Minimum intron size"/>
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481 <param argument="--alignIntronMax" type="integer" min="0" value="0" label="Maximum intron size"/>
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482 <param argument="--alignMatesGapMax" type="integer" min="0" value="0" label="Maximum gap between two mates"/>
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483 <param argument="--alignSJoverhangMin" type="integer" min="1" value="5" label="Minimum overhang for spliced alignments"/>
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484 <section name="alignSJstitchMismatchNmax" title="Maximum number of mismatches for stitching of the splice junctions (-1: no limit)" expanded="true">
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485 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax1" type="integer" min="-1" value="0" label="Non-canonical motifs"/>
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486 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax2" type="integer" min="-1" value="-1" label="GT/AG and CT/AC motif"/>
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
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parents: 20
diff changeset
487 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax3" type="integer" min="-1" value="0" label="GC/AG and CT/GC motif"/>
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents: 20
diff changeset
488 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax4" type="integer" min="-1" value="0" label="AT/AC and GT/AT motif"/>
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
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parents: 20
diff changeset
489 </section>
10
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parents: 9
diff changeset
490 <param argument="--alignSJDBoverhangMin" type="integer" min="1" value="3" label="Minimum overhang for annotated spliced alignments"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
491 <param argument="--alignSplicedMateMapLmin" type="integer" min="0" value="0" label="Minimum mapped length for a read mate that is spliced"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
492 <param argument="--alignSplicedMateMapLminOverLmate" type="float" min="0" value="0.66" label="Minimum mapped length for a read mate that is spliced, normalized to mate length"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
493 <param argument="--alignWindowsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of windows per read"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
494 <param argument="--alignTranscriptsPerWindowNmax" type="integer" min="1" value="100" label="Maximum number of transcripts per window"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
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495 <param argument="--alignTranscriptsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of different alignments per read to consider"/>
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parents: 22
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496 <param argument="--alignEndsType" type="select" label="type of read ends alignment">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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parents: 22
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497 <option value="Local">standard local alignment with soft-clipping allowed</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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parents: 22
diff changeset
498 <option value="EndToEnd">force end-to-end read alignment, do not soft-clip</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
499 <option value="Extend5pOfRead1">fully extend only the 5p of the read1, all other ends: local alignment</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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parents: 22
diff changeset
500 <option value="Extend5pOfReads12">fully extend only the 5p of the both read1 and read2, all other ends: local alignment</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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parents: 22
diff changeset
501 </param>
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parents: 9
diff changeset
502 <param argument="--peOverlapNbasesMin" type="integer" min="0" value="0"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
503 label="minimum number of overlap bases to trigger mates merging and realignment" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
504 <param argument="--peOverlapMMp" type="float" min="0" max="1" value="0.01"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
505 label="maximum proportion of mismatched bases in the overlap area" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
506 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
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507 <section name="chim_settings" title="Chimeric alignment parameters" expanded="false">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
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508 <param argument="--chimSegmentMin" type="integer" min="1" value="12"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
509 label="Minimum length of chimeric segment"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
510 help="For small numbers this will cause large number of chimeric alignments. A value of 12 is commonly used." />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
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511 <param argument="--chimScoreMin" type="integer" min="0" value="0"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
512 label="Minimum total (summed) score of chimeric segments"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
513 <param argument="--chimScoreDropMax" type="integer" min="0" value="20"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
514 label="Maximum difference of chimeric score from read length"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
515 <param argument="--chimScoreSeparation" type="integer" min="0" value="10"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
516 label="Minimum difference between the best chimeric score and the next one"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
517 <param argument="--chimScoreJunctionNonGTAG" type="integer" value="-1"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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518 label="Penalty for a non-GT/AG chimeric junction"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
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519 <param argument="--chimJunctionOverhangMin" type="integer" min="0" value="20"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
520 label="Minimum overhang for a chimeric junction"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
521 <param argument="--chimSegmentReadGapMax" type="integer" min="0" value="0"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
522 label="Maximum gap in the read sequence between chimeric segments" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
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523 <param argument="--chimFilter" type="boolean" truevalue="banGenomicN" falsevalue="None" checked="true"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
524 label="Discard chimeric alignments with Ns in the genome sequence around the chimeric junction" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
525 <param argument="--chimMainSegmentMultNmax" type="integer" min="1" value="10"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
526 label="Maximum number of multi-alignments for the main chimeric segment."
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
527 help="A value of 1 prohibits multimapping main segments"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
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528 <param argument="--chimMultimapNmax" type="integer" min="1" value="1"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
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529 label="Maximum number of chimeric multi-alignments"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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diff changeset
530 help="The default value of 1 only considers unique alignments. If you chose to report chimeric alignments alongside regular ones in the BAM output, this setting is ignored and only uniquely mapping chimeric reads get reported. " />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
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531 <param argument="--chimMultimapScoreRange" type="integer" min="0" value="1"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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532 label="Score range for multi-mapping chimeras"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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diff changeset
533 help="The threshold below the best chimeric score that a multimapping chimera must have to be output. This is ignored unless --chimMultimapNmax is above 1" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
534 </section>
23
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parents: 22
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535 <expand macro="limits" />
10
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536 </when>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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537 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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538 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
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539 <section name="perf" title="Performance tweaks / Troubleshooting" expanded="false">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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diff changeset
540 <param argument="--outBAMsortingBinsN" type="integer" value="50" min="1" label="Number of genome bins for coordinate-sorting" help="Higher values result in lower RAM requirements during the sorting step. The default value is 50. Tweak this if you are facing memory-related errors." />
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parents: 18
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541 <param argument="--winAnchorMultimapNmax" type="integer" value="50" min="50" label="Maximum number of loci anchors are allowed to map to" help="Higher value can increase the runtime singificantly. This value should be set greater or equal to --outFilterMultimapNmax" />
10
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542 </section>
23
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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parents: 22
diff changeset
543 <expand macro="outWig"/>
0
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544 </inputs>
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545
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
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546 <outputs>
8
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parents: 7
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547 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out">
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167
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parents: 7
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548 <expand macro="dbKeyActions" />
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167
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parents: 7
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549 </data>
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
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550
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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parents: 2
diff changeset
551 <data format="interval" name="chimeric_junctions" label="${tool.name} on ${on_string}: chimeric junctions" from_work_dir="Chimeric.out.junction">
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d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
552 <filter>('Junctions' in chimOutType)</filter>
8
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167
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parents: 7
diff changeset
553 <expand macro="dbKeyActions" />
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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parents: 2
diff changeset
554 </data>
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parents: 2
diff changeset
555
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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parents: 2
diff changeset
556 <data format="interval" name="splice_junctions" label="${tool.name} on ${on_string}: splice junctions.bed" from_work_dir="SJ.out.tab">
8
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167
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parents: 7
diff changeset
557 <expand macro="dbKeyActions" />
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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parents: 2
diff changeset
558 </data>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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parents: 2
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559
10
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parents: 9
diff changeset
560 <data name="mapped_reads" format="bam" label="${tool.name} on ${on_string}: mapped.bam">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
561 <expand macro="dbKeyActions" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
562 </data>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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diff changeset
563
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
564 <data name="transcriptome_mapped_reads" format="unsorted.bam" label="${tool.name} on ${on_string}: transcriptome-mapped.bam" >
23
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
565 <filter>'TranscriptomeSAM' in refGenomeSource['GTFconditional']['quantmode_output']['quantMode']</filter>
8
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167
iuc
parents: 7
diff changeset
566 <expand macro="dbKeyActions" />
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
567 </data>
9
0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7
iuc
parents: 8
diff changeset
568
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
569 <data name="reads_per_gene" format="tabular" label="${tool.name} on ${on_string}: reads per gene" from_work_dir="ReadsPerGene.out.tab">
23
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
570 <filter>'GeneCounts' in refGenomeSource['GTFconditional']['quantmode_output']['quantMode']</filter>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
571 <expand macro="outCountActions" />
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
572 </data>
23
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
573 <expand macro="outWigOutputs"/>
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
574 </outputs>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
575 <tests>
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
576 <test expect_num_outputs="3">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
577 <conditional name="singlePaired">
30
4014de1b6daf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
iuc
parents: 28
diff changeset
578 <param name="sPaired" value="paired" />
4014de1b6daf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
iuc
parents: 28
diff changeset
579 <param name="input1" value="pbmc_1k_v2_L001.R1.10k.fastq.gz" ftype="fastqsanger.gz" />
4014de1b6daf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
iuc
parents: 28
diff changeset
580 <param name="input2" value="pbmc_1k_v2_L001.R2.10k.fastq.gz" ftype="fastqsanger.gz" />
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
581 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
582 <conditional name="refGenomeSource">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
583 <param name="geneSource" value="history" />
30
4014de1b6daf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
iuc
parents: 28
diff changeset
584 <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" />
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
585 <param name="genomeSAindexNbases" value="5" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
586 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
587 <section name="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
588 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
30
4014de1b6daf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
iuc
parents: 28
diff changeset
589 <conditional name="wasp_conditional">
4014de1b6daf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
iuc
parents: 28
diff changeset
590 <param name="waspOutputMode" value="wasp_mode"/>
4014de1b6daf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
iuc
parents: 28
diff changeset
591 <param name="varVCFfile" value="filtered3.vcf" ftype="vcf" />
4014de1b6daf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
iuc
parents: 28
diff changeset
592 </conditional>
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
593 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
594 <section name="algo">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
595 <conditional name="params">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
596 <param name="settingsType" value="default" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
597 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
598 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
599 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
30
4014de1b6daf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
iuc
parents: 28
diff changeset
600 <output name="splice_junctions" file="rnastar_test_splicejunctions_wasp.bed"/>
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
601 </test>
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
602 <!-- test with cached genome index -->
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
603 <test expect_num_outputs="3">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
604 <conditional name="singlePaired">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
605 <param name="sPaired" value="single" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
606 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
607 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
608 <conditional name="refGenomeSource">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
609 <param name="geneSource" value="indexed" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
610 <conditional name="GTFconditional">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
611 <param name="GTFselect" value="with-gtf" />
11
41929aa1e7f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2911002ccd79fe062f6346ee5699ea262f92f04f"
iuc
parents: 10
diff changeset
612 <param name="genomeDir" value="001" />
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
613 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
614 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
615 <section name="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
616 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
617 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
618 <section name="algo">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
619 <conditional name="params">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
620 <param name="settingsType" value="default" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
621 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
622 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
623 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
624 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
625 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
626 </test>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
627 <!-- test gtf file and GeneCounts mode -->
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
628 <test expect_num_outputs="4">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
629 <conditional name="singlePaired">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
630 <param name="sPaired" value="single" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
631 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
632 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
633 <conditional name="refGenomeSource">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
634 <param name="geneSource" value="history" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
635 <param name="genomeFastaFiles" value="tophat_test.fa" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
636 <param name="genomeSAindexNbases" value="5" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
637 <conditional name="GTFconditional">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
638 <param name="GTFselect" value="with-gtf" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
639 <param name="sjdbOverhang" value="75"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
640 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/>
23
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
641 <conditional name="quantmode_output">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
642 <param name="quantMode" value="GeneCounts"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
643 </conditional>
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
644 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
645 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
646 <section name="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
647 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
648 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
649 <section name="algo">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
650 <conditional name="params">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
651 <param name="settingsType" value="default" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
652 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
653 </section>
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
654
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
655 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
656 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
657 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
24
4df95e2d7f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 23
diff changeset
658 <output name="reads_per_gene" file="tophat_test_reads_per_gene.txt">
4df95e2d7f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 23
diff changeset
659 <metadata name="column_names" value="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" />
4df95e2d7f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents: 23
diff changeset
660 </output>
1
bc685d13b637 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
parents: 0
diff changeset
661 </test>
27
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
662 <!-- Test if an alternative feature can be provided as a splicing unit.
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
663 If the splice feature set is not set correctly,
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
664 "Fatal INPUT FILE error, no exon lines in the GTF file" is expected -->
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
665 <test expect_num_outputs="4">
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
666 <conditional name="singlePaired">
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
667 <param name="sPaired" value="single" />
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
668 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
669 </conditional>
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
670 <conditional name="refGenomeSource">
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
671 <param name="geneSource" value="history" />
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
672 <param name="genomeFastaFiles" value="tophat_test.fa" />
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
673 <param name="genomeSAindexNbases" value="5" />
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
674 <conditional name="GTFconditional">
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
675 <param name="GTFselect" value="with-gtf" />
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
676 <param name="sjdbOverhang" value="75"/>
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
677 <param name="sjdbGTFfile" value="no_exon.gtf" ftype="gtf"/>
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
678 <param name="sjdbGTFfeatureExon" value="fakexon"/>
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
679 <conditional name="quantmode_output">
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
680 <param name="quantMode" value="GeneCounts"/>
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
681 </conditional>
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
682 </conditional>
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
683 </conditional>
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
684 <section name="oformat">
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
685 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
686 </section>
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
687 <section name="algo">
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
688 <conditional name="params">
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
689 <param name="settingsType" value="default" />
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
690 </conditional>
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
691 </section>
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
692
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
693 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
694 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
695 <output name="mapped_reads" file="rnastar_test_mapped_reads_fakexon.bam" compare="sim_size" delta="634" />
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
696 <output name="reads_per_gene" file="tophat_test_reads_per_gene.txt">
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
697 <metadata name="column_names" value="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" />
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
698 </output>
79de45b5069b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents: 24
diff changeset
699 </test>
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
700 <!-- test gtf file and TranscriptomeSAM mode -->
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
701 <test expect_num_outputs="4">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
702 <conditional name="singlePaired">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
703 <param name="sPaired" value="single" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
704 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
705 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
706 <conditional name="refGenomeSource">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
707 <param name="geneSource" value="history" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
708 <param name="genomeFastaFiles" value="tophat_test.fa" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
709 <param name="genomeSAindexNbases" value="5" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
710 <conditional name="GTFconditional">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
711 <param name="GTFselect" value="with-gtf" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
712 <param name="sjdbOverhang" value="75"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
713 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/>
23
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
714 <conditional name="quantmode_output">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
715 <param name="quantMode" value="TranscriptomeSAM"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
716 </conditional>
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
717 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
718 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
719 <section name="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
720 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
721 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
722 <section name="algo">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
723 <conditional name="params">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
724 <param name="settingsType" value="default" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
725 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
726 </section>
9
0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7
iuc
parents: 8
diff changeset
727
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
728 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
729 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
730 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
22
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents: 20
diff changeset
731 <output name="transcriptome_mapped_reads" file="rnastar_test_transcriptome_mapped_reads.bam" compare="sim_size" delta="634" />
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
732 </test>
23
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
733 <!-- test cached no index but gtf file and GeneCounts TranscriptomeSAM mode -->
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
734 <test expect_num_outputs="5">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
735 <conditional name="singlePaired">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
736 <param name="sPaired" value="single" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
737 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
738 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
739 <conditional name="refGenomeSource">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
740 <param name="geneSource" value="indexed" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
741 <conditional name="GTFconditional">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
742 <param name="GTFselect" value="without-gtf-with-gtf" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
743 <param name="genomeDir" value="000" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
744 <param name="sjdbOverhang" value="75"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
745 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
746 <conditional name="quantmode_output">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
747 <param name="quantMode" value="TranscriptomeSAM GeneCounts"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
748 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
749 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
750 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
751 <section name="oformat">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
752 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
753 </section>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
754 <section name="algo">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
755 <conditional name="params">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
756 <param name="settingsType" value="default" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
757 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
758 </section>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
759
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
760 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
761 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
762 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
763 <output name="reads_per_gene" file="tophat_test_reads_per_gene.txt" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
764 <output name="transcriptome_mapped_reads" file="rnastar_test_transcriptome_mapped_reads.bam" compare="sim_size" delta="634" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
765 </test>
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
766 <test expect_num_outputs="3">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
767 <conditional name="singlePaired">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
768 <param name="sPaired" value="single" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
769 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
770 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
771 <conditional name="refGenomeSource">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
772 <param name="geneSource" value="history" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
773 <param name="genomeFastaFiles" value="tophat_test.fa" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
774 <param name="genomeSAindexNbases" value="5" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
775 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
776 <section name="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
777 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch,XS" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
778 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
779 <section name="filter">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
780 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
781 <conditional name="output_params2">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
782 <param name="output_select2" value="yes" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
783 <param name="outFilterScoreMinOverLread" value="0.9" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
784 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
785 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
786 <section name="algo">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
787 <conditional name="params">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
788 <param name="settingsType" value="full" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
789 <section name="seed">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
790 <param name="seed_select" value="yes" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
791 <param name="seedSearchStartLmax" value="25" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
792 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
793 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
794 </section>
9
0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7
iuc
parents: 8
diff changeset
795
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
796 <output name="output_log" file="rnastar_test2.log" compare="re_match_multiline" />
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
797 <output name="splice_junctions" file="rnastar_test2_splicejunctions.bed"/>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
798 <output name="mapped_reads" file="rnastar_test2_mapped_reads.bam" compare="sim_size" delta="200" />
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
799 </test>
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
800 <test expect_num_outputs="4">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
801 <conditional name="singlePaired">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
802 <param name="sPaired" value="single" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
803 <param name="input1" value="test3.fastqsanger" ftype="fastqsanger" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
804 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
805 <conditional name="refGenomeSource">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
806 <param name="geneSource" value="history" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
807 <param name="genomeFastaFiles" value="test3.ref.fa" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
808 <param name="genomeSAindexNbases" value="5" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
809 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
810 <param name="chimOutType" value="Junctions" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
811 <section name="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
812 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch,XS" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
813 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
814 <section name="algo">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
815 <conditional name="params">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
816 <param name="settingsType" value="star_fusion" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
817 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
818 </section>
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
819
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
820 <output name="chimeric_junctions" file="test3.chimjunc.tabular" compare="diff" lines_diff="2"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
821 </test>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
822 <test expect_num_outputs="4"><!-- tests fastqsanger.gz -->
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
823 <conditional name="singlePaired">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
824 <param name="sPaired" value="single" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
825 <param name="input1" value="test3.fastqsanger.gz" ftype="fastqsanger.gz" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
826 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
827 <conditional name="refGenomeSource">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
828 <param name="geneSource" value="history" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
829 <param name="genomeFastaFiles" value="test3.ref.fa" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
830 <param name="genomeSAindexNbases" value="5" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
831 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
832 <param name="chimOutType" value="Junctions" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
833 <section name="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
834 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch,XS" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
835 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
836 <section name="algo">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
837 <conditional name="params">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
838 <param name="settingsType" value="star_fusion" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
839 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
840 </section>
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
841
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
842 <output name="chimeric_junctions" file="test3.chimjunc.tabular" compare="diff" lines_diff="2"/>
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
843 </test>
28
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents: 27
diff changeset
844 <!-- test 10 -->
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
845 <test expect_num_outputs="3">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
846 <conditional name="singlePaired">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
847 <param name="sPaired" value="single" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
848 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
849 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
850 <conditional name="refGenomeSource">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
851 <param name="geneSource" value="history" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
852 <param name="genomeFastaFiles" value="tophat_test.fa" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
853 <param name="genomeSAindexNbases" value="5" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
854 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
855 <section name="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
856 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
857 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
858 <section name="filter">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
859 <param name="basic_filters" value="--outFilterIntronMotifs RemoveNoncanonical" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
860 <conditional name="output_params2">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
861 <param name="output_select2" value="yes" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
862 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
863 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
864 <section name="algo">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
865 <conditional name="params">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
866 <param name="settingsType" value="full" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
867 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
868 </section>
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
869
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
870 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
871 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
28
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents: 27
diff changeset
872 <output name="mapped_reads" file="rnastar_test_mapped_reads_test10.bam" compare="sim_size" delta="634" />
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
873 </test>
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
874 <!-- twopass mode tests -->
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
875 <!-- test Basic twopass -->
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
876 <test expect_num_outputs="3">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
877 <conditional name="singlePaired">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
878 <param name="sPaired" value="single" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
879 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
880 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
881 <conditional name="refGenomeSource">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
882 <param name="geneSource" value="history" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
883 <param name="genomeFastaFiles" value="tophat_test.fa" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
884 <param name="genomeSAindexNbases" value="5" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
885 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
886 <conditional name="twopass">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
887 <param name="twopassMode" value="Basic" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
888 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
889 <section name="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
890 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
891 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
892 <section name="filter">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
893 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
894 <conditional name="output_params2">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
895 <param name="output_select2" value="yes" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
896 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
897 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
898 <section name="algo">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
899 <conditional name="params">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
900 <param name="settingsType" value="full" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
901 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
902 </section>
9
0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7
iuc
parents: 8
diff changeset
903
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
904 <output name="output_log" file="rnastar_test_twopass.log" compare="re_match_multiline" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
905 <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
906 <output name="mapped_reads" file="rnastar_test_mapped_reads_twopass.bam" compare="sim_size" delta="634" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
907 </test>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
908 <!-- test Basic twopass without a gtf file option -->
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
909 <test expect_num_outputs="3">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
910 <conditional name="singlePaired">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
911 <param name="sPaired" value="single" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
912 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
913 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
914 <conditional name="refGenomeSource">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
915 <param name="geneSource" value="indexed" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
916 <conditional name="GTFconditional">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
917 <param name="GTFselect" value="without-gtf" />
11
41929aa1e7f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2911002ccd79fe062f6346ee5699ea262f92f04f"
iuc
parents: 10
diff changeset
918 <param name="genomeDir" value="000" />
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
919 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
920 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
921 <conditional name="twopass">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
922 <param name="twopassMode" value="Basic" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
923 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
924 <section name="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
925 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
926 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
927 <section name="filter">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
928 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
929 <conditional name="output_params2">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
930 <param name="output_select2" value="yes" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
931 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
932 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
933 <section name="algo">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
934 <conditional name="params">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
935 <param name="settingsType" value="full" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
936 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
937 </section>
9
0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7
iuc
parents: 8
diff changeset
938
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
939 <output name="output_log" file="rnastar_test_twopass.log" compare="re_match_multiline" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
940 <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
941 <output name="mapped_reads" file="rnastar_test_mapped_reads_twopass.bam" compare="sim_size" delta="634" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
942 </test>
20
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
943 <!-- test Basic twopass with a built-in gtf index option -->
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
944 <test expect_num_outputs="3">
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
945 <conditional name="singlePaired">
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
946 <param name="sPaired" value="single" />
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
947 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
948 </conditional>
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
949 <conditional name="refGenomeSource">
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
950 <param name="geneSource" value="indexed" />
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
951 <conditional name="GTFconditional">
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
952 <param name="GTFselect" value="with-gtf" />
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
953 <param name="genomeDir" value="001" />
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
954 </conditional>
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
955 </conditional>
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
956 <conditional name="twopass">
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
957 <param name="twopassMode" value="Basic" />
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
958 </conditional>
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
959 <section name="oformat">
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
960 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
961 </section>
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
962 <section name="filter">
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
963 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" />
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
964 <conditional name="output_params2">
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
965 <param name="output_select2" value="yes" />
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
966 </conditional>
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
967 </section>
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
968 <section name="algo">
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
969 <conditional name="params">
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
970 <param name="settingsType" value="full" />
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
971 </conditional>
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
972 </section>
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
973
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
974 <output name="output_log" file="rnastar_test_twopass.log" compare="re_match_multiline" />
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
975 <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/>
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
976 <output name="mapped_reads" file="rnastar_test_mapped_reads_twopass.bam" compare="sim_size" delta="634" />
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents: 19
diff changeset
977 </test>
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
978 <!-- test "multisample" twopass -->
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
979 <test expect_num_outputs="3">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
980 <conditional name="singlePaired">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
981 <param name="sPaired" value="single" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
982 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
983 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
984 <conditional name="refGenomeSource">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
985 <param name="geneSource" value="history" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
986 <param name="genomeFastaFiles" value="tophat_test.fa" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
987 <param name="genomeSAindexNbases" value="5" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
988 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
989 <conditional name="twopass">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
990 <param name="twopassMode" value="None --sjdbFileChrStartEnd" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
991 <param name="sj_precalculated" value="rnastar_test_splicejunctions_twopass.bed" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
992 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
993 <section name="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
994 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
995 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
996 <section name="filter">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
997 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonicalUnannotated,--outFilterIntronMotifs RemoveNoncanonical" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
998 <conditional name="output_params2">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
999 <param name="output_select2" value="yes" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1000 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1001 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1002 <section name="algo">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1003 <conditional name="params">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1004 <param name="settingsType" value="full" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1005 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1006 </section>
9
0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7
iuc
parents: 8
diff changeset
1007
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1008 <output name="output_log" file="rnastar_test_twopass.log" compare="re_match_multiline" />
9
0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7
iuc
parents: 8
diff changeset
1009 <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/>
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1010 <output name="mapped_reads" file="rnastar_test_mapped_reads_twopass.bam" compare="sim_size" delta="634" />
9
0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7
iuc
parents: 8
diff changeset
1011 </test>
18
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1012 <!-- test "genomeSAindexNbases" parameter -->
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1013 <test expect_num_outputs="3">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1014 <conditional name="singlePaired">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1015 <param name="sPaired" value="single" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1016 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1017 </conditional>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1018 <conditional name="refGenomeSource">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1019 <param name="geneSource" value="history" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1020 <param name="genomeFastaFiles" value="tophat_test.fa" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1021 <param name="genomeSAindexNbases" value="14" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1022 </conditional>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1023 <section name="oformat">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1024 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1025 </section>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1026 <section name="algo">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1027 <conditional name="params">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1028 <param name="settingsType" value="default" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1029 </conditional>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1030 </section>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1031 <output name="output_log" file="rnastar_test_genomeSAindexNbases.log" compare="re_match_multiline" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1032 <output name="splice_junctions" file="rnastar_test_genomeSAindexNbases.bed"/>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1033 <output name="mapped_reads" file="rnastar_test_mapped_reads_genomeSAindexNbases.bam" compare="sim_size" delta="634" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1034 </test>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1035 <test expect_num_outputs="3">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1036 <conditional name="singlePaired">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1037 <param name="sPaired" value="single" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1038 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1039 </conditional>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1040 <conditional name="refGenomeSource">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1041 <param name="geneSource" value="history" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1042 <param name="genomeFastaFiles" value="tophat_test.fa" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1043 <param name="genomeSAindexNbases" value="10" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1044 </conditional>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1045 <section name="oformat">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1046 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1047 </section>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1048 <section name="algo">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1049 <conditional name="params">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1050 <param name="settingsType" value="default" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1051 </conditional>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1052 </section>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1053 <output name="output_log" file="rnastar_test_genomeSAindexNbases_02.log" compare="re_match_multiline" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1054 <output name="splice_junctions" file="rnastar_test_genomeSAindexNbases_02.bed"/>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1055 <output name="mapped_reads" file="rnastar_test_mapped_reads_genomeSAindexNbases_02.bam" compare="sim_size" delta="634" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1056 </test>
23
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1057 <!-- test paired-end input and outWig -->
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1058 <test expect_num_outputs="6">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1059 <conditional name="singlePaired">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1060 <param name="sPaired" value="paired" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1061 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1062 <param name="input2" value="tophat_in3.fastqsanger" ftype="fastqsanger" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1063 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1064 <conditional name="refGenomeSource">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1065 <param name="geneSource" value="history" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1066 <param name="genomeFastaFiles" value="tophat_test.fa" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1067 <param name="genomeSAindexNbases" value="5" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1068 <conditional name="GTFconditional">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1069 <param name="GTFselect" value="with-gtf" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1070 <param name="sjdbOverhang" value="75"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1071 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1072 <conditional name="quantmode_output">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1073 <param name="quantMode" value="GeneCounts"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1074 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1075 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1076 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1077 <section name="oformat">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1078 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1079 </section>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1080 <section name="algo">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1081 <conditional name="params">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1082 <param name="settingsType" value="default" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1083 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1084 </section>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1085 <conditional name="outWig">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1086 <param name="outWigType" value="wiggle" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1087 <param name="outWigTypeSecondWord" value="read2"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1088 <param name="outWigStrand" value="false" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1089 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1090 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1091 <output name="splice_junctions" file="rnastar_test_splicejunctions_PE.bed"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1092 <output name="mapped_reads" file="rnastar_test_mapped_reads_PE.bam" compare="sim_size" delta="634" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1093 <output name="reads_per_gene" file="tophat_test_reads_per_gene_PE.txt" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1094 <output name="signal_unique_str1" file="tophat_Signal.Unique.both.read2.out.wig" ftype="wig"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1095 <output name="signal_uniquemultiple_str1" file="tophat_Signal.Unique.both.read2.out.wig" ftype="wig" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1096 </test>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1097 <!-- test paired-end input as collection and outWig stranded -->
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1098 <test expect_num_outputs="8">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1099 <conditional name="singlePaired">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1100 <param name="sPaired" value="paired_collection" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1101 <param name="input" >
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1102 <collection type="paired">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1103 <element name="forward" value="tophat_revlib_R1.fastqsanger" ftype="fastq"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1104 <element name="reverse" value="tophat_revlib_R2.fastqsanger" ftype="fastq"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1105 </collection>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1106 </param>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1107 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1108 <conditional name="refGenomeSource">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1109 <param name="geneSource" value="history" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1110 <param name="genomeFastaFiles" value="tophat_test.fa" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1111 <param name="genomeSAindexNbases" value="5" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1112 <conditional name="GTFconditional">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1113 <param name="GTFselect" value="with-gtf" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1114 <param name="sjdbOverhang" value="75"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1115 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1116 <conditional name="quantmode_output">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1117 <param name="quantMode" value="GeneCounts"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1118 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1119 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1120 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1121 <section name="oformat">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1122 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1123 </section>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1124 <section name="algo">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1125 <conditional name="params">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1126 <param name="settingsType" value="default" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1127 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1128 </section>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1129 <conditional name="outWig">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1130 <param name="outWigType" value="bedGraph" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1131 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1132
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1133 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1134 <output name="splice_junctions">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1135 <assert_contents>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1136 <has_n_lines n="2"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1137 <has_line_matching expression="test_chromosome\s+251\s+350\s+1\s+1\s+0\s+24\s+0\s+33"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1138 <has_line_matching expression="test_chromosome\s+401\s+500\s+1\s+1\s+0\s+25\s+0\s+36"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1139 </assert_contents>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1140 </output>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1141 <output name="mapped_reads" >
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1142 <assert_contents>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1143 <has_size value="4711" delta="800"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1144 </assert_contents>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1145 </output>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1146 <output name="reads_per_gene" file="tophat_test_reads_per_gene_PE_rev.txt" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1147 <output name="signal_unique_str1" file="tophat_rev_Signal.Unique.str1.out.bg" ftype="bedgraph"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1148 <output name="signal_uniquemultiple_str1" file="tophat_rev_Signal.Unique.str1.out.bg" ftype="bedgraph"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1149 <output name="signal_unique_str2" file="tophat_rev_Signal.Unique.str2.out.bg" ftype="bedgraph" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1150 <output name="signal_uniquemultiple_str2" file="tophat_rev_Signal.Unique.str2.out.bg" ftype="bedgraph" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1151 </test>
28
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents: 27
diff changeset
1152 <!-- test diploid mode -->
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents: 27
diff changeset
1153 <test expect_num_outputs="3">
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents: 27
diff changeset
1154 <conditional name="singlePaired">
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents: 27
diff changeset
1155 <param name="sPaired" value="single" />
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents: 27
diff changeset
1156 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents: 27
diff changeset
1157 </conditional>
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents: 27
diff changeset
1158 <conditional name="refGenomeSource">
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents: 27
diff changeset
1159 <param name="geneSource" value="history" />
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents: 27
diff changeset
1160 <param name="genomeFastaFiles" value="tophat_test.fa.gz" />
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents: 27
diff changeset
1161 <param name="genomeSAindexNbases" value="5" />
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents: 27
diff changeset
1162 </conditional>
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents: 27
diff changeset
1163 <conditional name="diploidconditional">
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents: 27
diff changeset
1164 <param name="diploid" value="Yes" />
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents: 27
diff changeset
1165 <!-- generated from rnastar_test_mapped_reads.bam with
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents: 27
diff changeset
1166 bcftools mpileup and bcftools call -->
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents: 27
diff changeset
1167 <param name="genomeTransformVCF" value="rnastar_test_mapped_reads.vcf" ftype="vcf" />
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents: 27
diff changeset
1168 <param name="genomeTransformOutput" value="true" />
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents: 27
diff changeset
1169 </conditional>
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents: 27
diff changeset
1170 <output name="output_log" file="rnastar_test_diploid.log" compare="re_match_multiline" />
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents: 27
diff changeset
1171 <output name="splice_junctions" file="rnastar_test_splicejunctions_diploid.bed"/>
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents: 27
diff changeset
1172 <output name="mapped_reads" file="rnastar_test_mapped_reads_diploid.bam" compare="sim_size" delta="634" />
3e94726bfa9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents: 27
diff changeset
1173 </test>
18
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents: 16
diff changeset
1174 </tests>
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1175 <help><![CDATA[
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
1176 **What it does**
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
1177
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1178 STAR_ is an ultrafast universal RNA-seq aligner.
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
1179
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1180 **Compatibility Notes**
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1181
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1182 STAR has a huge amount of options to filter alignments and to configure the
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1183 exact format of its output.
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
1184
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1185 Some tools you may plan to use in your downstream analysis of the results are known to be sensitive to these settings or combinations of them.
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1186
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1187 *STAR-Fusion*
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
1188
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1189 STAR-Fusion_ can use the chimeric junctions output of STAR as input, but you
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1190 need to enable **chimeric alignment detection** by STAR for that dataset to be
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1191 generated. Hence, be sure to select:
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
1192
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1193 **Report chimeric alignments?**: `As separate tabular "Junctions" output (Junctions)`.
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1194
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1195 In addition, for best results it is recommended_ that you
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1196
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1197 - use **2-pass mapping** for more sensitive novel splice junction discovery
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
1198
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1199 - under *BAM output format specification*,
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1200 **Read alignment tags to include in the BAM output**: select `XS` as an
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1201 additional tag to generate (this is the equivalent of using
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1202 `--outSAMstrandField intronMotif` on the command line)
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
1203
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1204 - under *Algorithmic settings*, **Configure seed, alignment and limits options**:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1205 `use parameters suggested for STAR-Fusion`.
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
1206
22
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents: 20
diff changeset
1207 *Arriba*
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents: 20
diff changeset
1208
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents: 20
diff changeset
1209 Arriba_ can use the BAM with chimeric junctions or both files separately, generated by STAR, as input, but you
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents: 20
diff changeset
1210 need to enable **chimeric alignment detection** by STAR for those datasets to be
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents: 20
diff changeset
1211 generated. Hence, be sure to select either:
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents: 20
diff changeset
1212
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents: 20
diff changeset
1213 **Report chimeric alignments?**: `As separate tabular "Junctions" output (Junctions)` or **Report chimeric alignments?**: `Within the BAM output (together with regular alignments; WithinBAM)`.
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents: 20
diff changeset
1214
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents: 20
diff changeset
1215 In addition, the following parameters_ related to chimeric alignment are recommended for improved sensitivity
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents: 20
diff changeset
1216
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents: 20
diff changeset
1217 - under *Output filter criteria*,
23
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 22
diff changeset
1218 **Would you like to set additional output filters?**: select `Yes` to set
22
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents: 20
diff changeset
1219 **Maximum number of alignments to output a read's alignment results, plus 1** to 50
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents: 20
diff changeset
1220
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents: 20
diff changeset
1221 - under *Algorithmic settings*, **Configure seed, alignment and limits options**:
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents: 20
diff changeset
1222 `use parameters suggested for Arriba`.
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents: 20
diff changeset
1223
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1224 *Cufflinks*
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
1225
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1226 .. class:: infomark
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
1227
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1228 Cufflinks is not considered to be the best tool for use downstream of STAR
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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diff changeset
1229 anymore. Consider using *Stringtie* instead, which also should pose no
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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diff changeset
1230 compatibility issues.
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
1231
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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diff changeset
1232 To avoid compatibility issues with Cufflinks you should:
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
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parents:
diff changeset
1233
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1234 - select **XS** as a *Read alignment tag to include in the BAM output* if (and
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1235 only if) your sequenced reads come from an unstranded library prep
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1236 - *not* select the *jM* and *jI* tags for inclusion
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1237 - keep the **HI** tag selected and
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1238 - select *HI tag values should be* **zero-based**
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1239 - exclude **All alignments across non-canonical junctions** under *Output
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1240 filter criteria -> Exclude the following records from the BAM output*
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1241
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1242 -----
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
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parents:
diff changeset
1243
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1244 Attribution
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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diff changeset
1245
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1246 Minor tweaks to output names to suit downstream purposes, toolshed automated
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1247 dependencies and odds and ends of other code and documentation comprising
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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diff changeset
1248 this tool were originally written by Ross Lazarus and have been licensed under
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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diff changeset
1249 the creative commons
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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diff changeset
1250 `BY-NC_ND 3.0 license <http://creativecommons.org/licenses/by-nc-nd/3.0/>`__.
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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parents: 9
diff changeset
1251
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1252 .. _STAR: https://github.com/alexdobin/STAR
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
1253 .. _STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion
22
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
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diff changeset
1254 .. _Arriba: https://github.com/suhrig/arriba
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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diff changeset
1255 .. _recommended: https://github.com/STAR-Fusion/STAR-Fusion/wiki#alternatively-kickstart-mode-running-star-yourself-and-then-running-star-fusion-using-the-existing-outputs
22
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
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diff changeset
1256 .. _parameters: https://arriba.readthedocs.io/en/latest/workflow/
10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents: 9
diff changeset
1257 ]]></help>
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
1258 <expand macro="citations"/>
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b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
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diff changeset
1259 </tool>