Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/SMART/galaxy/mergeTranscriptLists.xml @ 4:1fc014126d55
Uploaded
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:45:50 -0500 |
parents | e0f8dcca02ed |
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rev | line source |
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0
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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1 <tool id="mergeTranscriptLists" name="merge transcript lists"> |
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2 <description>Merge the elements of two lists of genomic coordinates.</description> |
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3 <command interpreter="python"> |
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4 ../Java/Python/mergeTranscriptLists.py -i $formatType.inputFileName1 |
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5 #if $formatType.FormatInputFileName1 == 'bed': |
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6 -f bed |
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7 #elif $formatType.FormatInputFileName1 == 'gff': |
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8 -f gff |
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9 #elif $formatType.FormatInputFileName1 == 'gff2': |
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10 -f gff2 |
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11 #elif $formatType.FormatInputFileName1 == 'gff3': |
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12 -f gff3 |
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13 #elif $formatType.FormatInputFileName1 == 'sam': |
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14 -f sam |
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15 #elif $formatType.FormatInputFileName1 == 'gtf': |
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16 -f gtf |
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17 #end if |
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18 |
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19 -j $formatType2.inputFileName2 |
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20 #if $formatType2.FormatInputFileName2 == 'bed': |
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21 -g bed |
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22 #elif $formatType2.FormatInputFileName2 == 'gff': |
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23 -g gff |
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24 #elif $formatType2.FormatInputFileName2 == 'gff2': |
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25 -g gff2 |
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26 #elif $formatType2.FormatInputFileName2 == 'gff3': |
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27 -g gff3 |
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28 #elif $formatType2.FormatInputFileName2 == 'sam': |
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29 -g sam |
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30 #elif $formatType2.FormatInputFileName2 == 'gtf': |
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31 -g gtf |
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32 #end if |
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33 |
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34 $all |
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35 $normalize |
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36 |
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37 #if $OptionDistance.dis == 'Yes': |
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38 -d $OptionDistance.disVal |
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39 #end if |
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40 |
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41 #if $OptionColinearOrAntiSens.OptionCA == 'Colinear': |
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42 -c |
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43 #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens': |
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44 -a |
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45 #end if |
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46 |
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47 -o $outputFileGff |
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48 |
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49 |
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50 |
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51 </command> |
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52 |
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53 <inputs> |
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54 <conditional name="formatType"> |
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55 <param name="FormatInputFileName1" type="select" label="Input File Format 1"> |
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56 <option value="bed">bed</option> |
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57 <option value="gff">gff</option> |
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58 <option value="gff2">gff2</option> |
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59 <option value="gff3">gff3</option> |
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60 <option value="sam">sam</option> |
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61 <option value="gtf">gtf</option> |
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62 </param> |
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63 <when value="bed"> |
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64 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/> |
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65 </when> |
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66 <when value="gff"> |
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67 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/> |
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68 </when> |
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69 <when value="gff2"> |
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70 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/> |
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71 </when> |
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72 <when value="gff3"> |
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73 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/> |
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74 </when> |
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75 <when value="sam"> |
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76 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/> |
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77 </when> |
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78 <when value="gtf"> |
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79 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/> |
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80 </when> |
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81 </conditional> |
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82 |
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83 <conditional name="formatType2"> |
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84 <param name="FormatInputFileName2" type="select" label="Input File Format 2"> |
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85 <option value="bed">bed</option> |
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86 <option value="gff">gff</option> |
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87 <option value="gff2">gff2</option> |
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88 <option value="gff3">gff3</option> |
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89 <option value="sam">sam</option> |
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90 <option value="gtf">gtf</option> |
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91 </param> |
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92 <when value="bed"> |
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93 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/> |
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94 </when> |
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95 <when value="gff"> |
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96 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/> |
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97 </when> |
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98 <when value="gff2"> |
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99 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/> |
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100 </when> |
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101 <when value="gff3"> |
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102 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/> |
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103 </when> |
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104 <when value="sam"> |
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105 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/> |
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106 </when> |
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107 <when value="gtf"> |
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108 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/> |
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109 </when> |
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110 </conditional> |
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111 |
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112 |
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113 <param name="all" type="boolean" truevalue="-k" falsevalue="" checked="false" label="print all the transcripts, not only those overlapping"/> |
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114 <param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="normalize the number of reads per cluster by the number of mappings per read "/> |
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115 |
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116 <conditional name="OptionDistance"> |
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117 <param name="dis" type="select" label="provide the number of reads" > |
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118 <option value="Yes">Yes</option> |
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119 <option value="No" selected="true">No</option> |
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120 </param> |
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121 <when value="Yes"> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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122 <param name="disVal" type="integer" value="0" label="max. distance between two transcripts" /> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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123 </when> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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124 <when value="No"> |
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125 </when> |
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126 </conditional> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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127 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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128 <conditional name="OptionColinearOrAntiSens"> |
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129 <param name="OptionCA" type="select" label="Colinear or anti-sens"> |
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130 <option value="Colinear">Colinear</option> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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131 <option value="AntiSens">AntiSens</option> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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132 <option value="NONE" selected="true">NONE</option> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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133 </param> |
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134 <when value="Colinear"> |
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135 </when> |
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136 <when value="AntiSens"> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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137 </when> |
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138 <when value="NONE"> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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139 </when> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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140 </conditional> |
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141 |
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142 </inputs> |
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143 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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144 <outputs> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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145 <data name="outputFileGff" format="gff3" label="[mergeTranscriptLists]out file"/> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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146 </outputs> |
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147 |
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148 </tool> |