annotate SMART/galaxy/getDistance.xml @ 6:769e306b7933

Change the repository level.
author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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children 440ceca58672
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6
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1 <tool id="GetDistance" name="get distance">
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2 <description>Give the distances between every data from the first input set and the data from the second input set</description>
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3 <command interpreter="python">
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4 ../Java/Python/getDistance.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
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35 $absolute $proportion
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36
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37 #if $OptionColinearOrAntiSens.OptionCA == "Colinear":
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38 -c
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39 #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens':
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40 -a
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41 #end if
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42
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43 #if $OptionFirstNucl5.FirstNu5 == "Yes":
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44 -s $OptionFirstNucl5.first5File1
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45 -S $OptionFirstNucl5.first5File2
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46 #end if
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47
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48 #if $OptionFirstNucl3.FirstNu3 == "Yes":
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49 -e $OptionFirstNucl3.first3File1
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50 -E $OptionFirstNucl3.first3File2
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51 #end if
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52
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53 #if $OptionMinDistance.MinD == "Yes":
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54 -m $OptionMinDistance.minDistance
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55 #end if
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56
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57 #if $OptionMaxDistance.MaxD == "Yes":
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58 -M $OptionMaxDistance.maxDistance
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59 #end if
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60
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61 $fivePrime $threePrime $spearMan
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62
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63 #if $OptionBuckets.OBuckets == "Yes":
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64 -u $OptionBuckets.buckets
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65 #end if
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66
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67 #if $OptionMinXaxis.MinX == "Yes":
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68 -x $OptionMinXaxis.minXaxis
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69 #end if
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70
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71 #if $OptionMaxXaxis.MaxX == "Yes":
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72 -X $OptionMaxXaxis.maxXaxis
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73 #end if
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74
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75 #if $OptionTitle.OTitle == "Yes":
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76 -t $OptionTitle.title
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77 #end if
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78
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79 -o $outputFilePng
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80 $outputDistance $outputFileDistance
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81
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82 </command>
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83
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84 <inputs>
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85 <conditional name="formatType">
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86 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
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87 <option value="bed">bed</option>
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88 <option value="gff">gff</option>
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89 <option value="gff2">gff2</option>
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90 <option value="gff3">gff3</option>
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91 <option value="sam">sam</option>
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92 <option value="gtf">gtf</option>
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93 </param>
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94 <when value="bed">
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95 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
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96 </when>
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97 <when value="gff">
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98 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
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99 </when>
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100 <when value="gff2">
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101 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
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102 </when>
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103 <when value="gff3">
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104 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
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105 </when>
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106 <when value="sam">
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107 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
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108 </when>
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109 <when value="gtf">
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110 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
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111 </when>
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112 </conditional>
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113
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114 <conditional name="formatType2">
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115 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
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116 <option value="bed">bed</option>
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117 <option value="gff">gff</option>
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118 <option value="gff2">gff2</option>
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119 <option value="gff3">gff3</option>
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120 <option value="sam">sam</option>
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121 <option value="gtf">gtf</option>
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122 </param>
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123 <when value="bed">
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124 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
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125 </when>
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126 <when value="gff">
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127 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
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128 </when>
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129 <when value="gff2">
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130 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
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131 </when>
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132 <when value="gff3">
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133 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
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134 </when>
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135 <when value="sam">
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136 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
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137 </when>
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138 <when value="gtf">
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139 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
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140 </when>
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141 </conditional>
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142
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143 <param name="outputDistance" type="boolean" truevalue="-O" falsevalue="" checked="false" label="distance option" help="This option create a GFF3 output file containing the distance for each element of the query."/>
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144
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145 <param name="absolute" type="boolean" truevalue="-b" falsevalue="" checked="false" label="absolute value option" help="This option gives the absolute value of the distance."/>
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146 <param name="proportion" type="boolean" truevalue="-p" falsevalue="" checked="false" label="proportion option" help="This option gives the proportion on the y-axis instead of the number of distances."/>
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147
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148 <conditional name="OptionColinearOrAntiSens">
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149 <param name="OptionCA" type="select" label="Colinear or anti-sens">
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150 <option value="Colinear">Colinear</option>
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151 <option value="AntiSens">AntiSens</option>
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152 <option value="NONE" selected="true">NONE</option>
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153 </param>
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154 <when value="Colinear">
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155 </when>
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156 <when value="AntiSens">
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157 </when>
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158 <when value="NONE">
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159 </when>
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160 </conditional>
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161
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162 <conditional name="OptionFirstNucl5">
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163 <param name="FirstNu5" type="select" label="only consider the n first 5' nucleotides for input files">
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164 <option value="Yes">Yes</option>
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165 <option value="No" selected="true">No</option>
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166 </param>
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167 <when value="Yes">
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168 <param name="first5File1" type="integer" value="1" label="in file 1" help="Be Careful! The value must be upper than 0"/>
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169 <param name="first5File2" type="integer" value="1" label="in file 2" help="Be Careful! The value must be upper than 0"/>
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170 </when>
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171 <when value="No">
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172 </when>
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173 </conditional>
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174
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175 <conditional name="OptionFirstNucl3">
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176 <param name="FirstNu3" type="select" label="only consider the n first 3' nucleotides for input files">
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177 <option value="Yes">Yes</option>
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178 <option value="No" selected="true">No</option>
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179 </param>
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180 <when value="Yes">
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181 <param name="first3File1" type="integer" value="1" label="in file 1" help="Be Careful! The value must be upper than 0"/>
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182 <param name="first3File2" type="integer" value="1" label="in file 2" help="Be Careful! The value must be upper than 0"/>
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183 </when>
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184 <when value="No">
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185 </when>
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186 </conditional>
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187
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188 <conditional name="OptionMinDistance">
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189 <param name="MinD" type="select" label="minimum distance considered between two transcripts">
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190 <option value="Yes">Yes</option>
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191 <option value="No" selected="true">No</option>
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192 </param>
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193 <when value="Yes">
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194 <param name="minDistance" type="integer" value="1"/>
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195 </when>
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196 <when value="No">
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yufei-luo
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197 </when>
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198 </conditional>
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199
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200 <conditional name="OptionMaxDistance">
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201 <param name="MaxD" type="select" label="maximum distance considered between two transcripts">
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202 <option value="Yes">Yes</option>
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203 <option value="No" selected="true">No</option>
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204 </param>
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205 <when value="Yes">
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206 <param name="maxDistance" type="integer" value="1000"/>
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207 </when>
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208 <when value="No">
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209 </when>
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210 </conditional>
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211
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212 <param name="fivePrime" type="boolean" truevalue="-5" falsevalue="" checked="false" label="five prime option" help="Consider the elements from input file 1 which are upstream of elements of input file 2"/>
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213 <param name="threePrime" type="boolean" truevalue="-3" falsevalue="" checked="false" label="three prime option" help="Consider the elements from input file1 which are downstream of elements of input file 2"/>
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214 <param name="spearMan" type="boolean" truevalue="-r" falsevalue="" checked="false" label="spearman option" help="Compute Spearman rho."/>
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215
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216
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217 <conditional name="OptionBuckets">
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218 <param name="OBuckets" type="select" label="Plots histogram instead of line plot with given interval size.">
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219 <option value="Yes">Yes</option>
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220 <option value="No" selected="true">No</option>
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221 </param>
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222 <when value="Yes">
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223 <param name="buckets" type="integer" value="1" label="Interval size"/>
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224 </when>
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225 <when value="No">
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226 </when>
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227 </conditional>
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228
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229 <conditional name="OptionMinXaxis">
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230 <param name="MinX" type="select" label="Minimum value on the x-axis to plot.">
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231 <option value="Yes">Yes</option>
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232 <option value="No" selected="true">No</option>
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233 </param>
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234 <when value="Yes">
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235 <param name="minXaxis" type="integer" value="1"/>
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236 </when>
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237 <when value="No">
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yufei-luo
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238 </when>
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yufei-luo
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239 </conditional>
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240
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241 <conditional name="OptionMaxXaxis">
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242 <param name="MaxX" type="select" label="Maximum value on the x-axis to plot.">
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243 <option value="Yes">Yes</option>
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244 <option value="No" selected="true">No</option>
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245 </param>
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246 <when value="Yes">
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247 <param name="maxXaxis" type="integer" value="1"/>
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yufei-luo
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248 </when>
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249 <when value="No">
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yufei-luo
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250 </when>
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251 </conditional>
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252
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253 <conditional name="OptionTitle">
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254 <param name="OTitle" type="select" label="Title for the graph.">
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255 <option value="Yes">Yes</option>
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256 <option value="No" selected="true">No</option>
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257 </param>
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258 <when value="Yes">
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yufei-luo
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259 <param name="title" type="text" value=""/>
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260 </when>
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261 <when value="No">
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yufei-luo
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262 </when>
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yufei-luo
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263 </conditional>
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264
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265 </inputs>
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266
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267
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268 <outputs>
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269 <data name="outputFilePng" format="png"/>
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270 <data name="outputFileDistance" format="gff3">
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271 <filter>outputDistance</filter>
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272 </data>
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273 </outputs>
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274
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275 </tool>