annotate SMART/galaxy/getSizes.xml @ 36:44d5973c188c

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author m-zytnicki
date Tue, 30 Apr 2013 15:02:29 -0400
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1 <tool id="GetSizes" name="get sizes">
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2 <description>Get the sizes of a set of genomic coordinates.</description>
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3 <command interpreter="python">
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4 ../Java/Python/getSizes.py -i $formatType.inputFileName $formatType.FormatInputFileName
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5
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6 #if $OptionQuery.OptionQ == 'NONE':
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7 -q size
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8 #else:
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9 $OptionQuery.OptionQ
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10 #end if
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11
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12 -o $outputFile
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13
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14 #if $OptionXMax.xMax == "Yes":
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15 -x $OptionXMax.maxValue
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16 #end if
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17 #if $OptionX.xLab == "Yes":
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18 -a $OptionX.xLabValue
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19 #end if
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20 #if $OptionY.yLab == "Yes":
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21 -b $OptionY.yLabValue
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22 #end if
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23 $barPlot
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24 </command>
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25
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26 <inputs>
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27 <conditional name="formatType">
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28 <param name="FormatInputFileName" type="select" label="Input File Format">
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29 <option value="-f bed">bed</option>
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30 <option value="-f gff">gff</option>
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31 <option value="-f gff2">gff2</option>
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32 <option value="-f gff3">gff3</option>
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33 <option value="-f sam">sam</option>
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34 <option value="-f gtf">gtf</option>
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35 <option value="-f fasta">fasta</option>
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36 <option value="-f fastq">fastq</option>
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37 </param>
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38 <when value="-f bed">
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39 <param name="inputFileName" format="bed" type="data" label="Input File"/>
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40 </when>
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41 <when value="-f gff">
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42 <param name="inputFileName" format="gff" type="data" label="Input gff File"/>
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43 </when>
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44 <when value="-f gff2">
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45 <param name="inputFileName" format="gff" type="data" label="Input gff2 File"/>
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46 </when>
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47 <when value="-f gff3">
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48 <param name="inputFileName" format="gff3" type="data" label="Input gff3 File"/>
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49 </when>
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50 <when value="-f sam">
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51 <param name="inputFileName" format="sam" type="data" label="Input gff2 File"/>
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52 </when>
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53 <when value="-f gtf">
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54 <param name="inputFileName" format="gtf" type="data" label="Input gff3 File"/>
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55 </when>
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56 <when value="-f fasta">
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57 <param name="inputFileName" format="fasta" type="data" label="Input fasta File"/>
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58 </when>
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59 <when value="-f fastq">
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60 <param name="inputFileName" format="fastq" type="data" label="Input fastq File"/>
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61 </when>
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62 </conditional>
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63
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64 <conditional name="OptionQuery">
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65 <param name="OptionQ" type="select" label="mesure type">
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66 <option value="-q size">size</option>
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67 <option value="-q intron size">intron size</option>
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68 <option value="-q exon size">exon size</option>
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69 <option value="-q 1st exon size">1st exon size</option>
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70 <option value="NONE" selected="true">NONE</option>
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71 </param>
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72 <when value="-q size">
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73 </when>
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74 <when value="-q intron size">
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75 </when>
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76 <when value="-q exon size">
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77 </when>
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78 <when value="-q 1st exon size">
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79 </when>
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80 <when value="NONE">
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81
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82 </when>
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83 </conditional>
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84
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85 <conditional name="OptionXMax">
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86 <param name="xMax" type="select" label="maximum x-value to plot">
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87 <option value="Yes">Yes</option>
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88 <option value="No" selected="true">No</option>
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89 </param>
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90 <when value="Yes">
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91 <param name="maxValue" type="integer" value="1000"/>
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92 </when>
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93 <when value="No">
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94 </when>
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95 </conditional>
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96
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97 <conditional name="OptionX">
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98 <param name="xLab" type="select" label="X label title">
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99 <option value="Yes">Yes</option>
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100 <option value="No" selected="true">No</option>
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101 </param>
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102 <when value="Yes">
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103 <param name="xLabValue" type="text" value="Size" label="Notice: The title should not have spaces. EX. Size_of_transcript"/>
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104 </when>
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105 <when value="No">
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106 </when>
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107 </conditional>
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108
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109 <conditional name="OptionY">
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110 <param name="yLab" type="select" label="Y label title">
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111 <option value="Yes">Yes</option>
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112 <option value="No" selected="true">No</option>
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113 </param>
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114 <when value="Yes">
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115 <param name="yLabValue" type="text" value="#_reads" label="Notice: The title should not have spaces. EX. Number_of_reads"/>
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116 </when>
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117 <when value="No">
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118 </when>
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119 </conditional>
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120
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121 <param name="barPlot" type="boolean" truevalue="-B" falsevalue="" checked="false" label="use barplot representation"/>
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122 </inputs>
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123
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124 <outputs>
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125 <data name="outputFile" format="png" label="[Get sizes] output file"/>
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126 </outputs>
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127
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128 <help>
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129 Get the sequence/annotation size distribution. A point (*x*, *y*) means that *y* elements have a size of *x* nucleotides.
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130
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131 When your mapping include exon/intron structures, you can decide to count the size of the introns, the sizes of the exons or the size of the first exons.
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132 </help>
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133 </tool>