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1 <tool id="mapperAnalyzer" name="mapper analyzer">
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2 <description>Read the output of an aligner, print statistics and possibly translate into BED or GBrowse formats. </description>
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3 <command interpreter="python">
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4 ../Java/Python/mapperAnalyzer.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 == 'gff3':
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8 -f gff3
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9 #elif $formatType.FormatInputFileName1 == 'sam':
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10 -f sam
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11 #elif $formatType.FormatInputFileName1 == 'bam':
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12 -f bam
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13 #elif $formatType.FormatInputFileName1 == 'seqmap':
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14 -f seqmap
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15 #end if
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16
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17 -q $formatType2.inputFileName2
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18 #if $formatType2.FormatInputFileName2 == 'fasta':
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19 -k fasta
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20 #elif $formatType2.FormatInputFileName2 == 'fastq':
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21 -k fastq
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22 #end if
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23
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24
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25 #if $optionnumber.number == 'Yes':
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26 -n $optionnumber.numberVal
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27 #end if
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28 #if $optionsize.size == 'Yes':
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29 -s $optionsize.sizeVal
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30 #end if
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31 #if $optionidentity.identity == 'Yes':
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32 -d $optionidentity.identityVal
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33 #end if
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34 #if $optionmismatch.mismatch == 'Yes':
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35 -m $optionmismatch.mismatchVal
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36 #end if
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37 #if $optiongap.gap == 'Yes':
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38 -p $optiongap.gapVal
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39 #end if
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40 #if $optiontitle.title == 'Yes':
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41 -t $optiontitle.titleVal
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42 #end if
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43 #if $optionappend.append == 'Yes':
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44 -a $optionappend.appendfile
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45 #end if
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46
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47 $merge
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48 $remove
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49 $remain
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50 -o $outputFileGFF
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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 mapping Format">
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56 <option value="bed">bed</option>
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57 <option value="gff3">gff3</option>
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58 <option value="sam">sam</option>
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59 <option value="bam">bam</option>
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60 <option value="seqmap" selected="true">seqmap</option>
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61 </param>
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62 <when value="bed">
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63 <param name="inputFileName1" format="bed" type="data" label="Input File"/>
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64 </when>
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65 <when value="gff3">
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66 <param name="inputFileName1" format="gff3" type="data" label="Input File"/>
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67 </when>
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68 <when value="sam">
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69 <param name="inputFileName1" format="sam" type="data" label="Input File"/>
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70 </when>
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71 <when value="bam">
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72 <param name="inputFileName1" format="bam" type="data" label="Input File"/>
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73 </when>
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74 <when value="seqmap">
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75 <param name="inputFileName1" format="seqmap" type="data" label="Input File"/>
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76 </when>
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77 </conditional>
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78
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79 <conditional name="formatType2">
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80 <param name="FormatInputFileName2" type="select" label="Reference sequence File Format">
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81 <option value="fasta" selected="true">fasta</option>
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82 <option value="fastq">fastq</option>
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83 </param>
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84 <when value="fasta">
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85 <param name="inputFileName2" format="fasta" type="data" label="Reference sequence File Format"/>
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86 </when>
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87 <when value="fastq">
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88 <param name="inputFileName2" format="fastq" type="data" label="Reference sequence File Format"/>
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89 </when>
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90 </conditional>
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91
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92
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93 <conditional name="optionnumber">
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94 <param name="number" type="select" label="max. number of occurrences of a sequence">
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95 <option value="Yes">Yes</option>
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96 <option value="No" selected="true">No</option>
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97 </param>
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98 <when value="Yes">
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99 <param name="numberVal" type="integer" value="0"/>
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100 </when>
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101 <when value="No">
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102 </when>
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103 </conditional>
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104
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105 <conditional name="optionsize">
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106 <param name="size" type="select" label="minimum pourcentage of size ">
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107 <option value="Yes">Yes</option>
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108 <option value="No" selected="true">No</option>
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109 </param>
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110 <when value="Yes">
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111 <param name="sizeVal" type="integer" value="0"/>
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112 </when>
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113 <when value="No">
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114 </when>
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115 </conditional>
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116
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117 <conditional name="optionidentity">
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118 <param name="identity" type="select" label="minimum pourcentage of identity ">
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119 <option value="Yes">Yes</option>
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120 <option value="No" selected="true">No</option>
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121 </param>
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122 <when value="Yes">
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123 <param name="identityVal" type="integer" value="0"/>
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124 </when>
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125 <when value="No">
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126 </when>
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127 </conditional>
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128
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129 <conditional name="optionmismatch">
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130 <param name="mismatch" type="select" label="maximum number of mismatches">
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131 <option value="Yes">Yes</option>
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132 <option value="No" selected="true">No</option>
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133 </param>
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134 <when value="Yes">
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135 <param name="mismatchVal" type="integer" value="0"/>
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136 </when>
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137 <when value="No">
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138 </when>
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139 </conditional>
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140
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141 <conditional name="optiongap">
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142 <param name="gap" type="select" label="maximum number of gaps">
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143 <option value="Yes">Yes</option>
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144 <option value="No" selected="true">No</option>
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145 </param>
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146 <when value="Yes">
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147 <param name="gapVal" type="integer" value="0"/>
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148 </when>
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149 <when value="No">
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150 </when>
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151 </conditional>
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152
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153 <conditional name="optiontitle">
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154 <param name="title" type="select" label="title of the plots ">
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155 <option value="Yes">Yes</option>
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156 <option value="No" selected="true">No</option>
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157 </param>
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158 <when value="Yes">
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159 <param name="titleVal" type="text" value="title of the UCSC track" />
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160 </when>
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161 <when value="No">
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162 </when>
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163 </conditional>
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164
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165 <conditional name="optionappend">
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166 <param name="append" type="select" label="append to GFF3 file">
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167 <option value="Yes">Yes</option>
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168 <option value="No" selected="true">No</option>
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169 </param>
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170 <when value="Yes">
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171 <param name="appendfile" type="data" format="gff3" label="append a file"/>
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172 </when>
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173 <when value="No">
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174 </when>
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175 </conditional>
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176
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177 <param name="merge" type="boolean" truevalue="-e" falsevalue="" checked="false" label="merge exons when introns are short "/>
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178 <param name="remove" type="boolean" truevalue="-x" falsevalue="" checked="false" label="remove transcripts when exons are short"/>
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179 <param name="remain" type="boolean" truevalue="-r" falsevalue="" checked="false" label="print the unmatched sequences "/>
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180 </inputs>
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181
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182 <outputs>
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183 <data name="outputFileGFF" format="gff3" label="[mapperAnalyzer] out file"/>
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184 </outputs>
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185
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186 </tool>
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