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1 <tool id="cg_junctiondiff" name="junctiondiff(beta) 1.6" version="1.0.1">
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2 <!--
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3 This tool creates a GUI for the junctiondiff function of cgatools from Complete Genomics, Inc.
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4 written 6-18-2012 by bcrain@completegenomics.com
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5 updated 8-14-2012 by bcrain@completegenomics.com
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6 -->
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7
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8 <description>reports difference between junction calls</description>
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9
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10 <command>
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11 <!-- print version of cgatools to STDOUT-->
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12 cgatools | head -1;
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13
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14 <!-- print command lines to STDOUT-->
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15 echo "cgatools junctiondiff --beta
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16 --reference $crr.fields.path
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17 --junctionsA $data_sources.inputA
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18 --junctionsB $data_sources.inputB
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19 --scoreThresholdA $scoreA
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20 --scoreThresholdB $scoreB
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21 --distance $distance
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22 --minlength $minlength
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23 --output-prefix cg_
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24 $stat
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25 ";
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26
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27 <!-- execute cgatools-->
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28 cgatools junctiondiff --beta
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29 --reference $crr.fields.path
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30 --junctionsA $data_sources.inputA
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31 --junctionsB $data_sources.inputB
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32 --scoreThresholdA $scoreA
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33 --scoreThresholdB $scoreB
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34 --distance $distance
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35 --minlength $minlength
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36 --output-prefix cg_
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37 $stat
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38 ;
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39 mv cg_diff-*tsv cg_diff.tsv
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40 </command>
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41
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42 <outputs>
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43 <data format="tabular" name="output1" from_work_dir="cg_diff.tsv" label="${tool.name} diff"/>
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44 <data format="tabular" name="output2" from_work_dir="cg_report.tsv" label="${tool.name} report">
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45 <filter>(stat == '--statout')</filter>
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46 </data>
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47 </outputs>
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48
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49 <inputs>
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50 <!--form field to select crr file-->
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51 <param name="crr" type="select" label="Reference genome (.crr file)">
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52 <options from_data_table="cg_crr_files" />
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53 </param>
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54
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55 <!--conditional to select variant file input-->
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56 <conditional name="data_sources">
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57 <param name="data_source" type="select" label="Where are the input junction files?">
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58 <option value="in" selected="true">imported into Galaxy</option>
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59 <option value="out">located outside Galaxy (data on server or mounted drive)</option>
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60 </param>
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61
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62 <!--form field to select junction files-->
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63 <when value="in">
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64 <param name="inputA" type="data" format="tabluar" label="Junction file A">
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65 <validator type="dataset_ok_validator" />
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66 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
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67 metadata_name="dbkey" metadata_column="1"
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68 message="cgatools is not currently available for this build."/>
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69 </param>
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70 <param name="inputB" type="data" format="tabluar" label="Junction file B">
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71 <validator type="dataset_ok_validator" />
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72 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
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73 metadata_name="dbkey" metadata_column="1"
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74 message="cgatools is not currently available for this build."/>
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75 </param>
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76 </when>
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77
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78 <!--form field to enter external input files-->
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79 <when value="out">
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80 <param name="inputA" type="text" label="Junction file A (/path/junction_file)" size="40" help="e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01_2000/ASM/SV/allJunctionsBeta-GS00000YYYY-ASM.tsv">
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81 <validator type="empty_field" message="You must supply a junction file"/>
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82 </param>
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83 <param name="inputB" type="text" label="Junction file B (/path/junction_file)" size="40" help="e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01_2000/ASM/SV/allJunctionsBeta-GS00000YYYY-ASM.tsv">
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84 <validator type="empty_field" message="You must supply a junction file"/>
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85 </param>
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86 </when>
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87 </conditional>
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88
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89 <!--form field to select stats output-->
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90 <param name="stat" type="select" label="Print input file stats">
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91 <option value="">no</option>
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92 <option value="--statout">yes</option>
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93 </param>
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94
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95 <!--other parameters-->
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96 <param name="scoreA" type="integer" label="Score threshold value for input file A (default 10)" value="10">
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97 <validator type="empty_field" message="You must enter a value, the default is 10" />
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98 </param>
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99 <param name="scoreB" type="integer" label="Score threshold value for input file B (default 0)" value="0">
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100 <validator type="empty_field" message="You must enter a value, the default is 0" />
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101 </param>
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102 <param name="distance" type="integer" label="Max distance between coordinates of potentially compatible junctions (default 200)" value="200">
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103 <validator type="empty_field" message="You must enter a value, the default is 200" />
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104 </param>
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105 <param name="minlength" type="integer" label="Minimum deletion junction length to be included into the difference file (default 500)" value="500">
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106 <validator type="empty_field" message="You must enter a value, the default is 500" />
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107 </param>
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108 </inputs>
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109
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110
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111 <help>
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112
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113 **What it does**
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114
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115 This tool uses cgatools junctiondiff to report difference between junction calls of two Complete Genomics junctions files
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116
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117 **cgatools 1.6.0 Documentation**
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118
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119 Userguide: http://cgatools.sourceforge.net/docs/1.6.0/cgatools-user-guide.pdf
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120
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121 Release notes: http://cgatools.sourceforge.net/docs/1.6.0/cgatools-release-notes.pdf
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122
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123 **Command line reference**::
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124
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125 COMMAND NAME
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126 junctiondiff - Reports difference between junction calls of Complete Genomics junctions files.
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127
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128 DESCRIPTION
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129 junctiondiff takes two junction files A and B as input and produces the
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130 following output:
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131 - "diff-inputFileName" - the junctions from an input file A that are not
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132 present in input file B.
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133 - "report.txt" - a brief summary report (if --statout is used)
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134
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135 Two junctions are considered equivalent if:
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136 - they come from different files
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137 - left and right positions of one junction are not more than "--distance"
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138 bases apart from the corresponding positions of another junction
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139 - the junction scores are equal or above the scoreThreshold
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140 - they are on the same strands
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141
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142 OPTIONS
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143 -h [ --help ]
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144 Print this help message.
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145
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146 --beta
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147 This is a beta command. To run this command, you must pass the --beta
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148 flag.
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149
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150 -s [ --reference ] arg
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151 Reference file.
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152
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153 -a [ --junctionsA ] arg
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154 input junction file A.
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155
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156 -b [ --junctionsB ] arg
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157 input junction file B.
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158
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159 -A [ --scoreThresholdA ] arg (=10)
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160 score threshold value for the input file A.
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161
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162 -B [ --scoreThresholdB ] arg (=0)
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163 score threshold value for the input file B.
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164
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165 -d [ --distance ] arg (=200)
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166 Max distance between coordinates of potentially compatible junctions.
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167
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168 -l [ --minlength ] arg (=500)
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169 Minimum deletion junction length to be included into the difference
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170 file.
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171
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172 -o [ --output-prefix ] arg
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173 The path prefix for all the output reports.
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174
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175 -S [ --statout ]
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176 (Debug) Report various input file statistics. Experimental feature.
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177
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178 SUPPORTED FORMAT_VERSION
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179 1.5 or later
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180 </help>
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181 </tool>
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