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1 <tool id="cg_junctiondiff" name="junctiondiff(beta) 1.5" version="1.0.0">
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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 -->
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6
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7 <description>reports difference between junction calls</description> <!--adds description in toolbar-->
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8
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9 <requirements>
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10 <requirement type="binary">cgatools</requirement>
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11 </requirements>
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12
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13 <command> <!--run executable-->
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14 cgatools | head -1;
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15 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 $stat
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24 --output-prefix cg_
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25 ;
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26 mv cg_diff-*tsv cg_diff.tsv
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27 </command>
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28
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29 <outputs>
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30 <data format="tabular" name="output1" from_work_dir="cg_diff.tsv" label="${tool.name} on ${on_string}: diff"/>
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31 <data format="tabular" name="output2" from_work_dir="cg_report.tsv" label="${tool.name} on ${on_string}: report">
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32 <filter>(stat == '--statout')</filter>
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33 </data>
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34 </outputs>
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35
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36 <inputs>
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37 <!--form field to select crr file-->
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38 <param name="crr" type="select" label="Reference genome (.crr file)">
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39 <options from_data_table="cg_crr_files" />
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40 </param>
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41
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42 <!--conditional to select variant file input-->
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43 <conditional name="data_sources">
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44 <param name="data_source" type="select" label="Where are the input junction files?">
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45 <option value="in" selected="true">imported into Galaxy</option>
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46 <option value="out">located outside Galaxy (available only for local Galaxy instances)</option>
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47 </param>
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48 <when value="in">
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49 <!--form field to select variant files-->
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50 <param name="inputA" type="data" format="tabluar" label="Junction file A">
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51 <validator type="unspecified_build" />
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52 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
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53 metadata_name="dbkey" metadata_column="1"
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54 message="cgatools is not currently available for this build."/>
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55 </param>
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56 <param name="inputB" type="data" format="tabluar" label="Junction file B">
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57 <validator type="unspecified_build" />
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58 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
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59 metadata_name="dbkey" metadata_column="1"
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60 message="cgatools is not currently available for this build."/>
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61 </param>
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62 </when>
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63 <when value="out">
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64 <!--form field to enter external input files-->
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65 <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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66 <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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67 </when>
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68 </conditional>
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69
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70 <!--form field to select stats output-->
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71 <param name="stat" type="select" label="Print input file stats">
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72 <option value="">no</option>
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73 <option value="--statout">yes</option>
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74 </param>
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75
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76 <param name="scoreA" type="integer" label="Score threshold value for input file A (default 10)" value="10"/>
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77 <param name="scoreB" type="integer" label="Score threshold value for input file B (default 0)" value="0"/>
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78 <param name="distance" type="integer" label="Max distance between coordinates of potentially compatible junctions (default 200)" value="200"/>
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79 <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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80 </inputs>
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81
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82
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83 <help>
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84
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85 **What it does**
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86
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87 This tool reports difference between junction calls of Complete Genomics junctions files
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88
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89 **cgatools 1.5.0 Documentation**
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90
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91 Userguide: http://cgatools.sourceforge.net/docs/1.5.0/cgatools-user-guide.pdf
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92
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93 Release notes: http://cgatools.sourceforge.net/docs/1.5.0/cgatools-release-notes.pdf
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94
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95 **Command line reference**::
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96
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97 COMMAND NAME
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98 junctiondiff - Reports difference between junction calls of Complete Genomics junctions files.
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99
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100 DESCRIPTION
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101 junctiondiff takes two junction files A and B as input and produces the
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102 following output:
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103 - "diff-inputFileName" - the junctions from an input file A that are not
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104 present in input file B.
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105 - "report.txt" - a brief summary report (if --statout is used)
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106
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107 Two junctions are considered equivalent if:
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108 - they come from different files
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109 - left and right positions of one junction are not more than "--distance"
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110 bases apart from the corresponding positions of another junction
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111 - the junction scores are equal or above the scoreThreshold
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112 - they are on the same strands
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113
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114 OPTIONS
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115 -h [ --help ]
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116 Print this help message.
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117
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118 --beta
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119 This is a beta command. To run this command, you must pass the --beta
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120 flag.
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121
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122 -s [ --reference ] arg
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123 Reference file.
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124
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125 -a [ --junctionsA ] arg
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126 input junction file A.
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127
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128 -b [ --junctionsB ] arg
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129 input junction file B.
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130
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131 -A [ --scoreThresholdA ] arg (=10)
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132 score threshold value for the input file A.
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133
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134 -B [ --scoreThresholdB ] arg (=0)
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135 score threshold value for the input file B.
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136
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137 -d [ --distance ] arg (=200)
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138 Max distance between coordinates of potentially compatible junctions.
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139
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140 -l [ --minlength ] arg (=500)
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141 Minimum deletion junction length to be included into the difference
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142 file.
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143
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144 -o [ --output-prefix ] arg
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145 The path prefix for all the output reports.
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146
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147 -S [ --statout ]
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148 (Debug) Report various input file statistics. Experimental feature.
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149
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150 SUPPORTED FORMAT_VERSION
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151 1.5 or later
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152 </help>
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153 </tool>
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