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1 <tool id="cga_junctiondiff" name="junctiondiff(beta)" version="0.0.1">
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2
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3 <description>reports difference between junction calls</description> <!--adds description in toolbar-->
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4
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5 <requirements>
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6 <requirement type="binary">cgatools</requirement>
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7 </requirements>
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8
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9 <command> <!--run executable-->
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10 cgatools junctiondiff --beta
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11 --reference $crr.fields.path
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12 --junctionsA $data_sources.inputA
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13 --junctionsB $data_sources.inputB
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14 --scoreThresholdA $scoreA
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15 --scoreThresholdB $scoreB
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16 --distance $distance
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17 --minlength $minlength
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18 $stat
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19 --output-prefix cg_
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20 ;
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21 mv cg_diff-*tsv cg_diff.tsv
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22 </command>
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23
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24 <outputs>
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25 <data format="tabular" name="output1" from_work_dir="cg_diff.tsv" label="${tool.name} on ${on_string}: diff"/>
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26 <data format="tabular" name="output2" from_work_dir="cg_report.tsv" label="${tool.name} on ${on_string}: report">
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27 <filter>(stat == '--statout')</filter>
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28 </data>
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29 </outputs>
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30
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31 <inputs>
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32 <!--form field to select crr file-->
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33 <param name="crr" type="select" label="Genome build">
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34 <options from_data_table="cg_crr_files" />
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35 </param>
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36
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37 <!--conditional to select variant file input-->
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38 <conditional name="data_sources">
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39 <param name="data_source" type="select" label="Where are the input junction files?">
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40 <option value="in" selected="true">imported into Galaxy</option>
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41 <option value="out">located outside Galaxy (available only for local Galaxy instances)</option>
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42 </param>
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43 <when value="in">
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44 <!--form field to select variant files-->
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45 <param name="inputA" type="data" format="tabluar" label="Junction file A">
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46 <validator type="unspecified_build" />
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47 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
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48 metadata_name="dbkey" metadata_column="1"
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49 message="cgatools is not currently available for this build."/>
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50 </param>
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51 <param name="inputB" type="data" format="tabluar" label="Junction file B">
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52 <validator type="unspecified_build" />
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53 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
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54 metadata_name="dbkey" metadata_column="1"
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55 message="cgatools is not currently available for this build."/>
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56 </param>
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57 </when>
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58 <when value="out">
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59 <!--form field to enter external input files-->
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60 <param name="inputA" type="text" label="Junction file A (path/file_name)" size="40" help="Junction file can be compressed (gz, bz2)."/>
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61 <param name="inputB" type="text" label="Junction file B (path/file_name)" size="40" help="Junction file can be compressed (gz, bz2)."/>
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62 </when>
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63 </conditional>
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64
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65 <!--form field to select stats output-->
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66 <param name="stat" type="select" label="Print input file stats">
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67 <option value="">no</option>
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68 <option value="--statout">yes</option>
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69 </param>
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70
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71 <param name="scoreA" type="integer" label="Score threshold value for input file A (default 10)" value="10"/>
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72 <param name="scoreB" type="integer" label="Score threshold value for input file B (default 0)" value="0"/>
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73 <param name="distance" type="integer" label="Max distance between coordinates of potentially compatible junctions (default 200)" value="200"/>
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74 <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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75 </inputs>
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76
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77
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78 <help>
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79
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80 **What it does**
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81
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82 This tool reports difference between junction calls of Complete Genomics junctions files
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83
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84 cgatools: http://sourceforge.net/projects/cgatools/files/
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85
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86 -----
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87
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88 **cgatools Manual**::
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89
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90 COMMAND NAME
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91 junctiondiff - Reports difference between junction calls of Complete Genomics junctions files.
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92
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93 DESCRIPTION
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94 junctiondiff takes two junction files A and B as input and produces the
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95 following output:
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96 - "diff-inputFileName" - the junctions from an input file A that are not
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97 present in input file B.
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98 - "report.txt" - a brief summary report (if --statout is used)
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99
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100 Two junctions are considered equivalent if:
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101 - they come from different files
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102 - left and right positions of one junction are not more than "--distance"
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103 bases apart from the corresponding positions of another junction
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104 - the junction scores are equal or above the scoreThreshold
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105 - they are on the same strands
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106
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107 OPTIONS
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108 -h [ --help ]
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109 Print this help message.
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110
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111 --beta
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112 This is a beta command. To run this command, you must pass the --beta
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113 flag.
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114
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115 -s [ --reference ] arg
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116 Reference file.
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117
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118 -a [ --junctionsA ] arg
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119 input junction file A.
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120
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121 -b [ --junctionsB ] arg
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122 input junction file B.
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123
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124 -A [ --scoreThresholdA ] arg (=10)
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125 score threshold value for the input file A.
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126
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127 -B [ --scoreThresholdB ] arg (=0)
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128 score threshold value for the input file B.
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129
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130 -d [ --distance ] arg (=200)
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131 Max distance between coordinates of potentially compatible junctions.
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132
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133 -l [ --minlength ] arg (=500)
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134 Minimum deletion junction length to be included into the difference
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135 file.
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136
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137 -o [ --output-prefix ] arg
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138 The path prefix for all the output reports.
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139
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140 -S [ --statout ]
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141 (Debug) Report various input file statistics. Experimental feature.
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142
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143 SUPPORTED FORMAT_VERSION
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144 1.5 or later
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145 </help>
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146 </tool>
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