Mercurial > repos > saskia-hiltemann > cgatools_v17

annotate tools/cgatools17/junctiondiff_v17.xml @ 15:b5c879e950f5 draft default tip

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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 402ebee914f2286aa9d98223f501f06c1e4b9c22-dirty
author yhoogstrate
date Fri, 20 Nov 2015 03:50:36 -0500
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1
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1 <tool id="cg_junctiondiff" name="JunctionDiff" version="1.7.1">
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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="package" version="1">cgatools17</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 | head -1;
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11 cgatools junctiondiff --beta
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12 --reference ${crr.fields.crr_path}
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13 --junctionsA $inputA
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14 --junctionsB $inputB
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15 --scoreThresholdA $scoreA
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16 --scoreThresholdB $scoreB
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17 --distance $distance
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18 --minlength $minlength
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19 $stat
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20 --output-prefix cg_
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21 ;
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22 mv cg_diff-* cg_diff.tsv
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23 </command>
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24
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25 <inputs>
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26 <!-- reference -->
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27 <param name="crr" type="select" label="Reference Build">
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28 <options from_data_table="cg_anno_files" />
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29 </param>
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30
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31 <!--input files-->
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32 <param name="inputA" type="data" format="tabluar" label="Junction file A"/>
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33 <param name="inputB" type="data" format="tabluar" label="Junction file B"/>
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34
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35 <!--parameters-->
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36 <param name="stat" type="select" label="Print input file stats">
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37 <option value="">no</option>
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38 <option value="--statout">yes</option>
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39 </param>
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40
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41 <param name="scoreA" type="integer" label="Score threshold value for input file A (default 10)" value="10"/>
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42 <param name="scoreB" type="integer" label="Score threshold value for input file B (default 0)" value="0"/>
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43 <param name="distance" type="integer" label="Max distance between coordinates of potentially compatible junctions (default 200)" value="200"/>
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44 <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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45
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46 <!-- prefix for output file so you dont have to manually rename history items -->
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47 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
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48 </inputs>
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49
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50 <outputs>
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51 <data format="tabular" name="corrected_junctions" from_work_dir="cg_diff.tsv" label="$fname ${tool.name} on ${on_string}: diff"/>
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52 <data format="tabular" name="report" from_work_dir="cg_report.tsv" label="$fname ${tool.name} on ${on_string}: report">
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53 <filter>(stat == '--statout')</filter>
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54 </data>
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55 </outputs>
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56
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57
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58 <help>
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59 **What it does**
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60
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61 This tool reports difference between junction calls of Complete Genomics junctions files
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62
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63 **cgatools 1.7.1 Documentation**
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64
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65 Userguide: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-user-guide.pdf
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66
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67 Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf
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68
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69 **Command line reference**::
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70
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71 COMMAND NAME
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72 junctiondiff - Reports difference between junction calls of Complete Genomics junctions files.
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73
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74 DESCRIPTION
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75 junctiondiff takes two junction files A and B as input and produces the
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76 following output:
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77 - "diff-inputFileName" - the junctions from an input file A that are not
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78 present in input file B.
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79 - "report.txt" - a brief summary report (if --statout is used)
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80
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81 Two junctions are considered equivalent if:
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82 - they come from different files
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83 - left and right positions of one junction are not more than "--distance"
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84 bases apart from the corresponding positions of another junction
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85 - the junction scores are equal or above the scoreThreshold
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86 - they are on the same strands
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87
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88 OPTIONS
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89 -h [ --help ]
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90 Print this help message.
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91
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92 --beta
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93 This is a beta command. To run this command, you must pass the --beta
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94 flag.
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95
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96 -s [ --reference ] arg
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97 Reference file.
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98
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99 -a [ --junctionsA ] arg
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100 input junction file A.
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101
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102 -b [ --junctionsB ] arg
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103 input junction file B.
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104
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105 -A [ --scoreThresholdA ] arg (=10)
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106 score threshold value for the input file A.
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107
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108 -B [ --scoreThresholdB ] arg (=0)
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109 score threshold value for the input file B.
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110
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111 -d [ --distance ] arg (=200)
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112 Max distance between coordinates of potentially compatible junctions.
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113
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114 -l [ --minlength ] arg (=500)
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115 Minimum deletion junction length to be included into the difference
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116 file.
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117
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118 -o [ --output-prefix ] arg
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119 The path prefix for all the output reports.
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120
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121 -S [ --statout ]
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122 (Debug) Report various input file statistics. Experimental feature.
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123
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124 SUPPORTED FORMAT_VERSION
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125 1.5 or later
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126 </help>
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127 </tool>