Mercurial > repos > saskia-hiltemann > cgatools_v17

annotate tools/cgatools17/junctions2events_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="junctions2events" name="Junctions2Events" version="1.7.1">
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2 <description> Groups related junctions and annotates each group with information about the structural rearrangement (event) that these junctions represent </description>
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3
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4 <requirements>
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5 <requirement type="package" version="1">cgatools17</requirement>
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6 </requirements>
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7
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8 <command>
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9 cgatools | head -1;
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10 cgatools junctions2events --beta
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11 --reference ${refs.fields.crr_path}
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12 --junctions $junctions
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13 #if $alljunctions
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14 --all-junctions $alljunctions
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15 #end if
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16 --repmask-data ${refs.fields.repmask_path}
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17 --gene-data ${refs.fields.genedata_path}
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18 #if $more_options.options_type_selector == "more"
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19 --regulatory-region-length $regreglen
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20 --contained-genes-max-range $contgenmax
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21 --max-related-junction-distance $maxreljdist
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22 --max-pairing-distance $maxpairdist
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23 --max-copy-target-length $maxcopylen
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24 --max-simple-event-distance $maxsed
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25 #if $more_options.mobelname
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26 --mobile-element-names $mobelname
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27 #end if
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28 --max-distance-to-m-e $maxdisttome
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29 #end if
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30 </command>
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31
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32 <inputs>
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33 <!-- select reference -->
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34 <param name="refs" type="select" label="Reference Build">
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35 <options from_data_table="cg_anno_files" />
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36 </param>
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37
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38 <!-- select junction files -->
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39 <param name="junctions" type="data" format="tabular" label="Junctions file (allJunctions of highConfidenceJunction)"/>
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40 <param name="alljunctions" type="data" format="tabular" optional="true" label="Optional: allJunctions file"/>
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41
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42 <!-- advanced settings -->
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43 <conditional name="more_options">
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44 <param name="options_type_selector" type="select" label="Advanced Options">
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45 <option value="hide" selected="True">Less options</option>
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46 <option value="show">More options</option>
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47 </param>
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48 <when value="less">
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49 <!-- no options -->
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50 </when>
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51 <when value="show">
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52 <param name="regreglen" type="integer" value="7500" min="0" label="regulatory region length" help="Length of the region upstream of the gene that may contain regulatory sequence for the gene" />
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53 <param name="contgenmax" type="integer" value="-1" min="0" label="contained genes max range" help="Maximum length of a copy or deletion event to annotate with all genes that overlap the copied or deleted segment. (Negative value causes all events to be annotated regardless of the length)" />
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54 <param name="maxreljdist" type="integer" value="700" min="0" label="max related junctions distance" help="Junctions occurring within this distance are presumed to be related" />
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55 <param name="maxpairdist" type="integer" value="10000000" min="0" label="max pairing distance" help="Maximum allowed distance between junction sides wshen searching for paired junctions caused by the same event." />
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56 <param name="maxcopylen" type="integer" value="1000" min="0" label="max copy target length" help="Pairs of junctions will be classified as a copy event only if the length of the implied copy target region is below this threshold." />
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57 <param name="maxsed" type="integer" value="10000000" min="0" label="max simple event distance" help="When given a choice of identifying an event as a mobile element copy or as a simple deletion/duplication, prefer the latter explanation if the length of the affected sequence is below this threshold" />
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58 <param name="mobelname" type="select" multiple="true" display="checkboxes" label="mobile element names" help="Names of mobile elements that are known to be active and sometimes copy flanking 3' sequence" >
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59 <option value="L1HS"> L1HS </option>
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60 <option value="AluY"> AluY </option>
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61 <option value="SVA"> SVA </option>
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62 </param>
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63 <param name="maxdisttome" type="integer" value="2000" min="0" label="max distance to ME" help="Maximum allowed distance from the junction side to the element when searching for a mobile element related to a junction" />
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64 </when>
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65 </conditional>
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66
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67 <!-- prefix for output file so you dont have to manually rename history items -->
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68 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
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69 </inputs>
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70
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71 <outputs>
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72 <data format="tabular" name="annotatedjunctions" from_work_dir="AnnotatedJunctions.tsv" label="$fname AnnotatedJunctions file of ${tool.name} on ${on_string}"/>
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73 <data format="tabular" name="events" from_work_dir="Events.tsv" label="$fname Events file of ${tool.name} on ${on_string}"/>
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74 </outputs>
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75
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76 <help>
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77
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78 **What it does**
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79
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80 This tool searches for groups of related junctions and for every group
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81 attempts to determine the event that caused the junctions.
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82
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83 **cgatools 1.7.1 Documentation**
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84
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85 Userguide: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-user-guide.pdf
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86
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87 Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf
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88
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89 **Command line reference**::
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90
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91 COMMAND NAME
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92 junctions2events - Groups and annotates junction calls by event type.
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93
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94
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95 OPTIONS
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96 -h [ --help ]
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97 Print this help message.
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98
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99 --beta
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100 This is a beta command. To run this command, you must pass the --beta
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101 flag.
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102
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103 --reference arg
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104 Reference file.
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105
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106 --output-prefix arg
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107 The path prefix for all output reports.
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108
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109 --junctions arg
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110 Primary input junction file.
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111
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112 --all-junctions arg
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113 Superset of the input junction file to use when searching for the
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114 related junctions. The default is to use only the junctions in the
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115 primary junction file.
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116
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117 --repmask-data arg
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118 The file that contains repeat masker data.
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119
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120 --gene-data arg
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121 The file that contains gene location data.
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122
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123 --regulatory-region-length arg (=7500)
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124 Length of the region upstream of the gene that may contain regulatory
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125 sequence for the gene. Junctions that connect this region to another
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126 gene will be annotated as a special kind of gene fusion.
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127
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128 --contained-genes-max-range arg (=-1)
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129 Maximum length of a copy or deletion event to annotate with all genes
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130 that overlap the copied or deleted segment. Negative value causes all
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131 events to be annotated regardless of the length.
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132
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133 --max-related-junction-distance arg (=700)
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134 Junctions occurring within this distance are presumed to be related.
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135
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136 --max-pairing-distance arg (=10000000)
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137 When searching for paired junctions caused by the same event, maximum
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138 allowed distance between junction sides.
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139
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140 --max-copy-target-length arg (=1000)
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141 Pairs of junctions will be classified as a copy event only if the
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142 length of the implied copy target region is below this threshold.
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143
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144 --max-simple-event-distance arg (=10000000)
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145 When given a choice of explaining an event as a mobile element copy or
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146 as a simple deletion/duplication, prefer the latter explanation if the
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147 length of the affected sequence if below this threshold.
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148
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149 --mobile-element-names arg (=L1HS,SVA)
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150 Comma-separated list of the names of the mobile elements that are known
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151 to be active and sometimes copy flanking 3' sequence.
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152
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153 --max-distance-to-m-e arg (=2000)
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154 When searching for a mobile element related to a junction, maximum
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155 allowed distance from the junction side to the element.
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156
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157 --max-related-junction-output arg (=100)
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158 Maximum number of related junctions included into annotation field
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159
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160
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161 SUPPORTED FORMAT_VERSION
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162 1.5 or later
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163
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164 </help>
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165 </tool>
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166
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167