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comparison POGs.xml @ 12:752786fe211b draft default tip

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
author lecorguille
date Mon, 24 Sep 2018 03:57:14 -0400
parents 05985273b735
children
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11:05985273b735 12:752786fe211b
112 112
113 @HELP_AUTHORS@ 113 @HELP_AUTHORS@
114 114
115 <![CDATA[ 115 <![CDATA[
116 116
117 **Last Version** : Victor Mataigne and Gildas Le Corguillé
118
119 **Description** 117 **Description**
120 118
121 This tool parses homologous sequences obtained by pairwise and gather sequences into groups of orthologous sequences. 119 This tool parses homologous sequences obtained by pairwise and gather sequences into groups of orthologous sequences.
122 120
123 -------- 121 --------
128 126
129 -------- 127 --------
130 128
131 **Parameters** 129 **Parameters**
132 130
133 - Species minimum : drop orthogroups with less than n species : orthogroups with less than n species within won't be recorded. 131 - Species minimum : drop orthogroups with less than n species : orthogroups with less than n species within won't be recorded.
134 132 - verbose : check 'Yes' if you want a supplementary table : countings of orthogroups before the paralogous sequences removal.
135 - verbose : check 'Yes' if you want a supplementary table : countings of orthogroups before the paralogous sequences removal. 133 - paralogs : check 'Yes' if you also want to retrieve the orthogroups before the paralogous sequences removal.
136
137 - paralogs : check 'Yes' if you also want to retrieve the orthogroups before the paralogous sequences removal.
138 134
139 135
140 .. class:: warningmark 136 .. class:: warningmark
137
141 The minimum number of species per group only applies to the main output files. In the case of the 'paralogs' option, this parameter is more likely the minimum amount of sequences to keep. 138 The minimum number of species per group only applies to the main output files. In the case of the 'paralogs' option, this parameter is more likely the minimum amount of sequences to keep.
142 139
143 -------- 140 --------
144 141
145 **Outputs** 142 **Outputs**
155 --------- 152 ---------
156 153
157 **The AdaptSearch Pipeline** 154 **The AdaptSearch Pipeline**
158 155
159 .. image:: adaptsearch_picture_helps.png 156 .. image:: adaptsearch_picture_helps.png
157
158 ---------
160 159
161 Changelog 160 Changelog
162 --------- 161 ---------
163 162
164 **Version 2.1 - 04/01/2018** 163 **Version 2.1 - 04/01/2018**
182 181
183 ]]> 182 ]]>
184 183
185 </help> 184 </help>
186 185
187 <expand macro="citations" />
188
189 </tool> 186 </tool>