Mercurial > repos > abims-sbr > filter_assemblies

comparison filter_assembly.xml @ 7:948864b6ab4b draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 7c9540507076087e858141f9dd5df33409690dac
author abims-sbr
date Wed, 28 Feb 2018 06:03:31 -0500
parents 980b2f36e486
children e418021a8c69
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6:980b2f36e486 7:948864b6ab4b
1 <tool name="Filter assemblies" id="filter_assemblies" version="2.0.2"> 1 <tool name="Filter assemblies" id="filter_assemblies" version="2.0.3">
2 2
3 <description> 3 <description>
4 Filter the outputs of Velvet or Trinity assemblies 4 Filter the outputs of Velvet or Trinity assemblies
5 </description> 5 </description>
6 6
102 102
103 @HELP_AUTHORS@ 103 @HELP_AUTHORS@
104 104
105 <![CDATA[ 105 <![CDATA[
106 106
107 ---------
108
109 **Description** 107 **Description**
110 108
111 This tool reformats Velvet Oases or Trinity assemblies for the AdaptSearch galaxy suite and selects only one variant per gene according to its length and quality check. 109 This tool reformats Velvet Oases or Trinity assemblies for the AdaptSearch galaxy suite and selects only one variant per gene according to its length and quality check.
112 110
113 --------- 111 ---------
135 133
136 --------- 134 ---------
137 135
138 **Parameters** 136 **Parameters**
139 137
140 - 'Assembler' : specifies which assembler was used on the input files.
141 - 'Input files' : a collection of fasta files (one file per species). 138 - 'Input files' : a collection of fasta files (one file per species).
142 - 'Overlap percent identity cutoff' : cap3 -p parameter : minimum percent identity of an overlap. 139 - 'Overlap percent identity cutoff' : cap3 -p parameter : minimum percent identity of an overlap.
143 must be > 65 ; default : 100. 140 must be > 65 ; default : 100.
144 - 'Overlap length cutoff' (integer) : cap3 -o parameter : minimum length of an overlap (in base pairs). 141 - 'Overlap length cutoff' (integer) : cap3 -o parameter : minimum length of an overlap (in base pairs).
145 must be > 15 ; default : 60. 142 must be > 15 ; default : 60.