Mercurial > repos > iuc > chira_map

comparison chira_map.xml @ 8:3ba6fe6e7e82 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit a69b18084d0a9ade4e29869f8b0e2ce5fc4e0b73"
author iuc
date Sat, 06 Jun 2020 12:09:43 +0000
parents f11619faed12
children ef4058fbe025
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7:f11619faed12 8:3ba6fe6e7e82
72 <option value="rc">Reverse compliment of transcript strand only</option> 72 <option value="rc">Reverse compliment of transcript strand only</option>
73 <option value="both">Try both strands</option> 73 <option value="both">Try both strands</option>
74 </param> 74 </param>
75 <param name="seed_length1" type="integer" value="12" label="Seed length 1" min="1" 75 <param name="seed_length1" type="integer" value="12" label="Seed length 1" min="1"
76 help="Seed length for 1st mapping iteration. bwa-mem parameter -k"/> 76 help="Seed length for 1st mapping iteration. bwa-mem parameter -k"/>
77 <param name="seed_length2" type="integer" value="6" label="Seed length 2" min="1" 77 <param name="seed_length2" type="integer" value="16" label="Seed length 2" min="1"
78 help="Seed length for 2nd mapping iteration. bwa-mem parameter -k"/> 78 help="Seed length for 2nd mapping iteration. bwa-mem parameter -k"/>
79 <param name="align_score1" type="integer" value="18" min="1" 79 <param name="align_score1" type="integer" value="18" min="1"
80 label="Minimum alignmnet score for 1st mapping iteration" help="bwa-mem parameter '-T'"/> 80 label="Minimum alignmnet score for 1st mapping iteration" help="bwa-mem parameter '-T'"/>
81 <param name="align_score2" type="integer" value="10" min="1" 81 <param name="align_score2" type="integer" value="16" min="1"
82 label="Minimum alignmnet score for 2nd mapping iteration" help="bwa-mem parameter '-T'"/> 82 label="Minimum alignmnet score for 2nd mapping iteration" help="bwa-mem parameter '-T'"/>
83 <param name="match1" type="integer" value="1" label="Matching score for 1st mapping iteration"/> 83 <param name="match1" type="integer" value="1" label="Matching score for 1st mapping iteration"/>
84 <param name="mismatch1" type="integer" value="4" label="Mismatch penalty for 1st mapping iteration"/> 84 <param name="mismatch1" type="integer" value="4" label="Mismatch penalty for 1st mapping iteration"/>
85 <param name="match2" type="integer" value="1" label="Matching score for 2nd mapping iteration"/> 85 <param name="match2" type="integer" value="1" label="Matching score for 2nd mapping iteration"/>
86 <param name="mismatch2" type="integer" value="7" label="Mismatch penalty for 2nd mapping iteration"/> 86 <param name="mismatch2" type="integer" value="6" label="Mismatch penalty for 2nd mapping iteration"/>
87 <param name="gapo1" type="integer" value="6" label="Gap opening penalty for 1st mapping iteration"/> 87 <param name="gapo1" type="integer" value="6" label="Gap opening penalty for 1st mapping iteration"/>
88 <param name="gape1" type="integer" value="1" label="Gap extension penalty for 1st mapping iteration"/> 88 <param name="gape1" type="integer" value="1" label="Gap extension penalty for 1st mapping iteration"/>
89 <param name="gapo2" type="integer" value="100" label="Gap opening penalty for 2nd mapping iteration"/> 89 <param name="gapo2" type="integer" value="100" label="Gap opening penalty for 2nd mapping iteration"/>
90 <param name="gape2" type="integer" value="100" label="Gap extension penalty for 2nd mapping iteration"/> 90 <param name="gape2" type="integer" value="100" label="Gap extension penalty for 2nd mapping iteration"/>
91 <param name="nhits1" type="integer" value="50" 91 <param name="nhits1" type="integer" value="50"