Mercurial > repos > devteam > lastz
comparison lastz_wrapper.xml @ 4:60afcc2c1d05 draft
planemo upload commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
author | devteam |
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date | Fri, 09 Oct 2015 17:48:16 -0400 |
parents | 12d4359b7e2f |
children |
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3:d054d95585b1 | 4:60afcc2c1d05 |
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99 </param> | 99 </param> |
100 <param name="chain" type="select" label="Perform chaining of HSPs?"> | 100 <param name="chain" type="select" label="Perform chaining of HSPs?"> |
101 <option value="nochain">No</option> | 101 <option value="nochain">No</option> |
102 <option value="chain">Yes</option> | 102 <option value="chain">Yes</option> |
103 </param> | 103 </param> |
104 <param name="O" type="integer" size="5" value="400" label="Gap opening penalty"/> | 104 <param name="O" type="integer" value="400" label="Gap opening penalty"/> |
105 <param name="E" type="integer" size="5" value="30" label="Gap extension penalty"/> | 105 <param name="E" type="integer" value="30" label="Gap extension penalty"/> |
106 <param name="X" type="integer" size="5" value="910" label="X-drop threshold"/> | 106 <param name="X" type="integer" value="910" label="X-drop threshold"/> |
107 <param name="Y" type="integer" size="5" value="9370" label="Y-drop threshold"/> | 107 <param name="Y" type="integer" value="9370" label="Y-drop threshold"/> |
108 <param name="K" type="integer" size="5" value="3000" label="Set the threshold for HSPs (ungapped extensions scoring lower are discarded)"/> | 108 <param name="K" type="integer" value="3000" label="Set the threshold for HSPs (ungapped extensions scoring lower are discarded)"/> |
109 <param name="L" type="integer" size="5" value="3000" label="Set the threshold for gapped alignments (gapped extensions scoring lower are discarded)"/> | 109 <param name="L" type="integer" value="3000" label="Set the threshold for gapped alignments (gapped extensions scoring lower are discarded)"/> |
110 <param name="entropy" type="select" label="Involve entropy when filtering HSPs?"> | 110 <param name="entropy" type="select" label="Involve entropy when filtering HSPs?"> |
111 <option value="noentropy">No</option> | 111 <option value="noentropy">No</option> |
112 <option value="entropy">Yes</option> | 112 <option value="entropy">Yes</option> |
113 </param> | 113 </param> |
114 </when> | 114 </when> |
117 <param name="how_to_name" type="select" label="Do you want to modify the reference name?"> | 117 <param name="how_to_name" type="select" label="Do you want to modify the reference name?"> |
118 <option value="no">No</option> | 118 <option value="no">No</option> |
119 <option value="yes">Yes</option> | 119 <option value="yes">Yes</option> |
120 </param> | 120 </param> |
121 <when value="yes"> | 121 <when value="yes"> |
122 <param name="ref_name" type="text" size="25" value="Type sequence name here" label="Enter name for the Reference sequence"/> | 122 <param name="ref_name" type="text" value="Type sequence name here" label="Enter name for the Reference sequence"/> |
123 </when> | 123 </when> |
124 <when value="no" /> | 124 <when value="no" /> |
125 </conditional> | 125 </conditional> |
126 <param name="min_ident" type="integer" size="3" value="0" label="Do not report matches below this identity (%)"/> | 126 <param name="min_ident" type="integer" value="0" label="Do not report matches below this identity (%)"/> |
127 <param name="max_ident" type="integer" size="3" value="100" label="Do not report matches above this identity (%)"/> | 127 <param name="max_ident" type="integer" value="100" label="Do not report matches above this identity (%)"/> |
128 <param name="min_cvrg" type="integer" size="3" value="0" label="Do not report matches that cover less than this percentage of each read"/> | 128 <param name="min_cvrg" type="integer" value="0" label="Do not report matches that cover less than this percentage of each read"/> |
129 <param name="unmask" type="select" label="Convert lowercase bases to uppercase"> | 129 <param name="unmask" type="select" label="Convert lowercase bases to uppercase"> |
130 <option value="yes">Yes</option> | 130 <option value="yes">Yes</option> |
131 <option value="no">No</option> | 131 <option value="no">No</option> |
132 </param> | 132 </param> |
133 </inputs> | 133 </inputs> |