Mercurial > repos > iuc > hmmer_alimask
annotate macros.xml @ 6:92227c141aa5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit db615ae8a189ad988ec08090051a128355a4be70"
author | iuc |
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date | Thu, 14 Jan 2021 15:40:11 +0000 |
parents | b4dc65565864 |
children | 80c713789d13 |
rev | line source |
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0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
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1 <?xml version="1.0"?> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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2 <macros> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
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3 <xml name="requirements"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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4 <requirements> |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
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1
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5 <requirement type="package" version="@TOOL_VERSION@">hmmer</requirement> |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
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6 <yield/> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
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7 </requirements> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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8 </xml> |
5
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
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9 <token name="@TOOL_VERSION@">3.3</token> |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
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10 <xml name="stdio"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
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11 <stdio> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
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12 <!-- Anything other than zero is an error --> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
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13 <exit_code range="1:"/> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
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14 <exit_code range=":-1"/> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
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15 <!-- In case the return code has not been set propery check stderr too --> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
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16 <regex match="Error:"/> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
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17 <regex match="Exception:"/> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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18 </stdio> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
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19 </xml> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
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20 <token name="@THRESHOLDS@"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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21 -E $E |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
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22 --domE $domE |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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23 |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
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1
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24 #if str($T): |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents:
1
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25 -T $T |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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26 #end if |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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27 |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
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1
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changeset
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28 #if str($domT): |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents:
1
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29 --domT $domT |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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30 #end if |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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31 |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
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1
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32 #if str($incE): |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
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33 --incE $incE |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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34 #end if |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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35 |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
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1
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36 #if str($incdomE): |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents:
1
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37 --incdomE $incdomE |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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38 #end if |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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39 |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents:
1
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40 #if str($incT): |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents:
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41 --incT $incT |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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42 #end if |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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43 |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents:
1
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44 #if str($incdomT): |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents:
1
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45 --incdomT $incdomT |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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46 #end if |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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47 </token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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48 <xml name="thresholds_xml"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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49 <!-- Options controlling reporting thresholds --> |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents:
1
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50 <param argument="-E" type="float" min="0" value="10.0" label="report sequences <= this E-Value threshold in output" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents:
1
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51 <param argument="--domE" type="float" min="0" value="10.0" label="report domains <= this E-Value threshold in output" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents:
1
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52 <param argument="-T" type="float" optional="true" label="report sequences >= this score threshold in output" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents:
1
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53 <param argument="--domT" type="float" optional="true" label="report domains >= this score threshold in output" /> |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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54 <!-- Options controlling inclusion (significance) thresholds --> |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents:
1
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55 <param argument="--incE" type="float" optional="true" label="consider sequences <= this E-Value threshold as significant" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents:
1
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56 <param argument="--incdomE" type="float" optional="true" label="consider domains <= this E-Value threshold as significant" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents:
1
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57 <param argument="--incT" type="float" optional="true" label="consider sequences >= this score threshold as significant" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents:
1
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58 <param argument="--incdomT" type="float" optional="true" label="consider domains >= this score threshold as significant" /> |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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59 </xml> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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60 <token name="@THRESHOLDS_NODOM@"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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61 -E $E |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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62 |
3
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
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63 #if str($T): |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
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64 -T $T |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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65 #end if |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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66 |
3
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
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67 #if str($incE): |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
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68 --incE $incE |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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69 #end if |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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70 |
3
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
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71 #if str($incT): |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
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72 --incT $incT |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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73 #end if |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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74 </token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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75 <xml name="thresholds_nodom"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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76 <!-- Options controlling reporting thresholds --> |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents:
1
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77 <param argument="-E" type="float" min="0" value="10.0" label="report sequences <= this E-Value threshold in output" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents:
1
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78 <param argument="-T" type="float" optional="true" label="report sequences >= this score threshold in output" /> |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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79 <!-- Options controlling inclusion (significance) thresholds --> |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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80 <param argument="--incE" type="float" optional="true" label="consider sequences <= this E-Value threshold as significant" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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81 <param argument="--incT" type="float" optional="true" label="consider sequences >= this score threshold as significant" /> |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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82 </xml> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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83 <token name="@ACCEL_HEUR@"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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84 $max |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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85 --F1 $F1 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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86 --F2 $F2 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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87 --F3 $F3 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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88 $nobias |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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89 </token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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90 <xml name="accel_heur_xml"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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91 <!-- Options controlling acceleration heuristics --> |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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92 <param argument="--max" type="boolean" truevalue="--max" falsevalue="" label="Turn all heuristic filters off (less speed, more power)" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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93 <param argument="--F1" type="float" value="0.02" label="Stage 1 (MSV) threshold: promote hits w/ P <= F1" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
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94 <param argument="--F2" type="float" value="1e-3" label="Stage 2 (Vit) threshold: promote hits w/ P <= F2" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
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95 <param argument="--F3" type="float" value="1e-5" label="Stage 3 (Fwd) threshold: promote hits w/ P <= F3" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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96 <param argument="--nobias" type="boolean" truevalue="--nobias" falsevalue="" label="Turn off composition bias filter" /> |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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97 </xml> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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98 <token name="@EVAL_CALIB@"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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99 --EmL $EmL |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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100 --EmN $EmN |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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101 --EvL $EvL |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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102 --EvN $EvN |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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103 --EfL $EfL |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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104 --EfN $EfN |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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105 --Eft $Eft |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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106 </token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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107 <xml name="eval_calib_xml"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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108 <!-- Control of E-value calibration --> |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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109 <param argument="--EmL" type="integer" min="1" value="200" label="Length of sequences for MSV Gumbel mu fit" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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110 <param argument="--EmN" type="integer" min="1" value="200" label="Number of sequences for MSV Gumbel mu fit" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
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111 <param argument="--EvL" type="integer" min="1" value="200" label="Length of sequences for Viterbi Gumbel mu fit" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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112 <param argument="--EvN" type="integer" min="1" value="200" label="Number of sequences for Viterbi Gumbel mu fit" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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113 <param argument="--EfL" type="integer" min="1" value="100" label="Length of sequences for Forward exp tail tau fit" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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114 <param argument="--EfN" type="integer" min="1" value="200" label="Number of sequences for Forward exp tail tau fit" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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115 <param argument="--Eft" type="float" min="0" max="1" value="0.04" label="tail mass for Forward exponential tail tau fit" /> |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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116 </xml> |
5
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
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117 <token name="@OFORMAT_WITH_OPTS@"> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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118 #if $oformat: |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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119 #for o in str($oformat).split(','): |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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120 --$o '$getVar($o, 'MISSING_OUTPUT'+$o)' |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
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121 #end for |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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122 #end if |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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123 $acc $noali $notextw |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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124 </token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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125 <xml name="oformat_with_opts"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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126 <!-- Options directing output --> |
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819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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127 <param name="oformat" type="select" multiple="true" display="checkboxes" label="Output Formats"> |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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128 <option value="tblout" selected="true">Table of per-sequence hits (--tblout)</option> |
5
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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129 <yield/> |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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130 </param> |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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131 <param argument="--acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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132 <param argument="--noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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133 <param argument="--notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" /> |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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134 </xml> |
5
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
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135 |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
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136 <xml name="oformat_with_opts_dom"> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
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137 <expand macro="oformat_with_opts"> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
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138 <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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139 <yield/> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
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140 </expand> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
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141 </xml> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
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142 |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
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143 <xml name="oformat_with_opts_dom_pfam"> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
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144 <expand macro="oformat_with_opts_dom"> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
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145 <option value="pfamtblout" selected="true">Table of hits and domains in Pfam format (--pfamtblout)</option> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
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146 </expand> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
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147 </xml> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
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148 |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
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149 <xml name="oformat_with_opts_dfam_alisc"> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
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150 <!-- Options directing output --> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
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151 <expand macro="oformat_with_opts"> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
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152 <option value="dfamtblout" selected="true">Table of hits in Dfam format (--dfamtblout)</option> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
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153 <option value="aliscoresout">Scores for each position in each alignment to file (--aliscoresout)</option> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
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154 </expand> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
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155 </xml> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
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4
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changeset
|
156 |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
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changeset
|
157 <xml name="output" token_tool=""> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
diff
changeset
|
158 <data name="output" format="txt" label="@TOOL@ on ${on_string}"/> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
diff
changeset
|
159 <data name="tblout" format="txt" label="@TOOL@ on ${on_string}: per-sequence hits from HMM matches"> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
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changeset
|
160 <filter>oformat and 'tblout' in oformat</filter> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
diff
changeset
|
161 </data> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
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|
162 <yield/> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
diff
changeset
|
163 </xml> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
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changeset
|
164 <xml name="output_dom" token_tool=""> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
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changeset
|
165 <expand macro="output" tool="@TOOL@"> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
diff
changeset
|
166 <data name="domtblout" format="txt" label="@TOOL@ on ${on_string}: per-domain hits from HMM matches"> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
diff
changeset
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167 <filter>oformat and 'domtblout' in oformat</filter> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
diff
changeset
|
168 </data> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
diff
changeset
|
169 </expand> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
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changeset
|
170 <yield/> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
diff
changeset
|
171 </xml> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
diff
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|
172 <xml name="output_dom_pfam" token_tool=""> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
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changeset
|
173 <expand macro="output_dom" tool="@TOOL@"> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
diff
changeset
|
174 <data name="pfamtblout" format="txt" label="@TOOL@ on ${on_string}: per-sequence/per-domain hits from HMM matches"> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
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175 <filter>oformat and 'pfamtblout' in oformat</filter> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
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changeset
|
176 </data> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
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|
177 </expand> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
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|
178 </xml> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
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|
179 <xml name="output_dfam_alisc" token_tool="" token_ofvar="seqfile" token_invar="seqdb"> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
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changeset
|
180 <expand macro="output" tool="@TOOL@"> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
diff
changeset
|
181 <data name="dfamtblout" format="txt" label="@TOOL@ on ${on_string}: per-sequence/per-domain hits from HMM matches"> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
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182 <filter>oformat and 'dfamtblout' in oformat</filter> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
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|
183 </data> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
diff
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|
184 <data name="aliscoresout" format="txt" label="@TOOL@ on ${on_string}: scores for positional matches"> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
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185 <filter>oformat and 'aliscoresout' in oformat</filter> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
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|
186 </data> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
diff
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|
187 </expand> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
diff
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|
188 </xml> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
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189 |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
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190 <xml name="assert_out" token_tool=""> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
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|
191 <assert_contents> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
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|
192 <has_line_matching expression="# @TOOL@.*"/> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
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193 <has_line_matching expression="\[ok\]"/> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
diff
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|
194 </assert_contents> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
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195 </xml> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
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|
196 |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
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|
197 <xml name="assert_tblout" token_tool=""> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
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|
198 <assert_contents> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
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|
199 <has_line_matching expression="# Program: @TOOL@"/> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
diff
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|
200 <has_line_matching expression="# \[ok\]"/> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
diff
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|
201 </assert_contents> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
diff
changeset
|
202 </xml> |
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
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|
203 |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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204 <xml name="oformat_test"> |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
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1
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205 <param name="notextw" value="true" /> |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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|
206 </xml> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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|
207 <token name="@HSSI@"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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208 #if $hssi.hssi_select == "singlemx": |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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209 --popen $hssi.popen |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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210 --pextend $hssi.pextend |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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211 #end if |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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212 </token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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213 <xml name="hssi"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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214 <!-- Handling single sequence inputs --> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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|
215 <conditional name="hssi"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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|
216 <param name="hssi_select" type="select" label="Options for handling single sequence inputs"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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217 <option value="false" selected="true">Disable</option> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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218 <option value="singlemx">Use substitution score matrix for single-sequence inputs</option> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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|
219 </param> |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents:
1
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|
220 <when value="false" /> |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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221 <when value="singlemx"> |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
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1
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|
222 <param argument="--popen" type="float" min="0.0" max="0.5" value="0.02" label="Gap open probability" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
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1
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|
223 <param argument="--pextend" type="float" min="0.0" max="1.0" value="0.4" label="Gap extend probability" /> |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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|
224 </when> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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225 <!-- -mx <s> : substitution score matrix (built-in matrices, with -singlemx)--> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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|
226 <!-- -mxfile <f> : read substitution score matrix from file <f> (with -singlemx)--> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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227 </conditional> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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|
228 </xml> |
6
92227c141aa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit db615ae8a189ad988ec08090051a128355a4be70"
iuc
parents:
5
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|
229 <token name="@ADDTHREADS@"><![CDATA[ |
92227c141aa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit db615ae8a189ad988ec08090051a128355a4be70"
iuc
parents:
5
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|
230 ##compute the number of ADDITIONAL threads to be used (--cpu) |
92227c141aa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit db615ae8a189ad988ec08090051a128355a4be70"
iuc
parents:
5
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|
231 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) && |
92227c141aa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit db615ae8a189ad988ec08090051a128355a4be70"
iuc
parents:
5
diff
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|
232 ]]></token> |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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233 <token name="@CPU@"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit db615ae8a189ad988ec08090051a128355a4be70"
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234 --cpu \$addthreads |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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235 </token> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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236 <token name="@SEED@"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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237 --seed $seed |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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238 </token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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239 <xml name="seed"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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240 <param argument="--seed" type="integer" min="0" value="42" label="RNG seed, 0 generates a random seed" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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241 </xml> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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242 <xml name="seed_test"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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243 <param name="seed" value="4" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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244 </xml> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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245 <token name="@ADV_OPTS@"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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246 $nonull2 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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247 |
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248 #if str($Z): |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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249 -Z $Z |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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250 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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251 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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252 #if str($domZ): |
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253 --domZ $domZ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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254 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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255 </token> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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256 <xml name="adv_opts"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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257 <!-- Other options --> |
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258 <param argument="--nonull2" type="boolean" truevalue="--nonull2" falsevalue="" label="Turn off biased composition score corrections" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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259 <param argument="-Z" type="integer" optional="true" label="# of comparisons done for E-value calculation" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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260 <param argument="--domZ" type="integer" optional="true" label="# of significant sequences, for domain E-value calculation" /> |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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261 </xml> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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262 <token name="@FORMAT_SELECTOR@"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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263 $input_format_select |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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264 </token> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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265 <xml name="format_selector"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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266 <param name="input_format_select" type="select" label="Format of sequence and model"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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267 <option value="--amino">Protein</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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268 <option value="--dna">DNA</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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269 <option value="--rna">RNA</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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270 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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271 </xml> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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272 <xml name="format_selector_noprot"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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273 <param name="input_format_select" type="select" label="Format of sequence and model"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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274 <option value="--dna">DNA</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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275 <option value="--rna">RNA</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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276 </param> |
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277 </xml> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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278 <token name="@ARSWS@"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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279 $arsws.arsws_select |
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280 |
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281 #if $arsws.arsws_select == "--wblosum": |
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282 --wid $arsws.wid |
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283 #end if |
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284 </token> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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285 <xml name="arsws"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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286 <!-- Alternative relative sequence weighting strategies --> |
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287 <conditional name="arsws"> |
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288 <param name="arsws_select" type="select" label="Alternative relative sequence weighting strategies"> |
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289 <option value="--wpb" selected="true">Henikoff position-based weights (--wpb)</option> |
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290 <option value="--wgsc">Gerstein/Sonnhammer/Chothia tree weights (--wgsc)</option> |
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291 <option value="--wblosum">Henikoff simple filter weights (--wblosum)</option> |
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292 <option value="--wnone">don't do any relative weighting; set all to 1 (--wnnoe)</option> |
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293 <option value="--wgiven">use weights as given in MSA file (--wgiven)</option> |
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294 </param> |
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295 <when value="--wpb"> |
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296 </when> |
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297 <when value="--wgsc"> |
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298 </when> |
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299 <when value="--wblosum"> |
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300 <param argument="--wid" type="float" value="0.62" label="Set identity cutoff" /> |
0
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301 </when> |
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302 <when value="--wnone"> |
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303 </when> |
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304 <when value="--wgiven"> |
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305 </when> |
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306 </conditional> |
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307 </xml> |
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308 <token name="@AEEWS@"> |
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309 #if $aeews.aeews_select != "": |
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310 --$aeews.aeews_select |
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311 #if $aeews.aeews_select == "eent": |
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312 --eset $aeews.eset |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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313 --ere $aeews.ere |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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314 --esigma $aeews.esigma |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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315 #elif $aeews.aeews_select == "eclust": |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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316 --eset $aeews.eset |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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317 --eid $aeews.eid |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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318 #end if |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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319 #end if |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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320 </token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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321 <xml name="aeews"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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322 <!-- Alternative effective sequence weighting strategies --> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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323 <conditional name="aeews"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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324 <param name="aeews_select" type="select" label="Alternative effective sequence weighting strategies"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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325 <option value="">Disabled</option> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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326 <option value="eent">Adjust eff seq # to achieve relative entropy target (--eent)</option> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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327 <option value="eclust">Eff seq # is the # of single linkage clusters (--eclust)</option> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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328 <option value="enone">No effective seq # weighting: just use nseq (--enone)</option> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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329 </param> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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330 <when value=""> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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331 </when> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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332 <when value="eent"> |
3
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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333 <param argument="--eset" type="float" value="0" label="set eff seq # for all models" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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334 <param argument="--ere" type="float" value="0" label="set minimum rel entropy/position" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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335 <param argument="--esigma" type="float" value="45" label="set sigma param" /> |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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336 </when> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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337 <when value="eclust"> |
3
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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338 <param argument="--eset" type="float" value="0" label="set eff seq # for all models" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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339 <param argument="--eid" type="float" min="0" max="1" value="0.62" label="set fractional identity cutoff" /> |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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340 </when> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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341 <when value="enone"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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342 </when> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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343 </conditional> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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344 </xml> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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345 <token name="@CUT@"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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346 $cut_ga |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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347 $cut_nc |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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348 $cut_tc |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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349 </token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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350 <xml name="cut"> |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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351 <param argument="--cut_ga" type="boolean" truevalue="--cut_ga" falsevalue="" label="use profile's GA gathering cutoffs to set all thresholding" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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352 <param argument="--cut_nc" type="boolean" truevalue="--cut_nc" falsevalue="" label="use profile's NC gathering cutoffs to set all thresholding" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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353 <param argument="--cut_tc" type="boolean" truevalue="--cut_tc" falsevalue="" label="use profile's TC gathering cutoffs to set all thresholding" /> |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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354 </xml> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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355 <token name="@MCSS@"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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356 --$mcs.model_construction_strategy_select |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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357 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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358 #if $mcs.model_construction_strategy_select == "fast": |
3
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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359 --symfrac $mcs.symfrac |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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360 #end if |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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361 #if str($fragthresh) |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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362 --fragthresh $fragthresh |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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363 #end if |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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364 </token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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365 <xml name="mcss"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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366 <!-- Alternative model construction strategies --> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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367 <conditional name="mcs"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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368 <param name="model_construction_strategy_select" type="select" label="Model Construction Strategy"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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369 <option value="fast" selected="true">Assign columns with >= symfrac residues as consensus (--fast)</option> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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370 <option value="hand">Manual construction (requires reference annotation) (--hand)</option> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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371 </param> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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372 <when value="fast"> |
3
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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373 <param argument="--symfrac" value="0.5" type="float" label="Sets sym fraction controlling --fast construction"/> |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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374 </when> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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375 <when value="hand"></when> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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376 </conditional> |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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377 <param argument="--fragthresh" type="float" value="0.5" optional="true" label="Fraction of alignment length, under which sequences are excluded" help="HMMER infers fragments if the sequence length L is less than or equal to a fraction x times the alignment length in columns" /> |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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378 </xml> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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379 <token name="@PRIOR@"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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380 $aps_select |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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381 </token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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382 <xml name="prior"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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383 <param name="aps_select" type="select" label="Alternative Prior Strategies"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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384 <option value="" selected="true">Unspecified</option> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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385 <option value="--pnone">Don't use any prior; parameters are frequencies (--pnone)</option> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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386 <option value="--plaplace">Use a Laplace +1 prior (--plaplace)</option> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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387 </param> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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388 </xml> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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389 <xml name="citation"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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390 <citations> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
391 <citation type="doi">10.1093/nar/gkr367</citation> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
392 </citations> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
393 </xml> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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394 <token name="@LENGTHS@"> |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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395 #if str($w_beta): |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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396 --w_beta $w_beta |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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397 #end if |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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changeset
|
398 |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
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399 #if str($w_length): |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents:
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changeset
|
400 --w_length $w_length |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
401 #end if |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
402 </token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
403 <xml name="lengths"> |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents:
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diff
changeset
|
404 <param argument="--w_beta" type="float" optional="true" label="Tail mass at which window length is determined" /> |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents:
1
diff
changeset
|
405 <param argument="--w_length" type="integer" optional="true" label="Window Length" /> |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
406 </xml> |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
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|
407 <token name="@INPUTHMMCHOICE@"><![CDATA[ |
1
70cdf5a19b4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
parents:
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408 #if $input_hmm_conditional.input_hmm_source == "history": |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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409 #set $input_hmm_filename = "localref.hmm" |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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410 ln -s '${input_hmm_conditional.hmmfile}' '${input_hmm_filename}' && |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
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411 ## "Press" database |
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
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412 hmmpress '${input_hmm_filename}' && |
1
70cdf5a19b4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
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413 #else: |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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414 #set $input_hmm_filename = str($input_hmm_conditional.index.fields.db_path) |
1
70cdf5a19b4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
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415 #end if |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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416 ]]></token> |
1
70cdf5a19b4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
parents:
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417 <xml name="input_hmm_choice"> |
70cdf5a19b4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
parents:
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418 <conditional name="input_hmm_conditional"> |
70cdf5a19b4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
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419 <param name="input_hmm_source" type="select" label="Use a built-in HMM model database or own from your history" > |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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420 <option value="indexed" selected="true">Use a built-in HMM model database</option> |
1
70cdf5a19b4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
parents:
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421 <option value="history">Use a HMM database from history</option> |
70cdf5a19b4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
parents:
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changeset
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422 </param> |
70cdf5a19b4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
parents:
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diff
changeset
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423 <when value="indexed"> |
70cdf5a19b4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
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diff
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424 <param name="index" type="select" label="Select a HMM model database" help="If your database of interest is not listed, contact the Galaxy administrator"> |
70cdf5a19b4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
parents:
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425 <options from_data_table="hmm_database"> |
70cdf5a19b4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
parents:
0
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426 <filter type="sort_by" column="2"/> |
70cdf5a19b4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
parents:
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427 <validator type="no_options" message="No indexes are available for the selected input dataset"/> |
70cdf5a19b4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
parents:
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428 </options> |
70cdf5a19b4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
parents:
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429 </param> |
70cdf5a19b4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
parents:
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|
430 </when> |
70cdf5a19b4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
parents:
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431 <when value="history"> |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
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432 <param name="hmmfile" type="data" format="hmm2,hmm3" label="HMM model" /> |
1
70cdf5a19b4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
parents:
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433 </when> <!-- history --> |
70cdf5a19b4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
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434 </conditional> <!-- input_hmm_conditional --> |
70cdf5a19b4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
parents:
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435 </xml> |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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changeset
|
436 <xml name="input_hmm"> |
3
819d044451ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
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437 <param name="hmmfile" type="data" format="hmm2,hmm3" label="HMM model" /> |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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438 </xml> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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|
439 <xml name="input_msa"> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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|
440 <param name="msafile" type="data" label="Multiple Sequence Alignment" format="stockholm,clustal,fasta" |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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parents:
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441 help="in Stockholm, Clustal, or Fasta format. While this tool accepts fasta, please ensure that the sequences are not unaligned"/> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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|
442 </xml> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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changeset
|
443 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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|
444 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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445 <token name="@ACCEL_HEUR_HELP@"><![CDATA[ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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446 Acceleration Heuristicts (--F1, --F2, --F3) |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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447 ------------------------------------------- |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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|
448 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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449 **MSV filter** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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|
450 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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changeset
|
451 The sequence is aligned to the profile using a specialized model that |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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changeset
|
452 allows multiple high-scoring local ungapped segments to match. The |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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changeset
|
453 optimal alignment score (Viterbi score) is calculated under this multi- |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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454 segment model, hence the term MSV, for “multi-segment Viterbi”. This is |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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455 HMMER’s main speed heuristic. The MSV score is comparable to BLAST’s sum |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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changeset
|
456 score (optimal sum of ungapped alignment segments). Roughly speaking, |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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457 MSV is comparable to skipping the heuristic word hit and hit extension |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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changeset
|
458 steps of the BLAST acceleration algorithm. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
459 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
460 The MSV filter is very, very fast. In addition to avoiding indel |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
461 calculations in the dynamic programming table, it uses reduced precision |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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|
462 scores scaled to 8-bit integers, enabling acceleration via 16-way |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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463 parallel SIMD vector instructions. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
464 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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changeset
|
465 The MSV score is a true log-odds likelihood ratio, so it obeys |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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changeset
|
466 conjectures about the expected score distribution (Eddy, 2008) that |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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changeset
|
467 allow immediate and accurate calculation of the statistical significance |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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changeset
|
468 (P- value) of the MSV bit score. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
469 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
470 By default, comparisons with a P-value of ≤ 0.02 pass this filter, |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
471 meaning that about 2% of nonhomol- ogous sequences are expected to pass. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
472 You can use the --F1 option to change this threshold. For example, --F1 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
473 <0.05> would pass 5% of the comparisons, making a search more sensitive |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
474 but slower. Setting the threshold to ≥ 1.0 (--F1 99 for example) assures |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
475 that all comparisons will pass. Shutting off the MSV filter may be |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
476 worthwhile if you want to make sure you don’t miss comparisons that have |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
477 a lot of scattered insertions and deletions. Alternatively, the --max |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
478 option causes the MSV filter step (and all other filter steps) to be |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
479 bypassed. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
480 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
481 The MSV bit score is calculated as a log-odds score using the null model |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
482 for comparison. No correction for a biased composition or repetitive |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
483 sequence is done at this stage. For comparisons involving biased |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
484 sequences and/or profiles, more than 2% of comparisons will pass the MSV |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
485 filter. At the end of search output, there is a line like: |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
486 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
487 Passed MSV filter: 107917 (0.020272); expected 106468.8 (0.02) |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
488 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
489 which tells you how many and what fraction of comparisons passed the MSV |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
490 filter, versus how many (and what fraction) were expected. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
491 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
492 **Viterbi filter** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
493 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
494 The sequence is now aligned to the profile using a fast Viterbi algorithm for |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
495 optimal gapped alignment. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
496 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
497 This Viterbi implementation is specialized for speed. It is implemented in |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
498 8-way parallel SIMD vector instructions, using reduced precision scores that |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
499 have been scaled to 16-bit integers. Only one row of the dynamic programming |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
500 matrix is stored, so the routine only recovers the score, not the optimal |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
501 alignment itself. The reduced representation has limited range; local alignment |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
502 scores will not underflow, but high scoring comparisons can overflow and return |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
503 infinity, in which case they automatically pass the filter. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
504 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
505 The final Viterbi filter bit score is then computed using the appropriate null |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
506 model log likelihood (by default the biased composition filter model score, or |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
507 if the biased filter is off, just the null model score). If the P-value of this |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
508 score passes the Viterbi filter threshold, the sequence passes on to the next |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
509 step of the pipeline. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
510 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
511 The --F2 <x> option controls the P-value threshold for passing the Viterbi |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
512 filter score. The default is 0.001. The --max option bypasses all filters in |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
513 the pipeline. At the end of a search output, you will see a line like: |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
514 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
515 Passed Vit filter: 2207 (0.00443803); expected 497.3 (0.001) |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
516 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
517 which tells you how many and what fraction of comparisons passed the Viterbi |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
518 filter, versus how many were expected. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
519 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
520 **Forward filter/parser** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
521 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
522 The sequence is now aligned to the profile using the full Forward algorithm, |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
523 which calculates the likelihood of the target sequence given the profile, |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
524 summed over the ensemble of all possible alignments. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
525 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
526 This is a specialized time- and memory-efficient Forward implementation called |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
527 the “Forward parser”. It is implemented in 4-way parallel SIMD vector |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
528 instructions, in full precision (32-bit floating point). It stores just enough |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
529 information that, in combination with the results of the Backward parser |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
530 (below), posterior probabilities of start and stop points of alignments |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
531 (domains) can be calculated in the domain definition step (below), although the |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
532 detailed alignments themselves cannot be. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
533 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
534 The Forward filter bit score is calculated by correcting this score using the |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
535 appropriate null model log likelihood (by default the biased composition filter |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
536 model score, or if the biased filter is off, just the null model score). If the |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
537 P-value of this bit score passes the Forward filter threshold, the sequence |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
538 passes on to the next step of the pipeline. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
539 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
540 The bias filter score has no further effect in the pipeline. It is only used in |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
541 filter stages. It has no effect on final reported bit scores or P-values. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
542 Biased composition compensation for final bit scores is done by a more complex |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
543 domain-specific algorithm, described below. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
544 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
545 The --F3 <x> option controls the P-value threshold for passing the Forward |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
546 filter score. The default is 1e-5. The --max option bypasses all filters in the |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
547 pipeline. At the end of a search output, you will see a line like: |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
548 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
549 Passed Fwd filter: 1076 (0.00216371); expected 5.0 (1e-05) |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
550 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
551 which tells you how many and what fraction of comparisons passed the Forward |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
552 filter, versus how many were expected. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
553 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
554 **Bias Filter Options** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
555 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
556 The --max option bypasses all filters in the pipeline, including the bias |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
557 filter. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
558 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
559 The --nobias option turns off (bypasses) the biased composition filter. The |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
560 simple null model is used as a null hypothesis for MSV and in subsequent filter |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
561 steps. The biased composition filter step compromises a small amount of |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
562 sensitivity. Though it is good to have it on by default, you may want to shut |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
563 it off if you know you will have no problem with biased composition hits. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
564 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
565 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
566 **Advanced Documentation** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
567 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
568 A more detailed look at the internals of the various filter pipelines was |
6
92227c141aa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit db615ae8a189ad988ec08090051a128355a4be70"
iuc
parents:
5
diff
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|
569 posted on the `developer's blog <http://cryptogenomicon.org/hmmer3-is-stubborn.html>`__. |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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|
570 The information posted there may be useful to those who are struggling with |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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changeset
|
571 poor-scoring sequences. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
572 ]]></token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
573 <token name="@ADV_OPTS_HELP@"><![CDATA[ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
574 Advanced Options |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
575 ---------------- |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
576 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
577 **nonull2** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
578 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
579 can be too aggressive sometimes, causing you to miss homologs. You can turn the |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
580 biased-composition score correction off with the --nonull2 option (and if |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
581 you’re doing that, you may also want to set --nobias, to turn off another |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
582 biased composition step called the bias filter, which affects which sequences |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
583 get scored at all). |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
584 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
585 **domZ** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
586 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
587 Assert that the total number of targets in your searches is <x>, for the |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
588 purposes of per-domain conditional E-value calculations, rather than the number |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
589 of targets that passed the reporting thresholds. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
590 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
591 **Z** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
592 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
593 Assert that the total number of targets in your searches is <x>, for the |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
594 purposes of per-sequence E-value calculations, rather than the actual number of |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
595 targets seen. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
596 ]]></token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
597 <token name="@AEEWS_HELP@"><![CDATA[ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
598 Effective Sequence Number |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
599 ------------------------- |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
600 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
601 After relative weights are determined, they are normalized to sum to a total |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
602 effective sequence number, eff nseq. This number may be the actual number of |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
603 sequences in the alignment, but it is almost always smaller than that. The |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
604 default entropy weighting method (--eent) reduces the effective sequence num- |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
605 ber to reduce the information content (relative entropy, or average expected |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
606 score on true homologs) per consensus position. The target relative entropy is |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
607 controlled by a two-parameter function, where the two parameters are settable |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
608 with --ere and --esigma. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
609 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
610 **--eent** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
611 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
612 Adjust effective sequence number to achieve a specific relative entropy per |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
613 position (see --ere). This is the default. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
614 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
615 **--eclust** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
616 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
617 Set effective sequence number to the number of single-linkage clusters at a |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
618 specific identity threshold (see --eid). This option is not recommended; it’s |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
619 for experiments evaluating how much better --eent is. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
620 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
621 **--enone** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
622 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
623 Turn off effective sequence number determination and just use the actual number |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
624 of sequences. One reason you might want to do this is to try to maximize the |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
625 relative entropy/position of your model, which may be useful for short models. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
626 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
627 **--eset** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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628 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
629 Explicitly set the effective sequence number for all models to <x>. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
630 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
631 **--ere** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
632 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
633 Set the minimum relative entropy/position target to <x>. Requires --eent. Default |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
634 depends on the sequence alphabet. For protein sequences, it is 0.59 bits/position; |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
635 for nucleotide sequences, it is 0.45 bits/position. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
636 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
637 **--esigma** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
638 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
639 Sets the minimum relative entropy contributed by an entire model alignment, over |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
640 its whole length. This has the effect of making short models have higher relative |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
641 entropy per position than --ere alone would give. The default is 45.0 bits. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
642 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
643 **--eid** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
644 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
645 Sets the fractional pairwise identity cutoff used by single linkage clustering |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
646 with the --eclust option. The default is 0.62. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
647 ]]></token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
648 <token name="@ARSWS_HELP@"><![CDATA[ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
649 Options Controlling Relative Weights |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
650 ------------------------------------ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
651 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
652 HMMER uses an ad hoc sequence weighting algorithm to downweight closely related |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
653 sequences and up-weight distantly related ones. This has the effect of making |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
654 models less biased by uneven phylogenetic representation. For example, two |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
655 identical sequences would typically each receive half the weight that one |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
656 sequence would. These options control which algorithm gets used. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
657 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
658 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
659 **--wpb** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
660 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
661 Use the Henikoff position-based sequence weighting scheme [Henikoff and |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
662 Henikoff, J. Mol. Biol. 243:574, 1994]. This is the default. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
663 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
664 **--wgsc** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
665 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
666 Use the Gerstein/Sonnhammer/Chothia weighting algorithm [Gerstein et al, J. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
667 Mol. Biol. 235:1067, 1994]. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
668 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
669 **--wblosum** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
670 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
671 Use the same clustering scheme that was used to weight data in calculating |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
672 BLOSUM subsitution matrices [Henikoff and Henikoff, Proc. Natl. Acad. Sci |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
673 89:10915, 1992]. Sequences are single-linkage clustered at an identity |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
674 threshold (default 0.62; see --wid) and within each cluster of c sequences, |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
675 each sequence gets rela- tive weight 1/c. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
676 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
677 **--wnone** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
678 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
679 No relative weights. All sequences are assigned uniform weight. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
680 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
681 **--wid** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
682 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
683 Sets the identity threshold used by single-linkage clustering when using |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
684 --wblosum. Invalid with any other weighting scheme. Default is 0.62. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
685 ]]></token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
686 <token name="@BIAS_COMP_HELP@"><![CDATA[ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
687 Bias Composition |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
688 ---------------- |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
689 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
690 The next number, the bias, is a correction term for biased sequence composition |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
691 that has been applied to the sequence bit score.1 For instance, for the top hit |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
692 MYG PHYCA that scored 222.7 bits, the bias of 3.2 bits means that this sequence |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
693 originally scored 225.9 bits, which was adjusted by the slight 3.2 bit biased- |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
694 composition correction. The only time you really need to pay attention to the |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
695 bias value is when it’s large, on the same order of magnitude as the sequence |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
696 bit score. Sometimes (rarely) the bias correction isn’t aggressive enough, and |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
697 allows a non-homolog to retain too much score. Conversely, the bias correction |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
698 can be too aggressive sometimes, causing you to miss homologs. You can turn the |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
699 biased-composition score correction off with the --nonull2 option (and if |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
700 you’re doing that, you may also want to set --nobias, to turn off another |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
701 biased composition step called the bias filter, which affects which sequences |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
702 get scored at all). |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
703 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
704 ]]></token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
705 <token name="@CUT_HELP@"><![CDATA[ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
706 Options for Model-specific Score Thresholding |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
707 --------------------------------------------- |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
708 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
709 Curated profile databases may define specific bit score thresholds for each |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
710 profile, superseding any thresholding based on statistical significance alone. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
711 To use these options, the profile must contain the appropriate (GA, TC, and/or |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
712 NC) optional score threshold annotation; this is picked up by hmmbuild from |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
713 Stockholm format alignment files. Each thresholding option has two scores: the |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
714 per-sequence threshold <x1> and the per-domain threshold <x2> These act as if |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
715 -T<x1> --incT<x1> --domT<x2> --incdomT<x2> has been applied specifically using |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
716 each model’s curated thresholds. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
717 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
718 **--cut_ga** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
719 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
720 Use the GA (gathering) bit scores in the model to set per-sequence (GA1) and |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
721 per-domain (GA2) reporting and inclusion thresholds. GA thresholds are |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
722 generally considered to be the reliable curated thresholds defining family |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
723 membership; for example, in Pfam, these thresholds define what gets included in |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
724 Pfam Full alignments based on searches with Pfam Seed models. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
725 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
726 **--cut_nc** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
727 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
728 Use the NC (noise cutoff) bit score thresholds in the model to set |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
729 per-sequence (NC1) and per-domain (NC2) reporting and inclusion thresholds. NC |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
730 thresholds are generally considered to be the score of the highest-scoring |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
731 known false positive. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
732 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
733 **--cut_tc** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
734 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
735 Use the NC (trusted cutoff) bit score thresholds in the model to set |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
736 per-sequence (TC1) and per-domain (TC2) reporting and inclusion thresholds. TC |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
737 thresholds are generally considered to be the score of the lowest-scoring known |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
738 true positive that is above all known false positives. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
739 ]]></token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
740 <token name="@EVAL_CALIB_HELP@"><![CDATA[ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
741 Options Controlling H3 Parameter Estimation Methods |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
742 --------------------------------------------------- |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
743 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
744 H3 uses three short random sequence simulations to estimating the location |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
745 parameters for the expected score distributions for MSV scores, Viterbi scores, |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
746 and Forward scores. These options allow these simulations to be modified. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
747 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
748 **--EmL** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
749 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
750 Sets the sequence length in simulation that estimates the location parameter mu |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
751 for MSV E-values. Default is 200. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
752 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
753 **--EmN** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
754 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
755 Sets the number of sequences in simulation that estimates the location parameter |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
756 mu for MSV E-values. Default is 200. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
757 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
758 **--EvL** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
759 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
760 Sets the sequence length in simulation that estimates the location parameter mu |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
761 for Viterbi E-values. Default is 200. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
762 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
763 **--EvN** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
764 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
765 Sets the number of sequences in simulation that estimates the location parameter |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
766 mu for Viterbi E-values. Default is 200. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
767 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
768 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
769 **--EfL** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
770 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
771 Sets the sequence length in simulation that estimates the location parameter tau |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
772 for Forward E-values. Default is 100. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
773 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
774 **--EfN** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
775 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
776 Sets the number of sequences in simulation that estimates the location parameter |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
777 tau for Forward E-values. Default is 200. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
778 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
779 **--Eft** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
780 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
781 Sets the tail mass fraction to fit in the simulation that estimates the location param- |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
782 eter tau for Forward evalues. Default is 0.04. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
783 ]]></token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
784 <token name="@FORMAT_SELECTOR_HELP@"><![CDATA[ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
785 Options for Specifying the Alphabet |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
786 ----------------------------------- |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
787 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
788 The alphabet type (amino, DNA, or RNA) is autodetected by default, by looking |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
789 at the composition of the msafile. Autodetection is normally quite reliable, |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
790 but occasionally alphabet type may be ambiguous and autodetection can fail (for |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
791 instance, on tiny toy alignments of just a few residues). To avoid this, or to |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
792 increase robustness in automated analysis pipelines, you may specify the |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
793 alphabet type of msafile with these options. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
794 ]]></token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
795 <token name="@HSSI_HELP@"><![CDATA[ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
796 Options Controlling Single Sequence Scoring (first Iteration) |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
797 ------------------------------------------------------------- |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
798 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
799 By default, the first iteration uses a search model constructed from a single |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
800 query sequence. This model is constructed using a standard 20x20 substitution |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
801 matrix for residue probabilities, and two additional pa- rameters for |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
802 position-independent gap open and gap extend probabilities. These options allow |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
803 the default single-sequence scoring parameters to be changed. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
804 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
805 **Gap Open (--popen)** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
806 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
807 Set the gap open probability for a single sequence query model to <x> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
808 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
809 **Gap Extend (--pextend)** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
810 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
811 Set the gap extend probability for a single sequence query model to <x>. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
812 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
813 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
814 **--mx/--mxfile** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
815 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
816 These options are not currently supported |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
817 ]]></token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
818 <token name="@LENGTHS_HELP@"><![CDATA[ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
819 Tail Mass Options |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
820 ----------------- |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
821 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
822 **Window length tail mass (--w_beta)** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
823 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
824 The upper bound, W, on the length at which nhmmer expects to find an instance |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
825 of the model is set such that the fraction of all sequences generated by the |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
826 model with length >= W is less than <x>. The default is 1e-7. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
827 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
828 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
829 **Model instance length upper bound (--w length)** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
830 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
831 Override the model instance length upper bound, W, which is otherwise |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
832 controlled by --w beta. It should be larger than the model length. The value of |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
833 W is used deep in the acceleration pipeline, and modest changes are not |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
834 expected to impact results (though larger values of W do lead to longer run |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
835 time). |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
836 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
837 ]]></token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
838 <token name="@MCSS_HELP@"><![CDATA[ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
839 **Options Controlling Profile Construction** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
840 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
841 These options control how consensus columns are defined in an alignment. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
842 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
843 **--fast** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
844 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
845 Define consensus columns as those that have a fraction >= symfrac of residues |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
846 as opposed to gaps. (See below for the --symfrac option.) This is the default. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
847 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
848 **--hand** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
849 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
850 Define consensus columns in next profile using reference annotation to the multiple |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
851 alignment. This allows you to define any consensus columns you like. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
852 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
853 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
854 **--symfrac** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
855 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
856 Define the residue fraction threshold necessary to define a consensus column |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
857 when using the --fast option. The default is 0.5. The symbol fraction in each |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
858 column is calculated after taking relative sequence weighting into account, and |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
859 ignoring gap characters corresponding to ends of sequence fragments (as opposed |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
860 to internal insertions/deletions). Setting this to 0.0 means that every |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
861 alignment column will be assigned as consensus, which may be useful in some |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
862 cases. Setting it to 1.0 means that only columns that include 0 gaps (internal |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
863 insertions/deletions) will be assigned as consensus. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
864 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
865 **--fragthresh** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
866 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
867 We only want to count terminal gaps as deletions if the aligned sequence is |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
868 known to be full-length, not if it is a fragment (for instance, because only |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
869 part of it was sequenced). HMMER uses a simple rule to infer fragments: if the |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
870 sequence length L is less than or equal to a fraction <x> times the alignment |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
871 length in columns, then the sequence is handled as a fragment. The default is |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
872 0.5. Setting --fragthresh0 will define no (nonempty) sequence as a fragment; |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
873 you might want to do this if you know you’ve got a carefully curated alignment |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
874 of full-length sequences. Setting --fragthresh1 will define all sequences as |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
875 fragments; you might want to do this if you know your alignment is entirely |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
876 composed of fragments, such as translated short reads in metagenomic shotgun |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
877 data. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
878 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
879 ]]></token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
880 <token name="@OFORMAT_WITH_OPTS_HELP@"><![CDATA[ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
881 Options for Controlling Output |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
882 ------------------------------ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
883 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
884 **Table of hits** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
885 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
886 Save a simple tabular (space-delimited) file summarizing the per-target output, with |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
887 one data line per homologous target model found. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
888 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
889 **Table of per-domain hits** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
890 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
891 Save a simple tabular (space-delimited) file summarizing the per-domain output, |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
892 with one data line per homologous domain detected in a query sequence for each |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
893 homologous model. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
894 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
895 **Table of hits and domains in Pfam Format** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
896 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
897 Save an especially succinct tabular (space-delimited) file summarizing the |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
898 per-target output, with one data line per homologous target model found. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
899 ]]></token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
900 <token name="@OFORMAT_WITH_OPTS_NOPFAM_HELP@"><![CDATA[ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
901 Options for Controlling Output |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
902 ------------------------------ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
903 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
904 **Table of hits** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
905 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
906 Save a simple tabular (space-delimited) file summarizing the per-target output, with |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
907 one data line per homologous target model found. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
908 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
909 **Table of per-domain hits** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
910 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
911 Save a simple tabular (space-delimited) file summarizing the per-domain output, |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
912 with one data line per homologous domain detected in a query sequence for each |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
913 homologous model. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
914 ]]></token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
915 <token name="@OFORMAT_WITH_OPTS_N_HELP@"><![CDATA[ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
916 Options for Controlling Output |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
917 ------------------------------ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
918 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
919 **Table of hits** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
920 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
921 Save a simple tabular (space-delimited) file summarizing the per-target output, with |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
922 one data line per homologous target model found. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
923 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
924 **Table of hits (dfam)** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
925 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
926 Save a tabular (space-delimited) file summarizing the per-hit output, similar |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
927 to --tblout but more succinct. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
928 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
929 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
930 **List of per-position scores for each hit (--aliscoreout)** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
931 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
932 Save to file a list of per-position scores for each hit. This is useful, for |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
933 example, in identifying regions of high score density for use in resolving |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
934 overlapping hits from different models. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
935 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
936 ]]></token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
937 <token name="@PRIOR_HELP@"><![CDATA[ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
938 Options Controlling Priors |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
939 -------------------------- |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
940 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
941 By default, weighted counts are converted to mean posterior probability |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
942 parameter estimates using mixture Dirichlet priors. Default mixture Dirichlet |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
943 prior parameters for protein models and for nucleic acid (RNA and DNA) models |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
944 are built in. The following options allow you to override the default priors. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
945 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
946 **No priors (--pnone)** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
947 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
948 Don’t use any priors. Probability parameters will simply be the observed |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
949 frequencies, after relative sequence weighting. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
950 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
951 **Laplace +1 prior** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
952 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
953 Use a Laplace +1 prior in place of the default mixture Dirichlet prior. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
954 ]]></token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
955 <token name="@SEED_HELP@"><![CDATA[ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
956 Random Seeding |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
957 -------------- |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
958 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
959 Seed the random number generator with <n>, an integer >= 0. If <n> is nonzero, |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
960 any stochastic simulations will be reproducible; the same command will give the |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
961 same results. If <n> is 0, the random number generator is seeded arbitrarily, |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
962 and stochastic simulations will vary from run to run of the same command. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
963 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
964 ]]></token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
965 <token name="@THRESHOLDS_HELP@"><![CDATA[ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
966 Options for Reporting Thresholds |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
967 -------------------------------- |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
968 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
969 Reporting thresholds control which hits are reported in output files (the main |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
970 output, --tblout, and --domtblout). |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
971 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
972 **E-value (-E)** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
973 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
974 In the per-target output, report target profiles with an E-value of <= <x>. The |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
975 default is 10.0, meaning that on average, about 10 false positives will be |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
976 reported per query, so you can see the top of the noise and decide for yourself |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
977 if it’s really noise. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
978 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
979 **Bit score (-T)** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
980 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
981 Instead of thresholding per-profile output on E-value, instead report target profiles |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
982 with a bit score of >= <x>. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
983 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
984 **domain E-value (--domE)** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
985 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
986 In the per-domain output, for target profiles that have already satisfied the |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
987 per-profile reporting threshold, report individual domains with a conditional |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
988 E-value of <= <x>. The default is 10.0. A conditional E-value means the |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
989 expected number of additional false positive domains in the smaller search |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
990 space of those comparisons that already satisfied the per-profile reporting |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
991 threshold (and thus must have at least one homologous domain already). |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
992 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
993 **domain Bit scores (--domT)** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
994 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
995 Instead of thresholding per-domain output on E-value, instead report domains |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
996 with a bit score of >= <x>. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
997 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
998 Options for Inclusion Thresholds |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
999 -------------------------------- |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1000 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1001 Inclusion thresholds are stricter than reporting thresholds. Inclusion |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1002 thresholds control which hits are considered to be reliable enough to be |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1003 included in an output alignment or a subsequent search round. In hmmscan, which |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1004 does not have any alignment output (like hmmsearch or phmmer) nor any iterative |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1005 search steps (like jackhmmer), inclusion thresholds have little effect. They |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1006 only affect what domains get marked as significant (!) or questionable (?) in |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1007 domain output. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1008 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1009 **E-value of per target inclusion threshold** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1010 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1011 Use an E-value of <= <x> as the per-target inclusion threshold. The default is |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1012 0.01, meaning that on average, about 1 false positive would be expected in |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1013 every 100 searches with different query sequences. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1014 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1015 **Bit score of per target inclusion threshold** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1016 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1017 Instead of using E-values for setting the inclusion threshold, instead use a |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1018 bit score of >= <x> as the per-target inclusion threshold. It would be unusual |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1019 to use bit score thresholds with hmmscan, because you don’t expect a single |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1020 score threshold to work for different profiles; different profiles have |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1021 slightly different expected score distributions. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1022 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1023 **domain E-value per target inclusion treshold** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1024 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1025 Use a conditional E-value of <= <x> as the per-domain inclusion threshold, in |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1026 targets that have already satisfied the overall per-target inclusion threshold. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1027 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1028 **domain Bit score per target inclusion treshold** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1029 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1030 Instead of using E-values, instead use a bit score of >= <x> as the per-domain |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1031 inclusion threshold. As with --incT above, it would be unusual to use a single |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1032 bit score threshold in hmmscan. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1033 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1034 ]]></token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1035 <token name="@THRESHOLDS_NODOM_HELP@"><![CDATA[ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1036 Options for Reporting Thresholds |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1037 -------------------------------- |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1038 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1039 Reporting thresholds control which hits are reported in output files (the main |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1040 output, --tblout, and --domtblout). |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1041 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1042 **E-value (-E)** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1043 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1044 In the per-target output, report target profiles with an E-value of <= <x>. The |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1045 default is 10.0, meaning that on average, about 10 false positives will be |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1046 reported per query, so you can see the top of the noise and decide for yourself |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1047 if it’s really noise. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1048 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1049 **Bit score (-T)** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1050 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1051 Instead of thresholding per-profile output on E-value, instead report target profiles |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1052 with a bit score of >= <x>. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1053 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1054 Options for Inclusion Thresholds |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1055 -------------------------------- |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1056 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1057 Inclusion thresholds are stricter than reporting thresholds. Inclusion |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1058 thresholds control which hits are considered to be reliable enough to be |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1059 included in an output alignment or a subsequent search round. In hmmscan, which |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1060 does not have any alignment output (like hmmsearch or phmmer) nor any iterative |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1061 search steps (like jackhmmer), inclusion thresholds have little effect. They |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1062 only affect what domains get marked as significant (!) or questionable (?) in |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1063 domain output. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1064 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1065 **E-value of per target inclusion threshold** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1066 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1067 Use an E-value of <= <x> as the per-target inclusion threshold. The default is |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1068 0.01, meaning that on average, about 1 false positive would be expected in |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1069 every 100 searches with different query sequences. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1070 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1071 **Bit score of per target inclusion threshold** |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1072 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1073 Instead of using E-values for setting the inclusion threshold, instead use a |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1074 bit score of >= <x> as the per-target inclusion threshold. It would be unusual |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1075 to use bit score thresholds with hmmscan, because you don’t expect a single |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1076 score threshold to work for different profiles; different profiles have |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1077 slightly different expected score distributions. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1078 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1079 ]]></token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1080 <token name="@ATTRIBUTION@"><![CDATA[ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1081 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1082 Attribution |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1083 ----------- |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1084 |
1
70cdf5a19b4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
parents:
0
diff
changeset
|
1085 This Galaxy tool relies on HMMER3_ |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1086 Internally the software is cited as: |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1087 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1088 :: |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1089 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1090 # hmmscan :: search sequence(s) against a profile database |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1091 # HMMER 3.1 (February 2013); http://hmmer.org/ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1092 # Copyright (C) 2011 Howard Hughes Medical Institute. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1093 # Freely distributed under the GNU General Public License (GPLv3). |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1094 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1095 |
5
b4dc65565864
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents:
4
diff
changeset
|
1096 The wrappers were written by the IUC and are licensed under Apache2_. The |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1097 documentation is copied from the HMMER3 documentation. |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1098 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1099 .. _Apache2: http://www.apache.org/licenses/LICENSE-2.0 |
1
70cdf5a19b4b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
parents:
0
diff
changeset
|
1100 .. _HMMER3: http://hmmer.org/ |
0
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1101 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1102 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1103 ]]></token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1104 <token name="@HELP_PRE@"><![CDATA[ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1105 |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1106 What it does |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1107 ============ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1108 ]]></token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1109 <token name="@HELP_PRE_OTH@"><![CDATA[ |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1110 Options |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1111 ======= |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
|
1112 ]]></token> |
a20b2c7c5eee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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1113 </macros> |