Mercurial > repos > iuc > hmmer_hmmemit
annotate hmmemit.xml @ 1:855e2b978e3a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
author | iuc |
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date | Mon, 14 Nov 2016 15:10:53 -0500 |
parents | f48f9bbfcfd8 |
children | 7b7ff4d209f7 |
rev | line source |
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0
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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1 <?xml version="1.0"?> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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2 <tool id="hmmer_hmmemit" name="hmmemit" version="@WRAPPER_VERSION@.0"> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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3 <description>sample sequence(s) from a profile HMM</description> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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4 <macros> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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5 <import>macros.xml</import> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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6 </macros> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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7 <expand macro="requirements"/> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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8 <expand macro="stdio"/> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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9 <command><![CDATA[ |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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10 hmmemit |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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11 |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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12 #if $oformat.oformat_select == "fasta": |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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13 -N $oformat.N_fa |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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14 #elif $oformat.oformat_select == "aln": |
f48f9bbfcfd8
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 -N $oformat.N_aln |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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16 -a |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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17 #elif $oformat.oformat_select == "mrcs": |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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18 -c |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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19 #elif $oformat.oformat_select == "mrcsf": |
f48f9bbfcfd8
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 --minl $oformat.minl |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
changeset
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21 --minu $oformat.minu |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff
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22 -C |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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23 #else: |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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changeset
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24 -N $oformat.N_smp |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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25 -p |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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26 #if $oformat.L: |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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changeset
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27 -L $oformat.L |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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28 #end if |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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29 $oformat.emission_profiles |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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30 #end if |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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31 |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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32 |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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33 @SEED@ |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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34 |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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35 $hmmfile |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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36 > $output |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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37 ]]></command> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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38 <inputs> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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39 <expand macro="input_hmm" /> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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40 |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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41 <conditional name="oformat"> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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42 <param name="oformat_select" type="select" label="Output Format"> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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43 <option value="fasta" selected="true">Fasta</option> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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44 <option value="aln">Alignment</option> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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45 <option value="mrcs">Majority-Rule Concensus Sequence</option> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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46 <option value="mrcsf">Fancier Concensus Sequence</option> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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47 <option value="sample">Sample sequences from profile, not core model</option> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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48 </param> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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49 <when value="fasta"> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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50 <param name="N_fa" type="integer" value="1" min="1" help="(-N)" |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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51 label="Number of sequences to generate"/> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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52 </when> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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53 <when value="aln"> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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54 <param name="N_aln" type="integer" value="1" min="1" help="(-N)" |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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55 label="Number of sequences to generate"/> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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56 </when> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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57 <when value="mrcs"> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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58 </when> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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59 <when value="mrcsf"> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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60 <param name="minl" type="float" value="0.7" help="(--minl)" |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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61 label="show consensus as 'any' (X/N) unless >= this fraction"/> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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62 <param name="minu" type="float" value="0.2" help="(--minu)" |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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63 label="show consensus as upper case if >= this fraction"/> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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64 </when> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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65 <when value="sample"> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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66 <param name="N_smp" type="integer" value="1" min="1" help="(-N)" |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
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67 label="Number of sequences to generate"/> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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68 <param name="L" type="integer" optional="True" help="(-L)" |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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69 label="Expected length of profile"/> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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70 |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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71 <param name="emission_profiles" type="select" label="Emission profile options"> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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72 <option value="--local" selected="true">configure profile in multihit local mode</option> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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73 <option value="--unilocal">configure profile in unilocal mode</option> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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74 <option value="--glocal">configure profile in multihit glocal mode</option> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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75 <option value="--uniglocal">configure profile in unihit glocal mode</option> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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76 </param> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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77 </when> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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78 </conditional> |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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79 |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
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80 |
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81 <expand macro="seed"/> |
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82 </inputs> |
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83 <outputs> |
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84 <data format="fasta" name="output" label="Sequences generated from $hmmfile.name"> |
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85 <change_format> |
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86 <when input="oformat_select" value="aln" format="stockholm"/> |
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87 <!-- the rest are fasta --> |
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88 </change_format> |
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89 </data> |
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90 </outputs> |
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91 <tests> |
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92 <test> |
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93 <param name="hmmfile" value="globins4.hmm"/> |
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94 <param name="oformat_select" value="aln"/> |
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95 <param name="N_aln" value="10"/> |
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96 <expand macro="seed_test" /> |
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97 <output name="output" file="globins4-emit.sto" lines_diff="4"/> |
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98 </test> |
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99 <test> |
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100 <param name="hmmfile" value="globins4.hmm"/> |
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101 <param name="oformat_select" value="fasta"/> |
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102 <param name="N_aln" value="10"/> |
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103 <expand macro="seed_test" /> |
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104 <output name="output" file="globins4-emit-1.sto" lines_diff="4"/> |
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105 </test> |
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106 </tests> |
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107 <help><![CDATA[ |
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108 @HELP_PRE@ |
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109 |
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110 The hmmemit program samples (emits) sequences from the profile HMM(s) in |
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111 hmmfile, and writes them to output. Sampling sequences may be useful for a |
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112 variety of purposes, including creating synthetic true positives for benchmarks |
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113 or tests. |
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114 |
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115 The default is to sample one unaligned sequence from the core probability |
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116 model, which means that each sequence consists of one full-length domain. |
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117 Alternatively, with the -c option, you can emit a simple majority-rule |
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118 consensus sequence; or with the -a option, you can emit an alignment (in which |
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119 case, you probably also want to set -N to something other than its default of 1 |
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120 sequence per model). |
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121 |
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122 As another option, with the -p option you can sample a sequence from a fully |
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123 configured HMMER search profile. This means sampling a ‘homologous sequence’ by |
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124 HMMER’s definition, including nonhomologous flanking sequences, local |
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125 alignments, and multiple domains per sequence, depending on the length model |
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126 and alignment mode chosen for the profile. |
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127 |
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128 The hmmfile may contain a library of HMMs, in which case each HMM will be used |
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129 in turn. |
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130 |
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131 @HELP_PRE_OTH@ |
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132 |
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133 Output Formats |
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134 -------------- |
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135 |
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136 Several output formats are available, each with different options. |
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137 |
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138 **Fasta** |
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139 |
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140 Fasta option is the easiest to understand, given an input model, it will produce N sequences in fasta format from that model. |
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141 |
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142 **Alignment** |
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143 |
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144 Produces a stockholm alignment, of what the Fasta output would have produced. |
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145 |
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146 **Majority-Rule Concensus Sequence** |
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147 |
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148 Emit a plurality-rule consensus sequence, instead of sampling a sequence from |
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149 the profile HMM’s probability distribution. The consensus sequence is formed by |
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150 selecting the maximum probability residue at each match state. |
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151 |
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152 **Fancier Concensus Sequence** |
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153 |
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154 Emit a fancier plurality-rule consensus sequence than the -c option. If the |
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155 maximum probability residue has p < minl show it as a lower case ’any’ residue |
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156 (n or x); if p >= minl and < minu show it as a lower case residue; and if p >= |
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157 minu show it as an upper case residue. The default settings of minu and minl |
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158 are both 0.0, which means -C gives the same output as -c unless you also set |
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159 minu and minl to what you want. |
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160 |
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161 **Sample** |
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162 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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163 Sample unaligned sequences from the implicit search profile, not from the core |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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164 model. The core model consists only of the homologous states (between the begin |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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165 and end states of a HMMER Plan7 model). The profile includes the nonhomologous |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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166 N, C, and J states, local/glocal and uni/multihit algorithm configuration, and |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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167 the target length model. Therefore sequences sampled from a profile may in- |
f48f9bbfcfd8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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168 clude nonhomologous as well as homologous sequences, and may contain more than |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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169 one homologous sequence segment. By default, the profile is in multihit local |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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170 mode, and the target sequence length is configured for L=400. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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171 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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172 @ATTRIBUTION@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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173 ]]></help> |
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174 <expand macro="citation"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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175 </tool> |