Mercurial > repos > devteam > clustalw
annotate macros.xml @ 4:4755a32131c7 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw commit f7923954e747d05d1e70d653ef1b544c3e14622f
author | iuc |
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date | Sun, 02 Oct 2022 15:32:04 +0000 |
parents | fac9d3c091cb |
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fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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1 <macros> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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2 <token name="@TOOL_VERSION@">2.1</token> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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3 <token name="@VERSION_SUFFIX@">1</token> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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4 <xml name="requirements"> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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5 <requirements> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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6 <requirement type="package" version="@TOOL_VERSION@">clustalw</requirement> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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7 </requirements> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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8 </xml> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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9 <xml name="macro_options" token_algorithm="" token_multiple="" token_label="" token_default=""> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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10 <conditional name="algorithm_conditional"> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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11 <param name="selector" type="select" label="Algorithm for the alignment guide tree" help="Default: slow"> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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12 <option value="">Slow: dynamic programming (accurate)</option> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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13 <option value="-QUICKTREE">Fast: method of Wilbur and Lipman (approximate)</option> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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14 </param> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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15 <when value=""> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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16 <section name="slow_pairwise_alignments" title="Slow pairwise alignments options"> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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17 <param argument="-@ALGORITHM@" type="select" label="@LABEL@ weigth matrix" help="Default: @DEFAULT@"> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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18 <yield/> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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19 </param> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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20 <param argument="-PWGAPOPEN" type="integer" min="0" optional="true" label="Gap opening penalty" help="Default: 10" /> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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21 <param argument="-PWGAPEXT" type="float" min="0" optional="true" label="Gap extension penalty" help="Default: 0.1" /> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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22 </section> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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23 </when> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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24 <when value="-QUICKTREE"> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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25 <section name="fast_pairwise_alignments" title="Fast pairwise alignments options"> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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26 <param argument="-KTUPLE" type="integer" min="0" optional="true" label="Word size" |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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27 help="Size of exactly matching fragment that is used. Increase for speed, decrease for sensitivity. Maximum value for proteins is 2, and for DNA 4.Default: 1" /> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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28 <param argument="-TOPDIAGS" type="integer" min="0" optional="true" label="Number of best diagonals" |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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29 help="Number of k-tuple matches on each diagonal. Decrease for speed; increase for sensitivity. Default: 5" /> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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30 <param argument="-WINDOW" type="integer" min="0" optional="true" label="Window length" |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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31 help="This is the number of diagonals around each of the best diagonals that will be used. Decrease for speed; increase for sensitivity. Default: 5" /> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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32 <param argument="-PAIRGAP" type="integer" min="0" optional="true" label="Gap penalty" |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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33 help="Fast pairwise alignment gap penalty for each gap created. Default: 3" /> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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34 <param argument="-SCORE" type="select" label="Score type" help="Score type to output. Default: percent"> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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35 <option value="PERCENT">Percent</option> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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36 <option value="ABSOLUTE">Absolute</option> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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37 </param> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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38 </section> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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39 </when> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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40 </conditional> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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41 <section name="multiple_alignments" title="Multiple alignments options"> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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42 <param argument="-@MULTIPLE@" type="select" label="@LABEL@ weigth matrix" help="Default: @DEFAULT@"> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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43 <yield/> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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44 </param> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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45 <param argument="-GAPOPEN" type="integer" min="0" optional="true" label="Gap opening penalty" help="Default: 10" /> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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46 <param argument="-GAPEXT" type="float" min="0" optional="true" label="Gap extension penalty" help="Default: 0.2" /> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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47 <param argument="-ENDGAPS" type="boolean" truevalue="-ENDGAPS" falsevalue="" checked="false" label="End gap separation penalty" |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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48 help="End gap separation treats end gaps just like internal gaps for the purposes of avoiding gaps that are too close. If you turn this off, end gaps will be ignored for this purpose. |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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49 This is useful when you wish to align fragments where the end gaps are not biologically meaningful" /> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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50 <param argument="-GAPDIST" type="integer" min="0" optional="true" label="Gap separation penalty range" |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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51 help="Gap separation distance tries to decrease the chances of gaps being too close to each other. Gaps that are less than this distance apart are penalised more than other gaps. |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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52 This does not prevent close gaps; it makes them less frequent, promoting a block-like appearance of the alignment" /> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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53 <param argument="-NOPGAP" type="boolean" truevalue="-NOPGAP" falsevalue="" checked="false" label="Residue specific penalties" |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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54 help="Residue specific penalties are amino acid specific gap penalties that reduce or increase the gap opening penalties at each position in the alignment or sequence. As an example, |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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55 positions that are rich in glycine are more likely to have an adjacent gap than positions that are rich in valine" /> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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56 <param argument="-NOHGAP" type="boolean" truevalue="-NOHGAP" falsevalue="" checked="false" label="Hydrophilic gaps" help="Hydrophilic gap penalties are used to increase the chances of a gap |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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57 within a run (5 or more residues) of hydrophilic amino acids; these are likely to be loop or random coil regions where gaps are more common" /> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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58 <param argument="-MAXDIV" type="integer" min="0" max="100" optional="true" label="Delay divergent sequences" help="Percentage identity for delay" /> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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59 <param argument="-NEGATIVE" type="boolean" truevalue="-NEGATIVE" falsevalue="" checked="false" label="Negative values in matrix" help="Delays the alignment of the most distantly related sequences |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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60 until after the most closely related sequences have been aligned. The setting shows the percent identity level required to delay the addition of a sequence; sequences that are less identical |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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61 than this level to any other sequences will be aligned later" /> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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62 <param argument="-TRANSWEIGHT" type="float" min="0" max="1" optional="true" label="Transition weight" help="The transition weight option for aligning nucleotide sequences has been changed in version |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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63 1.7 from an on/off toggle to a weight between 0 and 1. A weight of zero means that the transitions are scored as mismatches; a weight of 1 gives transitions the full match score. For distantly |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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64 related DNA sequences, the weight should be near to zero; for closely related sequences it can be useful to assign a higher score" /> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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65 </section> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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66 </xml> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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67 <token name="@SLOW_PAIRWISE_ALIGNMENTS@"><![CDATA[ |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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68 #if str($type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPOPEN) |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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69 -PWGAPOPEN=$type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPOPEN |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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70 #end if |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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71 #if str($type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPEXT) |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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72 -PWGAPEXT=$type_conditional.algorithm_conditional.slow_pairwise_alignments.PWGAPEXT |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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73 #end ifx |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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74 ]]></token> |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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75 <token name="@FAST_PAIRWISE_ALIGNMENTS@"><![CDATA[ |
fac9d3c091cb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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76 #if str($type_conditional.algorithm_conditional.fast_pairwise_alignments.KTUPLE) |
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77 -KTUPLE=$type_conditional.algorithm_conditional.fast_pairwise_alignments.KTUPLE |
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78 #end if |
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79 #if str($type_conditional.algorithm_conditional.fast_pairwise_alignments.TOPDIAGS) |
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80 -TOPDIAGS=$type_conditional.algorithm_conditional.fast_pairwise_alignments.TOPDIAGS |
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81 #end if |
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82 #if str($type_conditional.algorithm_conditional.fast_pairwise_alignments.WINDOW) |
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83 -WINDOW=$type_conditional.algorithm_conditional.fast_pairwise_alignments.WINDOW |
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84 #end if |
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85 #if str($type_conditional.algorithm_conditional.fast_pairwise_alignments.PAIRGAP) |
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86 -PAIRGAP=$type_conditional.algorithm_conditional.fast_pairwise_alignments.PAIRGAP |
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87 #end if |
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88 -SCORE=$type_conditional.algorithm_conditional.fast_pairwise_alignments.SCORE |
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89 ]]></token> |
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90 <token name="@MULTIPLE_ALIGNMENTS@"><![CDATA[ |
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91 #if str($type_conditional.multiple_alignments.GAPOPEN) |
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92 -GAPOPEN=$type_conditional.multiple_alignments.GAPOPEN |
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93 #end if |
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94 #if str($type_conditional.multiple_alignments.GAPEXT) |
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95 -GAPEXT=$type_conditional.multiple_alignments.GAPEXT |
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96 #end if |
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97 $type_conditional.multiple_alignments.ENDGAPS |
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98 #if str($type_conditional.multiple_alignments.GAPDIST) |
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99 -GAPDIST=$type_conditional.multiple_alignments.GAPDIST |
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100 #end if |
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101 $type_conditional.multiple_alignments.NOPGAP |
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102 $type_conditional.multiple_alignments.NOHGAP |
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103 #if str($type_conditional.multiple_alignments.MAXDIV) |
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104 -MAXDIV=$type_conditional.multiple_alignments.MAXDIV |
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105 #end if |
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106 $type_conditional.multiple_alignments.NEGATIVE |
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107 #if str($type_conditional.multiple_alignments.TRANSWEIGHT) |
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108 -TRANSWEIGHT=$type_conditional.multiple_alignments.TRANSWEIGHT |
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109 #end if |
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110 ]]></token> |
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111 |
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112 </macros> |