Mercurial > repos > iuc > hmmer_hmmbuild

annotate hmmbuild.xml @ 8:84159da667ec draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit db615ae8a189ad988ec08090051a128355a4be70"
author iuc
date Thu, 14 Jan 2021 15:32:33 +0000
parents e0cb3d4bc688
children 5c83ba4417e6
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1 <?xml version="1.0"?>
8
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2 <tool id="hmmer_hmmbuild" name="hmmbuild" version="@TOOL_VERSION@+galaxy1">
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3 <description>Build a profile HMM from an input multiple alignment</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <command><![CDATA[
8
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10 @ADDTHREADS@
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11 hmmbuild
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13 #if $hmmname:
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14 -n '$hmmname'
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15 #end if
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17 @FORMAT_SELECTOR@
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18 @MCSS@
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19 @ARSWS@
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20 @AEEWS@
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21 @PRIOR@
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22 @HSSI@
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23 @EVAL_CALIB@
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24
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25 @CPU@
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26 @SEED@
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27
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28 @LENGTHS@
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29 #if str($maxinsertlen):
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30 --maxinsertlen $maxinsertlen
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31 #end if
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32
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33 '$hmmout'
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34 '$msafile'
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35 ]]></command>
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36 <inputs>
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37 <expand macro="input_msa" />
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38 <param name="hmmname" argument="-n" type="text" optional="true" label="Name for the HMM" />
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39 <expand macro="format_selector"/>
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40 <expand macro="mcss"/>
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41 <expand macro="arsws"/>
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42 <expand macro="aeews"/>
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43 <expand macro="prior"/>
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44 <expand macro="hssi"/>
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45 <expand macro="eval_calib_xml"/>
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46 <expand macro="seed"/>
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47
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48 <expand macro="lengths" />
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49 <param argument="--maxinsertlen" type="integer" optional="true" label="Pretend all inserts are length &lt;= n" />
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50 </inputs>
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51 <outputs>
5
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52 <data name="hmmout" format="hmm3" label="HMM profile from $msafile.name"/>
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="msafile" value="globins4.sto"/>
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57 <expand macro="seed_test" />
7
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58 <output name="hmmout" file="globins4.hmm" compare="sim_size">
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59 <assert_contents>
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60 <has_line_matching expression="HMMER3/f.*"/>
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61 <has_line_matching expression="ALPH amino"/>
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62 <has_line_matching expression="NSEQ 4"/>
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63 <has_line_matching expression="//"/>
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64 </assert_contents>
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65 </output>
0
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66 </test>
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67 <test>
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68 <param name="msafile" value="MADE1.sto"/>
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69 <param name="input_format_select" value="--dna"/>
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70 <expand macro="seed_test" />
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71 <output name="hmmout" file="MADE1.hmm" compare="sim_size">
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72 <assert_contents>
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73 <has_line_matching expression="HMMER3/f.*"/>
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74 <has_line_matching expression="ALPH DNA"/>
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75 <has_line_matching expression="NSEQ 1997"/>
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76 <has_line_matching expression="//"/>
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77 </assert_contents>
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78 </output>
0
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79 </test>
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80 </tests>
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81 <help><![CDATA[
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82 @HELP_PRE@
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83
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84 For each multiple sequence alignment in <msafile> build a profile HMM and save
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85 it to a new file <hmmfile out>.
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86
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87 @HELP_PRE_OTH@
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88
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89 @FORMAT_SELECTOR_HELP@
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90 @MCSS_HELP@
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91 @ARSWS_HELP@
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92 @AEEWS_HELP@
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93 @PRIOR_HELP@
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94 @HSSI_HELP@
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95 @EVAL_CALIB_HELP@
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96 @SEED_HELP@
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97 @LENGTHS_HELP@
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99 @ATTRIBUTION@
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100 ]]></help>
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101 <expand macro="citation"/>
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102 </tool>