Mercurial > repos > lecorguille > hmmer_hmmbuild

annotate hmmbuild.xml @ 0:31279c47259a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
author lecorguille
date Tue, 01 Nov 2016 17:12:07 -0400
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31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
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1 <?xml version="1.0"?>
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
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2 <tool id="hmmer_hmmbuild" name="hmmbuild" version="@WRAPPER_VERSION@.0">
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
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3 <description>Build a profile HMM from an input multiple alignment</description>
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
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4 <macros>
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5 <import>macros.xml</import>
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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6 </macros>
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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7 <expand macro="requirements"/>
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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8 <expand macro="stdio"/>
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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9 <command><![CDATA[
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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10 hmmbuild
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11
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12 #if $hmmname:
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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13 -n "$hmmname"
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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14 #end if
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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16 @FORMAT_SELECTOR@
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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17 @MCSS@
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18 @ARSWS@
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19 @AEEWS@
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20 @PRIOR@
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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21 @HSSI@
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22 @EVAL_CALIB@
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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24 @CPU@
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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25 @SEED@
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27 @LENGTHS@
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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28 #if $maxinsertlen:
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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29 --maxinsertlen $maxinsertlen
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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30 #end if
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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31
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32 $hmmout
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33 $msafile
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34 ]]></command>
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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35 <inputs>
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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36 <expand macro="input_msa" />
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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37 <param name="hmmname" type="text" optional="True" label="Name for the HMM" help="(-n)"/>
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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38 <expand macro="format_selector"/>
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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39 <expand macro="mcss"/>
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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40 <expand macro="arsws"/>
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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41 <expand macro="aeews"/>
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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42 <expand macro="prior"/>
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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43 <expand macro="hssi"/>
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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44 <expand macro="eval_calib_xml"/>
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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45 <expand macro="seed"/>
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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46
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47 <expand macro="lengths" />
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48 <param name="maxinsertlen" label="Pretend all inserts are length &lt;= n"
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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49 help="(--maxinsertlen)" optional="True" type="integer"/>
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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50 </inputs>
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51 <outputs>
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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52 <data format="hmm3" name="hmmout" label="HMM profile from $msafile.name"/>
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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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" />
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58 <output name="hmmout" file="globins4.hmm" lines_diff="10"/>
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59 </test>
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60 <test>
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61 <param name="msafile" value="MADE1.sto"/>
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62 <param name="input_format_select" value="--dna"/>
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63 <expand macro="seed_test" />
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64 <output name="hmmout" file="MADE1.hmm" lines_diff="14"/>
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65 </test>
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66 </tests>
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67 <help><![CDATA[
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68 @HELP_PRE@
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69
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70 For each multiple sequence alignment in <msafile> build a profile HMM and save
31279c47259a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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71 it to a new file <hmmfile out>.
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72
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73 @HELP_PRE_OTH@
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74
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75 @FORMAT_SELECTOR_HELP@
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76 @MCSS_HELP@
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77 @ARSWS_HELP@
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78 @AEEWS_HELP@
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79 @PRIOR_HELP@
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80 @HSSI_HELP@
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81 @EVAL_CALIB_HELP@
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82 @SEED_HELP@
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83 @LENGTHS_HELP@
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84
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85 @ATTRIBUTION@
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86 ]]></help>
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87 <expand macro="citation"/>
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88 </tool>