Mercurial > repos > iuc > hmmer_nhmmer

annotate nhmmer.xml @ 0:f239ab5f45f4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
author iuc
date Sat, 25 Jun 2016 15:07:17 -0400
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f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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1 <?xml version="1.0"?>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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2 <tool id="hmmer_nhmmer" name="nhmmer" version="@WRAPPER_VERSION@.0">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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3 <description>search a DNA model or alignment against a DNA database (BLASTN-like)</description>
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4 <macros>
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5 <import>macros.xml</import>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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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[
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10 nhmmer
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11
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12 @OFORMAT_WITH_OPTS_N@
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13 @HSSI@
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14 @THRESHOLDS_NODOM@
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15 @CUT@
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16 @ACCEL_HEUR@
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17 @FORMAT_SELECTOR@
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18 @ADV_OPTS@
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19 @LENGTHS@
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20 @CPU@
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21 @SEED@
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22
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23 $hmmfile
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24 $seqfile
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25 > $output
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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26 ]]></command>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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27 <inputs>
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28 <expand macro="input_hmm" />
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29 <param name="seqfile" type="data" format="fasta" label="Target sequence file"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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30 <expand macro="oformat_with_opts_n"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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31 <expand macro="hssi"/>
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32 <expand macro="thresholds_nodom"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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33 <expand macro="cut" />
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34 <expand macro="accel_heur_xml"/>
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35 <expand macro="format_selector_noprot"/>
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36 <expand macro="adv_opts"/>
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37 <expand macro="lengths"/>
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38 <!-- TODO: block_length toponly bottomonly -->
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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39 <expand macro="seed"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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40 </inputs>
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41 <outputs>
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42 <data format="txt" name="output" label="NHMMER search of $seqfile.name in $hmmfile.name"/>
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43
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44 <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name in $hmmfile.name">
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45 <filter>'tblout' in str(oformat)</filter>
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46 </data>
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47 <data format="txt" name="dfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name in $hmmfile.name">
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48 <filter>'pfamtblout' in str(oformat)</filter>
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49 </data>
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50 <data format="txt" name="aliscoresout" label="Scores for positional matches of $seqfile.name in $hmmfile.name">
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51 <filter>'aliscoresout' in str(oformat)</filter>
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52 </data>
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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="hmmfile" value="MADE1.hmm"/>
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57 <param name="seqfile" value="dna_target.fa"/>
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58 <expand macro="oformat_test" />
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59 <expand macro="seed_test" />
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60 <output name="output" file="nhmmer.out" lines_diff="32"/>
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61 </test>
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62 </tests>
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63 <help><![CDATA[
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64 @HELP_PRE@
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65
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66 nhmmer is used to search one or more nucleotide queries against a nucleotide
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67 sequence database. For each query in <queryfile>, use that query to search the
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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68 target database of sequences in <seqdb>, and output a ranked list of the hits
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69 with the most significant matches to the query. A query may be either a profile
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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70 model built using hmmbuild, a sequence alignment, or a single sequence.
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71 Sequence based queries can be in a number of formats (see --qformat), and can
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72 typically be autodetected. Note that only Stockholm format supports the use of
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73 multiple sequence-based queries.
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74
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75 @HELP_PRE_OTH@
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76
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77 @OFORMAT_WITH_OPTS_N_HELP@
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78 @HSSI_HELP@
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79 @THRESHOLDS_NODOM_HELP@
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80 @CUT_HELP@
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81 @ACCEL_HEUR_HELP@
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82 @FORMAT_SELECTOR_HELP@
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83 @ADV_OPTS_HELP@
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84 @LENGTHS_HELP@
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85 @SEED_HELP@
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86
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87 @ATTRIBUTION@
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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88 ]]></help>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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89 <expand macro="citation"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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90 </tool>