Mercurial > repos > iuc > hmmer_nhmmscan

annotate nhmmscan.xml @ 0:a6098dd0cb46 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 15:07:32 -0400
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a6098dd0cb46 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"?>
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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2 <tool id="hmmer_nhmmscan" name="nhmmscan" version="@WRAPPER_VERSION@.0">
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3 <description>search DNA sequence(s) against a DNA profile database</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[
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10 hmmpress $hmmfile;
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11
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12 nhmmscan
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13
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14 @OFORMAT_WITH_OPTS_N@
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15 @THRESHOLDS_NODOM@
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16 @CUT@
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17 @ACCEL_HEUR@
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18 --B1 $B1
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19 --B2 $B2
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20 --B3 $B3
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22 @ADV_OPTS@
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23 @LENGTHS@
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24 @CPU@
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25 @SEED@
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26
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27 $hmmfile
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28 $seqfile
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29 > $output
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30 ]]></command>
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31 <inputs>
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32 <expand macro="input_hmm" />
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33 <!-- todo use Galaxy features like data libraries/data tables/??? -->
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34 <param name="seqfile" type="data" format="fasta" label="Sequence file"/>
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35 <expand macro="oformat_with_opts_n"/>
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36 <expand macro="thresholds_nodom"/>
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37 <expand macro="cut"/>
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38 <expand macro="accel_heur_xml"/>
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39
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40 <param name="B1" type="integer" label="window length for biased-composition modifier (MSV)" help="(--B1)" value="110"/>
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41 <param name="B2" type="integer" label="window length for biased-composition modifier (Vit)" help="(--B2)" value="240"/>
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42 <param name="B3" type="integer" label="window length for biased-composition modifier (Fwd)" help="(--B3)" value="1000"/>
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43
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44 <expand macro="adv_opts"/>
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45 <expand macro="lengths"/>
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46 <expand macro="seed"/>
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47 </inputs>
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48 <outputs>
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49 <data format="txt" name="output" label="HMM matches of $seqfile.name in $hmmfile.name"/>
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50
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51 <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name in $hmmfile.name">
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52 <filter>'tblout' in str(oformat)</filter>
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53 </data>
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54 <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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55 <filter>'pfamtblout' in str(oformat)</filter>
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56 </data>
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57 <data format="txt" name="aliscoresout" label="Scores for positional matches of $seqfile.name in $hmmfile.name">
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58 <filter>'aliscoresout' in str(oformat)</filter>
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59 </data>
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60 </outputs>
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61 <tests>
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62 <test>
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63 <param name="hmmfile" value="MADE1.hmm"/>
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64 <param name="seqfile" value="dna_target.fa"/>
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65 <expand macro="oformat_test" />
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66 <expand macro="seed_test" />
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67 <output name="output" file="MADE1.out" lines_diff="140"/>
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68 <output name="tblout" file="MADE1.out.tblout" lines_diff="30"/>
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69 <output name="domtblout" file="MADE1.out.domtblout" lines_diff="30"/>
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70 <output name="pfamtblout" file="MADE1.out.pfamtblout" lines_diff="36"/>
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71 </test>
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72 </tests>
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73 <help><![CDATA[
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74 @HELP_PRE@
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75
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76 nhmmscan is used to search nucleotide sequences against collections of
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77 nucleotide profiles. For each sequence in <seqfile>, use that query sequence to
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78 search the target database of profiles in <hmmfile>, and output ranked lists of
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79 the profiles with the most significant matches to the sequence.
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80
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81 The <seqfile> may contain more than one query sequence. It can be in FASTA
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82 format, or several other common sequence file formats (genbank, embl, and
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83 uniprot, among others), or in alignment file formats (stockholm, aligned fasta,
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84 and others). See the --qformat option for a complete list.
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85
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86 @HELP_PRE_OTH@
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87
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88 @OFORMAT_WITH_OPTS_N_HELP@
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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89 @THRESHOLDS_NODOM_HELP@
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90 @CUT_HELP@
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91 @ACCEL_HEUR_HELP@
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92 @BIAS_COMP_HELP@
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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93 @ADV_OPTS_HELP@
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94 @LENGTHS_HELP@
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95 @SEED_HELP@
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96
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97
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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98 @ATTRIBUTION@
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99 ]]></help>
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100 <expand macro="citation"/>
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101 </tool>