Mercurial > repos > iuc > hmmer_nhmmscan

annotate nhmmscan.xml @ 2:c3075b7fdbdd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
author iuc
date Sat, 07 Apr 2018 03:49:11 -0400
parents a6098dd0cb46
children 2d406da5d34e
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1 <?xml version="1.0"?>
2
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2 <tool id="hmmer_nhmmscan" name="nhmmscan" version="@TOOL_VERSION@">
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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[
2
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10 @INPUTHMMCHOICE@
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11 nhmmscan
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12
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13 @OFORMAT_WITH_OPTS_N@
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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 --B1 $B1
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18 --B2 $B2
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19 --B3 $B3
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21 @ADV_OPTS@
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22 @LENGTHS@
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23 @CPU@
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24 @SEED@
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25
2
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26 '$input_hmm_filename'
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27 '$seqfile'
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28 > '$output'
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29 ]]></command>
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30 <inputs>
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31 <expand macro="input_hmm_choice" />
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32 <!-- todo use Galaxy features like data libraries/data tables/??? -->
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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33 <param name="seqfile" type="data" format="fasta" label="Sequence file"/>
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34 <expand macro="oformat_with_opts_n"/>
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35 <expand macro="thresholds_nodom"/>
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36 <expand macro="cut"/>
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37 <expand macro="accel_heur_xml"/>
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38
2
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39 <param argument="--B1" type="integer" value="110" label="window length for biased-composition modifier (MSV)" />
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40 <param argument="--B2" type="integer" value="240" label="window length for biased-composition modifier (Vit)" />
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41 <param argument="--B3" type="integer" value="1000" label="window length for biased-composition modifier (Fwd)" />
0
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43 <expand macro="adv_opts"/>
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44 <expand macro="lengths"/>
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45 <expand macro="seed"/>
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46 </inputs>
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47 <outputs>
2
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48 <data name="output" format="txt" label="HMM matches of $seqfile.name against the profile database"/>
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49
2
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50 <data name="tblout" format="txt" label="Table of per-sequence hits from HMM matches of $seqfile.name against the profile database">
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51 <filter>oformat and 'tblout' in oformat</filter>
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52 </data>
2
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53 <data name="dfamtblout" format="txt" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name against the profile database">
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54 <filter>oformat and 'dfamtblout' in oformat</filter>
0
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55 </data>
2
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56 <data name="aliscoresout" format="txt" label="Scores for positional matches of $seqfile.name against the profile database">
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57 <filter>oformat and 'aliscoresout' in oformat</filter>
0
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58 </data>
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59 </outputs>
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60 <tests>
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61 <test>
2
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62 <param name="input_hmm_conditional|input_hmm_source" value="history"/>
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63 <param name="input_hmm_conditional|hmmfile" value="MADE1.hmm"/>
0
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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" />
2
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67 <output name="output" file="MADE1.nhmmscan_out" lines_diff="12" />
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68 <output name="tblout" file="MADE1.nhmmscan_out.tblout" lines_diff="10" />
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69 <output name="dfamtblout" file="MADE1.nhmmscan_out.dfamtblout" />
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70 <output name="aliscoresout" file="MADE1.nhmmscan_out.aliscoresout" lines_diff="10" />
0
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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@
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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@
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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
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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>