Mercurial > repos > iuc > hmmer_nhmmscan

annotate nhmmscan.xml @ 9:2b2f6fcb2f17 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 15:36:07 +0000
parents 61de78a1f32e
children 393baf6165c4
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1 <?xml version="1.0"?>
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2 <tool id="hmmer_nhmmscan" name="nhmmscan" version="@TOOL_VERSION@+galaxy1">
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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 @ADDTHREADS@
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11 @INPUTHMMCHOICE@
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12 nhmmscan
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13
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14 @OFORMAT_WITH_OPTS@
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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 $B3
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22 @ADV_OPTS@
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23 @LENGTHS@
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24 @CPU@
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25 @SEED@
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26
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27 '$input_hmm_filename'
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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_choice" />
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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_dfam_alisc"/>
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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 argument="--B1" type="integer" value="110" label="window length for biased-composition modifier (MSV)" />
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41 <param argument="--B2" type="integer" value="240" label="window length for biased-composition modifier (Vit)" />
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42 <param argument="--B3" type="integer" value="1000" label="window length for biased-composition modifier (Fwd)" />
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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 <expand macro="output_dfam_alisc" tool="NHMMSCAN"/>
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50 </outputs>
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51 <tests>
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52 <test expect_num_outputs="3">
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53 <param name="input_hmm_conditional|input_hmm_source" value="history"/>
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54 <param name="input_hmm_conditional|hmmfile" value="MADE1.hmm"/>
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55 <param name="seqfile" value="dna_target.fa"/>
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56 <expand macro="oformat_test" />
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57 <expand macro="seed_test" />
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58 <output name="output" file="MADE1.nhmmscan_out" lines_diff="12">
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59 <expand macro="assert_out" tool="nhmmscan"/>
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60 </output>
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61 <output name="tblout" file="MADE1.nhmmscan_out.tblout" lines_diff="10">
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62 <!-- nhmmscan reports as hmmscan https://github.com/EddyRivasLab/hmmer/issues/190 -->
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63 <expand macro="assert_tblout" tool="hmmscan"/>
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64 </output>
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65 <output name="dfamtblout" file="MADE1.nhmmscan_out.dfamtblout">
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66 <assert_contents>
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67 <has_line_matching expression="# hit scores"/>
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68 </assert_contents>
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69 </output>
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70 <!--not test because https://github.com/EddyRivasLab/hmmer/issues/190 <output name="aliscoresout" file="MADE1.nhmmscan_out.aliscoresout" lines_diff="10" />-->
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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>