Mercurial > repos > iuc > hmmer_nhmmscan

annotate nhmmscan.xml @ 7:e7d281a290a6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 061757dd7b3bfe66b7738fd54bd6c5e135d9afe8
author iuc
date Mon, 06 Nov 2023 20:24:33 +0000
parents e07176c0925d
children fb1305d0d1c6
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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="bio_tools"/>
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8 <expand macro="requirements"/>
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9 <expand macro="stdio"/>
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10 <command><![CDATA[
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11 @ADDTHREADS@
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12 @INPUTHMMCHOICE@
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13 nhmmscan
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14
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15 @OFORMAT_WITH_OPTS@
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16 @THRESHOLDS@
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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 $B3
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22 @ADV_OPTS@
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23 @LENGTHS@
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24 @CPU@
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25 @SEED@
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26
2
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27 '$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_cut_xml"/>
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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)" />
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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>
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48 <expand macro="output_dfam_alisc" tool="NHMMSCAN"/>
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49 </outputs>
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50 <tests>
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51 <test expect_num_outputs="3">
2
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52 <param name="input_hmm_conditional|input_hmm_source" value="history"/>
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53 <param name="input_hmm_conditional|hmmfile" value="MADE1.hmm"/>
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54 <param name="seqfile" value="dna_target.fa"/>
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55 <expand macro="oformat_test" />
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56 <expand macro="seed_test" />
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57 <output name="output" file="MADE1.nhmmscan_out" lines_diff="12">
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58 <expand macro="assert_out" tool="nhmmscan"/>
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59 </output>
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60 <output name="tblout" file="MADE1.nhmmscan_out.tblout" lines_diff="10">
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61 <!-- nhmmscan reports as hmmscan https://github.com/EddyRivasLab/hmmer/issues/190 -->
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62 <expand macro="assert_tblout" tool="nhmmscan"/>
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63 </output>
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64 <output name="dfamtblout" file="MADE1.nhmmscan_out.dfamtblout">
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65 <assert_contents>
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66 <has_line_matching expression="# hit scores"/>
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67 </assert_contents>
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68 </output>
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69 <!--not test because https://github.com/EddyRivasLab/hmmer/issues/190 <output name="aliscoresout" file="MADE1.nhmmscan_out.aliscoresout" lines_diff="10" />-->
0
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70 </test>
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71 </tests>
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72 <help><![CDATA[
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73 @HELP_PRE@
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74
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75 nhmmscan is used to search nucleotide sequences against collections of
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76 nucleotide profiles. For each sequence in <seqfile>, use that query sequence to
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77 search the target database of profiles in <hmmfile>, and output ranked lists of
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78 the profiles with the most significant matches to the sequence.
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79
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80 The <seqfile> may contain more than one query sequence. It can be in FASTA
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81 format, or several other common sequence file formats (genbank, embl, and
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82 uniprot, among others), or in alignment file formats (stockholm, aligned fasta,
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83 and others). See the --qformat option for a complete list.
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84
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85 @HELP_PRE_OTH@
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86
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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87 @OFORMAT_WITH_OPTS_N_HELP@
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88 @THRESHOLDS_NODOM_HELP@
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89 @CUT_HELP@
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90 @ACCEL_HEUR_HELP@
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91 @BIAS_COMP_HELP@
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92 @ADV_OPTS_HELP@
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93 @LENGTHS_HELP@
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94 @SEED_HELP@
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95
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96
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97 @ATTRIBUTION@
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98 ]]></help>
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99 <expand macro="citation"/>
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100 </tool>