Mercurial > repos > iuc > hmmer_hmmsearch

annotate hmmsearch.xml @ 8:3bb58751f4ee 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 20:22:49 +0000
parents d753d9169482
children df7a52791be9
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1dde27bbdcba 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"?>
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2 <tool id="hmmer_hmmsearch" name="hmmsearch" version="@TOOL_VERSION@+galaxy1">
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3 <description>search profile(s) against a sequence 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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1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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12 hmmsearch
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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14 @OFORMAT_WITH_OPTS@
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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15 @THRESHOLDS@
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16 @THRESHOLDS_DOM@
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17 @ACCEL_HEUR@
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18 @ADV_OPTS@
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19 @CPU@
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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20 @SEED@
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21
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22 '$hmmfile'
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23 '$seqdb'
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24 > '$output'
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25 ]]></command>
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26 <inputs>
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27 <expand macro="input_hmm" />
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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28 <!-- todo use Galaxy features like data libraries/data tables/??? -->
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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29 <param name="seqdb" type="data" format="fasta" label="Sequence database to search against"/>
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30 <expand macro="oformat_with_opts_dom_pfam"/>
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31 <expand macro="thresholds_cut_dom_xml"/>
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32 <expand macro="accel_heur_xml"/>
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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33 <expand macro="adv_opts"/>
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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34 <expand macro="seed"/>
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35 </inputs>
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36 <outputs>
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37 <expand macro="output_dom_pfam" tool="PHMMER"/>
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38 </outputs>
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39 <tests>
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40 <test expect_num_outputs="4">
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1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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41 <param name="hmmfile" value="globins4.hmm"/>
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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42 <param name="seqdb" value="uniprot_matches.fasta"/>
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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43 <expand macro="oformat_test" />
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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44 <expand macro="seed_test" />
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45 <output name="output" file="uniprot_globins_match.out" lines_diff="20">
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46 <expand macro="assert_out" tool="hmmsearch"/>
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47 </output>
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48 <output name="domtblout" file="globins.domtblout" lines_diff="16">
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49 <expand macro="assert_tblout" tool="hmmsearch"/>
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50 </output>
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51 <output name="pfamtblout" file="globins.pfamtblout" lines_diff="12">
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52 <expand macro="assert_tblout" tool="hmmsearch"/>
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53 </output>
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54 <output name="tblout" file="globins.tblout" lines_diff="16">
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55 <expand macro="assert_tblout" tool="hmmsearch"/>
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56 </output>
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57 </test>
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58 <test expect_num_outputs="1">
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59 <param name="hmmfile" value="globins4.hmm"/>
b774ae8e1609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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60 <param name="seqdb" value="uniprot_matches.fasta"/>
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61 <expand macro="oformat_test" />
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62 <param name="oformat" value=""/>
b774ae8e1609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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63 <expand macro="seed_test" />
b774ae8e1609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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64 <output name="output" file="uniprot_globins_match.out" lines_diff="20">
b774ae8e1609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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65 <expand macro="assert_out" tool="hmmsearch"/>
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66 </output>
0
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67 </test>
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68 <test expect_num_outputs="1"><!-- test with additional evalue threshold options set -->
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69 <param name="hmmfile" value="fn3.hmm"/>
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70 <param name="seqdb" value="uniprot_matches.fasta"/>
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71 <conditional name="repopt">
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72 <param name="incE" value="0.00001"/>
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73 <param name="incdomE" value="0.0001"/>
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74 </conditional>
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75 <expand macro="oformat_test" />
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76 <param name="oformat" value=""/>
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77 <expand macro="seed_test" />
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78 <output name="output">
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79 <expand macro="assert_out" tool="hmmsearch"/>
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80 </output>
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81 <assert_command>
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82 <has_text text="-E 10"/>
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83 <has_text text="--incE 1e-05"/>
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84 <has_text text="--domE 10"/>
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85 <has_text text="--incdomE 0.0001"/>
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86 </assert_command>
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87 </test>
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88 <test expect_num_outputs="1"><!-- test with cut_ga set -->
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89 <param name="hmmfile" value="fn3.hmm"/>
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90 <param name="seqdb" value="uniprot_matches.fasta"/>
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91 <conditional name="repopt">
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92 <param name="repopt_sel" value="--cut_ga"/>
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93 </conditional>
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94 <expand macro="oformat_test" />
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95 <param name="oformat" value=""/>
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96 <expand macro="seed_test" />
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97 <output name="output" file="cut_ga_test.out" lines_diff="10">
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98 <expand macro="assert_out" tool="hmmsearch"/>
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99 </output>
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100 </test>
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101
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102
0
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103 </tests>
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104 <help><![CDATA[
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105 @HELP_PRE@
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106
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107 hmmsearch is used to search one or more profiles against a sequence database.
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108 For each profile in <hmmfile>, use that query profile to search the target
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109 database of sequences in <seqdb>, and output ranked lists of the sequences with
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110 the most significant matches to the profile. To build profiles from multiple
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111 alignments, see hmmbuild.
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112
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113 @HELP_PRE_OTH@
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114
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115 @OFORMAT_WITH_OPTS_HELP@
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116 @THRESHOLDS_HELP@
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117 @CUT_HELP@
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118 @ACCEL_HEUR_HELP@
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119 @ADV_OPTS_HELP@
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120 @SEED_HELP@
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121
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122 @ATTRIBUTION@
3
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123 ]]></help>
0
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124 <expand macro="citation"/>
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125 </tool>