annotate jackhmmer.xml @ 7:6e27bb3f0fa6 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 0bccf5220ed6549db7e053f85bbe917326b0a0be"
author iuc
date Wed, 21 Jul 2021 14:16:41 +0000
parents d9ce554da9b4
children
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1 <?xml version="1.0"?>
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2 <tool id="hmmer_jackhmmer" name="jackhmmer" version="@TOOL_VERSION@+galaxy0">
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3 <description>iteratively search a protein sequence against a protein database (PSIBLAST-like)</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@
0
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11 jackhmmer
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12 -N $N
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13 @OFORMAT_WITH_OPTS@
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14 @HSSI@
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15 @THRESHOLDS@
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16 @ACCEL_HEUR@
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17 @ARSWS@
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18 @AEEWS@
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19 @PRIOR@
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20
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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21 @EVAL_CALIB@
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22 @ADV_OPTS@
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23 @CPU@
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24 @SEED@
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25
3
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26 '$seqfile'
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27 '$seqdb'
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28 > '$output'
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29 ]]></command>
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30 <inputs>
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31 <param name="seqfile" type="data" format="fasta" label="Protein sequence to search with"/>
b23fd24e45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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32 <!-- todo use Galaxy features like data libraries/data tables/??? -->
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33 <param name="N" type="integer" value="5" min="1" label="Maximum number of iterations" help="(-N)"/>
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34 <param name="seqdb" type="data" format="fasta" label="Sequence Database"/>
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35 <expand macro="oformat_with_opts_dom"/>
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36 <expand macro="hssi"/>
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37 <expand macro="thresholds_xml"/>
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38 <expand macro="accel_heur_xml"/>
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39 <expand macro="arsws"/>
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40 <expand macro="aeews"/>
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41 <expand macro="prior"/>
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42 <expand macro="eval_calib_xml"/>
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43 <expand macro="adv_opts"/>
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44 <expand macro="seed"/>
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45 </inputs>
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46 <outputs>
5
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47 <expand macro="output_dom_pfam" tool="JACKHMMER"/>
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48 </outputs>
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49 <tests>
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50 <test expect_num_outputs="3">
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51 <param name="seqfile" value="uniprot_matches.fasta"/>
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52 <param name="seqdb" value="globins45.fa"/>
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53 <expand macro="oformat_test" />
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54 <expand macro="seed_test" />
5
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55 <output name="output" file="jackhmmer.out" lines_diff="180">
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56 <expand macro="assert_out" tool="jackhmmer"/>
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57 </output>
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58 <output name="domtblout" file="jackhmmer.domtblout" lines_diff="10">
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59 <expand macro="assert_tblout" tool="jackhmmer"/>
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60 </output>
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61 <output name="tblout" file="jackhmmer.tblout" lines_diff="10">
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62 <expand macro="assert_tblout" tool="jackhmmer"/>
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63 </output>
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64 </test>
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65 <test expect_num_outputs="1">
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66 <param name="seqfile" value="uniprot_matches.fasta"/>
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67 <param name="seqdb" value="globins45.fa"/>
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68 <expand macro="oformat_test" />
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69 <param name="oformat" value=""/>
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70 <expand macro="seed_test" />
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71 <output name="output" file="jackhmmer.out" lines_diff="180">
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72 <expand macro="assert_out" tool="jackhmmer"/>
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73 </output>
0
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74 </test>
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75 </tests>
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76 <help><![CDATA[
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77 @HELP_PRE@
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78
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79 jackhmmer iteratively searches each query sequence in <seqfile> against the
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80 target sequence(s) in <seqdb>. The first iteration is identical to a phmmer
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81 search. For the next iteration, a multiple alignment of the query together
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82 with all target sequences satisfying inclusion thresholds is assembled, a
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83 profile is constructed from this alignment (identical to using hmmbuild on the
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84 alignment), and profile search of the <seqdb> is done (identical to an
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85 hmmsearch with the profile).
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86
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88 @HELP_PRE_OTH@
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89
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90 @OFORMAT_WITH_OPTS_HELP_NOPFAM@
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91 @HSSI_HELP@
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92 @THRESHOLDS_HELP@
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93 @ACCEL_HEUR_HELP@
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94 @ARSWS_HELP@
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95 @AEEWS_HELP@
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96 @PRIOR_HELP@
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97 @EVAL_CALIB_HELP@
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98 @ADV_OPTS_HELP@
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99 @SEED_HELP@
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101 @ATTRIBUTION@
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102 ]]></help>
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103 <expand macro="citation"/>
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104 </tool>