Mercurial > repos > iuc > hmmer_phmmer

annotate phmmer.xml @ 11:5642d4cc1a99 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:41:22 +0000
parents 2bfb56f290d3
children
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1 <?xml version="1.0"?>
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2 <tool id="hmmer_phmmer" name="phmmer" version="@TOOL_VERSION@+galaxy0">
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3 <description>search a protein sequence against a protein database (BLASTP-like)</description>
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4 <expand macro="bio_tools"/>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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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 phmmer
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14 @OFORMAT_WITH_OPTS@
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15 @HSSI@
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16 @THRESHOLDS@
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17 @ACCEL_HEUR@
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18 @EVAL_CALIB@
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19 @ADV_OPTS@
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21 @CPU@
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22 @SEED@
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23
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24 '$seqfile'
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25 '$seqdb'
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26 > '$output'
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27 ]]></command>
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28 <inputs>
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29 <param name="seqfile" type="data" format="fasta" label="Protein sequence to search with"/>
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30 <!-- todo use Galaxy features like data libraries/data tables/??? -->
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31 <param name="seqdb" type="data" format="fasta" label="Sequence Database"/>
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32 <expand macro="oformat_with_opts_dom_pfam"/>
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33 <expand macro="hssi"/>
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34 <expand macro="thresholds_xml"/>
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35 <expand macro="accel_heur_xml"/>
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36 <expand macro="eval_calib_xml"/>
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37 <expand macro="adv_opts"/>
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38 <expand macro="seed"/>
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39 </inputs>
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40 <outputs>
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41 <expand macro="output_dom_pfam" tool="PHMMER"/>
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42 </outputs>
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43 <tests>
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44 <test expect_num_outputs="4">
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45 <param name="seqfile" value="globins45.fa"/>
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46 <param name="seqdb" value="uniprot_matches.fasta"/>
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47 <expand macro="oformat_test" />
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48 <expand macro="seed_test" />
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49 <output name="output" file="phmmer.out" lines_diff="200">
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50 <expand macro="assert_out" tool="phmmer"/>
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51 </output>
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52 <!-- Lines diff is high due to a line of cpu/timing information for EACH sequence -->
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53 <output name="domtblout" file="phmmer.domtblout" lines_diff="12">
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54 <expand macro="assert_tblout" tool="phmmer"/>
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55 </output>
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56 <output name="pfamtblout" file="phmmer.pfamtblout" lines_diff="12">
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57 <expand macro="assert_tblout" tool="phmmer"/>
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58 </output>
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59 <output name="tblout" file="phmmer.tblout" lines_diff="12">
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60 <expand macro="assert_tblout" tool="phmmer"/>
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61 </output>
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62 </test>
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63 <test expect_num_outputs="1">
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64 <param name="seqfile" value="globins45.fa"/>
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65 <param name="seqdb" value="uniprot_matches.fasta"/>
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66 <expand macro="oformat_test" />
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67 <param name="oformat" value=""/>
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68 <expand macro="seed_test" />
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69 <output name="output" file="phmmer.out" lines_diff="200">
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70 <expand macro="assert_out" tool="phmmer"/>
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71 </output>
0
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72 </test>
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73 </tests>
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74 <help><![CDATA[
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75 @HELP_PRE@
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77 phmmer is used to search one or more query protein sequences against a protein
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78 sequence database. For each query sequence in <seqfile>, use that sequence to
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79 search the target database of sequences in <seqdb>, and output ranked lists of
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80 the sequences with the most significant matches to the query.
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83 @HELP_PRE_OTH@
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84
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85 @OFORMAT_WITH_OPTS_HELP@
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86 @HSSI_HELP@
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87 @THRESHOLDS_HELP@
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88 @ACCEL_HEUR_HELP@
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89 @EVAL_CALIB_HELP@
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90 @ADV_OPTS_HELP@
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91 @SEED_HELP@
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92
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93 @ATTRIBUTION@
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94 ]]></help>
0
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95 <expand macro="citation"/>
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96 </tool>