Mercurial > repos > iuc > hmmer3

annotate jackhmmer.xml @ 2:ef9501a30bfe draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e5a5ad091c621348dc6ce2df861475ebc54a380e
author iuc
date Tue, 13 Oct 2015 17:23:53 -0400
parents afd1fd3095ad
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afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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1 <?xml version="1.0"?>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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2 <tool id="hmmer_jackhmmer" name="jackhmmer" version="@WRAPPER_VERSION@.0">
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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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>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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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 jackhmmer
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11 -N $N
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12 @OFORMAT_WITH_OPTS_NOPFAM@
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13 @HSSI@
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14 @THRESHOLDS@
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15 @ACCEL_HEUR@
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16 @MCSS@
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17 @ARSWS@
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18 @AEEWS@
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19 @PRIOR@
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20
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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
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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"/>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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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)"/>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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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_nopfam"/>
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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="mcss"/>
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40 <expand macro="arsws"/>
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41 <expand macro="aeews"/>
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42 <expand macro="prior"/>
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43 <expand macro="eval_calib_xml"/>
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44 <expand macro="adv_opts"/>
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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 <data format="txt" name="output" label="PHMMER search of $seqfile.name in $seqdb.name"/>
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49 <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name in $seqdb.name">
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50 <filter>'tblout' in str(oformat)</filter>
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51 </data>
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52 <data format="txt" name="domtblout" label="Table of per-domain hits from HMM matches of $seqfile.name in $seqdb.name">
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53 <filter>'domtblout' in str(oformat)</filter>
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54 </data>
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55 </outputs>
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56 <tests>
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57 <test>
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58 <param name="seqfile" value="uniprot_matches.fasta"/>
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59 <param name="seqdb" value="globins45.fa"/>
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60 <expand macro="oformat_test" />
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61 <expand macro="seed_test" />
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62 <output name="output" file="jackhmmer.out" lines_diff="180"/>
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63 <output name="domtblout" file="jackhmmer.domtblout" lines_diff="10"/>
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64 <output name="tblout" file="jackhmmer.tblout" lines_diff="10"/>
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65 </test>
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66 </tests>
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67 <help><![CDATA[
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68 @HELP_PRE@
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69
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70 jackhmmer iteratively searches each query sequence in <seqfile> against the
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71 target sequence(s) in <seqdb>. The first iteration is identical to a phmmer
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72 search. For the next iteration, a multiple alignment of the query together
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73 with all target sequences satisfying inclusion thresholds is assembled, a
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74 profile is constructed from this alignment (identical to using hmmbuild on the
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75 alignment), and profile search of the <seqdb> is done (identical to an
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76 hmmsearch with the profile).
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77
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78
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79 @HELP_PRE_OTH@
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80
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81 @OFORMAT_WITH_OPTS_HELP_NOPFAM@
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82 @HSSI_HELP@
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83 @THRESHOLDS_HELP@
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84 @ACCEL_HEUR_HELP@
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85 @MCSS_HELP@
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86 @ARSWS_HELP@
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87 @AEEWS_HELP@
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88 @PRIOR_HELP@
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89 @EVAL_CALIB_HELP@
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90 @ADV_OPTS_HELP@
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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91 @SEED_HELP@
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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92
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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93 @ATTRIBUTION@
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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94 ]]></help>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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95 <expand macro="citation"/>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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96 </tool>