Mercurial > repos > iuc > hmmer3

annotate phmmer.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_phmmer" name="phmmer" 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>search a protein sequence against a protein database (BLASTP-like)</description>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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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[
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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10 phmmer
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11
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12 @OFORMAT_WITH_OPTS@
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13 @HSSI@
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14 @THRESHOLDS@
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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15 @ACCEL_HEUR@
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16 @EVAL_CALIB@
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17 @ADV_OPTS@
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18
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19 @CPU@
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20 @SEED@
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21
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22 $seqfile
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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23 $seqdb
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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24 > $output
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25 ]]></command>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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26 <inputs>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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27 <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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28 <!-- todo use Galaxy features like data libraries/data tables/??? -->
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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29 <param name="seqdb" type="data" format="fasta" label="Sequence Database"/>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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30 <expand macro="oformat_with_opts"/>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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31 <expand macro="hssi"/>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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32 <expand macro="thresholds_xml"/>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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33 <expand macro="accel_heur_xml"/>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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34 <expand macro="eval_calib_xml"/>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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35 <expand macro="adv_opts"/>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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36 <expand macro="seed"/>
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37 </inputs>
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38 <outputs>
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39 <data format="txt" name="output" label="PHMMER search of $seqfile.name in $seqdb.name"/>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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40 <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name in $seqdb.name">
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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41 <filter>'tblout' in str(oformat)</filter>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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42 </data>
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43 <data format="txt" name="domtblout" label="Table of per-domain hits from HMM matches of $seqfile.name in $seqdb.name">
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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44 <filter>'domtblout' in str(oformat)</filter>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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45 </data>
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46 <data format="txt" name="pfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name in $seqdb.name">
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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47 <filter>'pfamtblout' in str(oformat)</filter>
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48 </data>
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49 </outputs>
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50 <tests>
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51 <test>
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52 <param name="seqfile" value="globins45.fa"/>
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53 <param name="seqdb" value="uniprot_matches.fasta"/>
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54 <expand macro="oformat_test" />
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55 <expand macro="seed_test" />
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56 <output name="output" file="phmmer.out" lines_diff="200"/>
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57 <!-- Lines diff is high due to a line of cpu/timing information for EACH sequence -->
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58 <output name="domtblout" file="phmmer.domtblout" lines_diff="10"/>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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59 <output name="pfamtblout" file="phmmer.pfamtblout" lines_diff="10"/>
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60 <output name="tblout" file="phmmer.tblout" lines_diff="10"/>
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61 </test>
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62 </tests>
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63 <help><![CDATA[
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64 @HELP_PRE@
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65
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66 phmmer is used to search one or more query protein sequences against a protein
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67 sequence database. For each query sequence in <seqfile>, use that sequence to
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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68 search the target database of sequences in <seqdb>, and output ranked lists of
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69 the sequences with the most significant matches to the query.
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70
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71
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72 @HELP_PRE_OTH@
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73
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74 @OFORMAT_WITH_OPTS_HELP@
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75 @HSSI_HELP@
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76 @THRESHOLDS_HELP@
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77 @ACCEL_HEUR_HELP@
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78 @EVAL_CALIB_HELP@
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79 @ADV_OPTS_HELP@
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80 @SEED_HELP@
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81
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82 @ATTRIBUTION@
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83 ]]></help>
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84 <expand macro="citation"/>
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85 </tool>