Mercurial > repos > iuc > hmmer3

annotate hmmscan.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_hmmscan" name="hmmscan" 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 sequence(s) against a profile database</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"/>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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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 ## "Press" database
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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11 hmmpress $hmmfile;
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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12 ## Scan
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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13 hmmscan
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14
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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15 @OFORMAT_WITH_OPTS@
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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16 @THRESHOLDS@
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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17 @CUT@
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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18 @ACCEL_HEUR@
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19 @ADV_OPTS@
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20 @CPU@
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21 @SEED@
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22
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23 $hmmfile
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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24 $seqfile
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25 > $output;
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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26 ## Remove pressed database. Eventually will be replaced with a dedicated tool/datatype
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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27 rm ${hmmfile}.h3m ${hmmfile}.h3i ${hmmfile}.h3f ${hmmfile}.h3p;
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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28 ]]></command>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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29 <inputs>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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30 <expand macro="input_hmm" />
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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31 <!-- 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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32 <param name="seqfile" type="data" format="fasta" label="Sequence file"/>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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33 <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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34 <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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35 <expand macro="cut"/>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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36 <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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37 <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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38 <expand macro="seed"/>
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39 </inputs>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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40 <outputs>
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41 <data format="txt" name="output" label="HMM matches of $seqfile.name in $hmmfile.name"/>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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42 <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name in $hmmfile.name">
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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43 <filter>'tblout' in oformat</filter>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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44 </data>
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45 <data format="txt" name="domtblout" label="Table of per-domain hits from HMM matches of $seqfile.name in $hmmfile.name">
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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46 <filter>'domtblout' in oformat</filter>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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47 </data>
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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48 <data format="txt" name="pfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name in $hmmfile.name">
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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49 <filter>'pfamtblout' in oformat</filter>
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50 </data>
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51 </outputs>
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52 <tests>
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53 <test>
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54 <param name="hmmfile" value="MADE1.hmm"/>
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55 <param name="seqfile" value="dna_target.fa"/>
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56 <expand macro="oformat_test" />
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57 <expand macro="seed_test" />
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58 <output name="output" file="MADE1.out" lines_diff="20"/>
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59 <output name="tblout" file="MADE1.out.tblout" lines_diff="20"/>
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60 <output name="domtblout" file="MADE1.out.domtblout" lines_diff="20"/>
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61 <output name="pfamtblout" file="MADE1.out.pfamtblout" lines_diff="20"/>
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62 </test>
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63 </tests>
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64 <help><![CDATA[
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65 @HELP_PRE@
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66
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67 hmmscan is used to search protein sequences against collections of protein
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68 profiles. For each sequence in <seqfile>, use that query sequence to search the
afd1fd3095ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
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69 target database of profiles in <hmmfile>, and output ranked lists of the profiles
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70 with the most significant matches to the sequence.
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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 @THRESHOLDS_HELP@
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76 @CUT_HELP@
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77 @ACCEL_HEUR_HELP@
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78 @ADV_OPTS_HELP@
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79 @SEED_HELP@
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80
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81 @ATTRIBUTION@
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82 ]]></help>
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83 <expand macro="citation"/>
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84 </tool>