Mercurial > repos > iuc > hmmer_hmmsearch

annotate hmmsearch.xml @ 3:284d40d6f5a1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
author iuc
date Sat, 07 Apr 2018 03:49:37 -0400
parents 4d2ba28f8c8c
children 6867ed975e25
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1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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1 <?xml version="1.0"?>
3
284d40d6f5a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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2 <tool id="hmmer_hmmsearch" name="hmmsearch" version="@TOOL_VERSION@">
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1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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3 <description>search profile(s) against a sequence database</description>
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4 <macros>
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5 <import>macros.xml</import>
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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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[
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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10 hmmsearch
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11
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12 @OFORMAT_WITH_OPTS@
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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13 @THRESHOLDS@
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14 @CUT@
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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15 @ACCEL_HEUR@
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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16 @ADV_OPTS@
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17 @CPU@
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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18 @SEED@
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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19
3
284d40d6f5a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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20 '$hmmfile'
284d40d6f5a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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21 '$seqdb'
284d40d6f5a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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22 > '$output'
284d40d6f5a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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23 ]]></command>
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1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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24 <inputs>
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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25 <expand macro="input_hmm" />
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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26 <!-- todo use Galaxy features like data libraries/data tables/??? -->
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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27 <param name="seqdb" type="data" format="fasta" label="Sequence database to search against"/>
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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28 <expand macro="oformat_with_opts"/>
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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29 <expand macro="thresholds_xml"/>
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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30 <expand macro="cut"/>
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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31 <expand macro="accel_heur_xml"/>
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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32 <expand macro="adv_opts"/>
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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33 <expand macro="seed"/>
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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34 </inputs>
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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35 <outputs>
3
284d40d6f5a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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36 <data name="output" format="txt" label="HMM matches of $hmmfile.name in $seqdb.name"/>
284d40d6f5a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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37 <data name="tblout" format="txt" label="Table of per-sequence hits from HMM matches of $hmmfile.name in $seqdb.name">
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38 <filter>oformat and 'tblout' in oformat</filter>
0
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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39 </data>
3
284d40d6f5a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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40 <data name="domtblout" format="txt" label="Table of per-domain hits from HMM matches of $hmmfile.name in $seqdb.name">
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41 <filter>oformat and 'domtblout' in oformat</filter>
0
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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42 </data>
3
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43 <data name="pfamtblout" format="txt" label="Table of per-sequence/per-domain hits from HMM matches of $hmmfile.name in $seqdb.name">
2
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44 <filter>oformat and 'pfamtblout' in oformat</filter>
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45 </data>
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46 </outputs>
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47 <tests>
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48 <test>
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49 <param name="hmmfile" value="globins4.hmm"/>
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50 <param name="seqdb" value="uniprot_matches.fasta"/>
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51 <expand macro="oformat_test" />
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52 <expand macro="seed_test" />
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53 <output name="output" file="uniprot_globins_match.out" lines_diff="20"/>
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54 <output name="domtblout" file="globins.domtblout" lines_diff="10"/>
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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55 <output name="pfamtblout" file="globins.pfamtblout" lines_diff="10"/>
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56 <output name="tblout" file="globins.tblout" lines_diff="10"/>
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57 </test>
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58 </tests>
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59 <help><![CDATA[
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60 @HELP_PRE@
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61
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62 hmmsearch is used to search one or more profiles against a sequence database.
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63 For each profile in <hmmfile>, use that query profile to search the target
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64 database of sequences in <seqdb>, and output ranked lists of the sequences with
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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65 the most significant matches to the profile. To build profiles from multiple
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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66 alignments, see hmmbuild.
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67
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68 @HELP_PRE_OTH@
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69
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70 @OFORMAT_WITH_OPTS_HELP@
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71 @THRESHOLDS_HELP@
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72 @CUT_HELP@
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73 @ACCEL_HEUR_HELP@
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74 @ADV_OPTS_HELP@
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75 @SEED_HELP@
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76
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77 @ATTRIBUTION@
3
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78 ]]></help>
0
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79 <expand macro="citation"/>
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80 </tool>