Mercurial > repos > iuc > hmmer_hmmalign

annotate jackhmmer.xml.orig @ 10:273dda94efb2 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 08:40:44 +0000
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10
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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1 <?xml version="1.0"?>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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2 <<<<<<< HEAD
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <tool id="hmmer_jackhmmer" name="jackhmmer" version="@TOOL_VERSION@+galaxy1">
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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4 <description>iteratively search a protein sequence against a protein database (PSIBLAST-like)</description>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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5 <macros>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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6 <import>macros.xml</import>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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7 </macros>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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8 <expand macro="requirements"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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9 <expand macro="stdio"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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10 <command><![CDATA[
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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11 @ADDTHREADS@
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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12 =======
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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13 <tool id="hmmer_jackhmmer" name="jackhmmer" version="@TOOL_VERSION@">
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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14 <description>iteratively search a protein sequence against a protein database (PSIBLAST-like)</description>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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15 <expand macro="bio_tools"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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16 <macros>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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17 <import>macros.xml</import>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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18 </macros>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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19 <expand macro="requirements"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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20 <expand macro="stdio"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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21 <command><![CDATA[
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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22 >>>>>>> c37d72558 (add more bio.tool IDs)
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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23 jackhmmer
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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24 -N $N
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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25 @OFORMAT_WITH_OPTS@
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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26 @HSSI@
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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27 @THRESHOLDS@
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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28 @ACCEL_HEUR@
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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29 @ARSWS@
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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30 @AEEWS@
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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31 @PRIOR@
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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32
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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33 @EVAL_CALIB@
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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34 @ADV_OPTS@
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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35 @CPU@
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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36 @SEED@
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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37
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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38 '$seqfile'
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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39 '$seqdb'
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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40 > '$output'
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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41 ]]></command>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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42 <inputs>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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43 <param name="seqfile" type="data" format="fasta" label="Protein sequence to search with"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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44 <!-- todo use Galaxy features like data libraries/data tables/??? -->
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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45 <param name="N" type="integer" value="5" min="1" label="Maximum number of iterations" help="(-N)"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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46 <param name="seqdb" type="data" format="fasta" label="Sequence Database"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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47 <expand macro="oformat_with_opts_dom"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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48 <expand macro="hssi"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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49 <expand macro="thresholds_xml"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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50 <expand macro="accel_heur_xml"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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51 <expand macro="arsws"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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52 <expand macro="aeews"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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53 <expand macro="prior"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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54 <expand macro="eval_calib_xml"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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55 <expand macro="adv_opts"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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56 <expand macro="seed"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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57 </inputs>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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58 <outputs>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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59 <expand macro="output_dom_pfam" tool="JACKHMMER"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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60 </outputs>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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61 <tests>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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62 <test expect_num_outputs="3">
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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63 <param name="seqfile" value="uniprot_matches.fasta"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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64 <param name="seqdb" value="globins45.fa"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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65 <expand macro="oformat_test" />
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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66 <expand macro="seed_test" />
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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67 <output name="output" file="jackhmmer.out" lines_diff="180">
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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68 <expand macro="assert_out" tool="jackhmmer"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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69 </output>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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70 <output name="domtblout" file="jackhmmer.domtblout" lines_diff="10">
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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71 <expand macro="assert_tblout" tool="jackhmmer"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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72 </output>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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73 <output name="tblout" file="jackhmmer.tblout" lines_diff="10">
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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74 <expand macro="assert_tblout" tool="jackhmmer"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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75 </output>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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76 </test>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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77 <test expect_num_outputs="1">
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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78 <param name="seqfile" value="uniprot_matches.fasta"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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79 <param name="seqdb" value="globins45.fa"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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80 <expand macro="oformat_test" />
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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81 <param name="oformat" value=""/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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82 <expand macro="seed_test" />
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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83 <output name="output" file="jackhmmer.out" lines_diff="180">
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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84 <expand macro="assert_out" tool="jackhmmer"/>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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85 </output>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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86 </test>
273dda94efb2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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87 </tests>
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88 <help><![CDATA[
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89 @HELP_PRE@
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90
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91 jackhmmer iteratively searches each query sequence in <seqfile> against the
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92 target sequence(s) in <seqdb>. The first iteration is identical to a phmmer
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93 search. For the next iteration, a multiple alignment of the query together
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94 with all target sequences satisfying inclusion thresholds is assembled, a
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95 profile is constructed from this alignment (identical to using hmmbuild on the
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96 alignment), and profile search of the <seqdb> is done (identical to an
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97 hmmsearch with the profile).
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98
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99
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100 @HELP_PRE_OTH@
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101
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102 @OFORMAT_WITH_OPTS_HELP_NOPFAM@
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103 @HSSI_HELP@
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104 @THRESHOLDS_HELP@
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105 @ACCEL_HEUR_HELP@
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106 @ARSWS_HELP@
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107 @AEEWS_HELP@
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108 @PRIOR_HELP@
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109 @EVAL_CALIB_HELP@
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110 @ADV_OPTS_HELP@
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111 @SEED_HELP@
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112
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113 @ATTRIBUTION@
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114 ]]></help>
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115 <expand macro="citation"/>
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116 </tool>