Mercurial > repos > iuc > hmmer_hmmscan

annotate hmmscan.xml @ 8:63f1dd395c05 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit db615ae8a189ad988ec08090051a128355a4be70"
author iuc
date Thu, 14 Jan 2021 15:35:24 +0000
parents d02bc72e520b
children 98f5c06a4231
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1 <?xml version="1.0"?>
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2 <tool id="hmmer_hmmscan" name="hmmscan" version="@TOOL_VERSION@+galaxy1">
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3 <description>search protein sequence(s) against a protein profile database</description>
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4 <macros>
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5 <import>macros.xml</import>
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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 @ADDTHREADS@
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11 @INPUTHMMCHOICE@
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12 hmmscan
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14 @OFORMAT_WITH_OPTS@
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15 @THRESHOLDS@
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16 @CUT@
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17 @ACCEL_HEUR@
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18 @ADV_OPTS@
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19 @CPU@
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20 @SEED@
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21
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22 '$input_hmm_filename'
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23 '$seqfile'
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24 > '$output'
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25 ]]></command>
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26 <inputs>
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27 <expand macro="input_hmm_choice" />
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28 <!-- todo use Galaxy features like data libraries/data tables/??? -->
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29 <param name="seqfile" type="data" format="fasta" label="Sequence file"/>
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30 <expand macro="oformat_with_opts_dom_pfam"/>
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31 <expand macro="thresholds_xml"/>
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32 <expand macro="cut"/>
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33 <expand macro="accel_heur_xml"/>
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34 <expand macro="adv_opts"/>
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35 <expand macro="seed"/>
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36 </inputs>
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37 <outputs>
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38 <expand macro="output_dom_pfam" tool="HMMSCAN"/>
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39 </outputs>
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40 <tests>
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41 <test expect_num_outputs="4">
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42 <param name="input_hmm_conditional|input_hmm_source" value="history"/>
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43 <param name="input_hmm_conditional|hmmfile" value="MADE1.hmm"/>
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44 <param name="seqfile" value="dna_target.fa"/>
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45 <expand macro="oformat_test" />
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46 <expand macro="seed_test" />
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47 <output name="output" file="MADE1.out" lines_diff="24">
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48 <expand macro="assert_out" tool="hmmscan"/>
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49 </output>
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50 <output name="tblout" file="MADE1.out.tblout" lines_diff="14">
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51 <expand macro="assert_tblout" tool="hmmscan"/>
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52 </output>
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53 <output name="domtblout" file="MADE1.out.domtblout" lines_diff="10">
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54 <expand macro="assert_tblout" tool="hmmscan"/>
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55 </output>
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56 <output name="pfamtblout" file="MADE1.out.pfamtblout" lines_diff="10">
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57 <expand macro="assert_tblout" tool="hmmscan"/>
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58 </output>
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59 </test>
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60 </tests>
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61 <help><![CDATA[
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62 @HELP_PRE@
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63
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64 hmmscan is used to search protein sequences against collections of protein
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65 profiles. For each sequence in <seqfile>, use that query sequence to search the
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66 target database of profiles in <hmmfile>, and output ranked lists of the profiles
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67 with the most significant matches to the sequence.
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69 @HELP_PRE_OTH@
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70
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71 @OFORMAT_WITH_OPTS_HELP@
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72 @THRESHOLDS_HELP@
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73 @CUT_HELP@
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74 @ACCEL_HEUR_HELP@
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75 @ADV_OPTS_HELP@
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76 @SEED_HELP@
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78 @ATTRIBUTION@
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79 ]]></help>
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80 <expand macro="citation"/>
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81 </tool>