Mercurial > repos > iuc > hmmer_hmmscan

annotate hmmscan.xml @ 3:4a09810b41ea draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
author iuc
date Mon, 14 Nov 2016 15:08:35 -0500
parents 6313ad2f168f
children 8e797aaf03fb
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1 <?xml version="1.0"?>
3
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2 <tool id="hmmer_hmmscan" name="hmmscan" version="@WRAPPER_VERSION@.1">
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3 <description>search sequence(s) against a 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[
3
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10 #if $input_hmm_conditional.input_hmm_source == "history":
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11 ## "Press" database
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12 hmmpress '$input_hmm_conditional.hmmfile' &&
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13 #end if
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14 ## Scan
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15 hmmscan
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16
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17 @OFORMAT_WITH_OPTS@
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18 @THRESHOLDS@
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19 @CUT@
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20 @ACCEL_HEUR@
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21 @ADV_OPTS@
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22 @CPU@
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23 @SEED@
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24
3
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25 @INPUTHMMCHOICE@
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26 '$seqfile'
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27 > '$output'
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28 #if $input_hmm_conditional.input_hmm_source == "history":
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29 ## Remove pressed database. Eventually will be replaced with a dedicated tool/datatype
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30 && rm '${input_hmm_conditional.hmmfile}.h3m' '${input_hmm_conditional.hmmfile}.h3i' '${input_hmm_conditional.hmmfile}.h3f' '${input_hmm_conditional.hmmfile}.h3p';
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31 #end if
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32 ]]></command>
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33 <inputs>
3
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34 <expand macro="input_hmm_choice" />
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35 <!-- todo use Galaxy features like data libraries/data tables/??? -->
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36 <param name="seqfile" type="data" format="fasta" label="Sequence file"/>
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37 <expand macro="oformat_with_opts"/>
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38 <expand macro="thresholds_xml"/>
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39 <expand macro="cut"/>
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40 <expand macro="accel_heur_xml"/>
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41 <expand macro="adv_opts"/>
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42 <expand macro="seed"/>
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43 </inputs>
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44 <outputs>
3
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45 <data format="txt" name="output" label="HMM matches of $seqfile.name against the profile database"/>
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46 <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name against the profile database">
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47 <filter>'tblout' in oformat</filter>
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48 </data>
3
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49 <data format="txt" name="domtblout" label="Table of per-domain hits from HMM matches of $seqfile.name against the profile database">
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50 <filter>'domtblout' in oformat</filter>
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51 </data>
3
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52 <data format="txt" name="pfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name against the profile database">
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53 <filter>'pfamtblout' in oformat</filter>
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54 </data>
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55 </outputs>
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56 <tests>
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57 <test>
3
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58 <param name="input_hmm_conditional|input_hmm_source" value="history"/>
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59 <param name="input_hmm_conditional|hmmfile" value="MADE1.hmm"/>
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60 <param name="seqfile" value="dna_target.fa"/>
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61 <expand macro="oformat_test" />
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62 <expand macro="seed_test" />
2
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63 <output name="output" file="MADE1.out" lines_diff="24"/>
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64 <output name="tblout" file="MADE1.out.tblout" lines_diff="20"/>
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65 <output name="domtblout" file="MADE1.out.domtblout" lines_diff="20"/>
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66 <output name="pfamtblout" file="MADE1.out.pfamtblout" lines_diff="20"/>
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67 </test>
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68 </tests>
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69 <help><![CDATA[
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70 @HELP_PRE@
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71
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72 hmmscan is used to search protein sequences against collections of protein
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73 profiles. For each sequence in <seqfile>, use that query sequence to search the
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74 target database of profiles in <hmmfile>, and output ranked lists of the profiles
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75 with the most significant matches to the sequence.
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76
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77 @HELP_PRE_OTH@
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78
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79 @OFORMAT_WITH_OPTS_HELP@
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80 @THRESHOLDS_HELP@
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81 @CUT_HELP@
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82 @ACCEL_HEUR_HELP@
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83 @ADV_OPTS_HELP@
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84 @SEED_HELP@
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85
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86 @ATTRIBUTION@
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
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87 ]]></help>
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
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88 <expand macro="citation"/>
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
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89 </tool>