Mercurial > repos > lecorguille > hmmer_hmmscan

annotate hmmscan.xml @ 0:8a93368dd5a5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
author lecorguille
date Tue, 01 Nov 2016 17:13:31 -0400
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0
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
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1 <?xml version="1.0"?>
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
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2 <tool id="hmmer_hmmscan" name="hmmscan" version="@WRAPPER_VERSION@.1">
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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3 <description>search sequence(s) against a profile database</description>
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
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4 <macros>
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5 <import>macros.xml</import>
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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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 #if $inputHmmConditional.inputHmmSource == "history":
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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11 ## "Press" database
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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12 hmmpress "$inputHmmConditional.hmmfile"
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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13 #end if
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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14 ## Scan
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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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
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25 @INPUTHMMCHOICE@
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26 $seqfile
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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27 > $output;
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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28 ## Remove pressed database. Eventually will be replaced with a dedicated tool/datatype
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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29 rm ${hmmfile}.h3m ${hmmfile}.h3i ${hmmfile}.h3f ${hmmfile}.h3p;
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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30 ]]></command>
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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31 <inputs>
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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32 <expand macro="input_hmm_choice" />
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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33 <!-- todo use Galaxy features like data libraries/data tables/??? -->
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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34 <param name="seqfile" type="data" format="fasta" label="Sequence file"/>
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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35 <expand macro="oformat_with_opts"/>
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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36 <expand macro="thresholds_xml"/>
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37 <expand macro="cut"/>
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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38 <expand macro="accel_heur_xml"/>
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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39 <expand macro="adv_opts"/>
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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40 <expand macro="seed"/>
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41 </inputs>
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42 <outputs>
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43 <data format="txt" name="output" label="HMM matches of $seqfile.name in $hmmfile.name"/>
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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44 <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name in $hmmfile.name">
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
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45 <filter>'tblout' in oformat</filter>
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46 </data>
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47 <data format="txt" name="domtblout" label="Table of per-domain hits from HMM matches of $seqfile.name in $hmmfile.name">
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48 <filter>'domtblout' in oformat</filter>
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49 </data>
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50 <data format="txt" name="pfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name in $hmmfile.name">
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51 <filter>'pfamtblout' in oformat</filter>
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52 </data>
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="hmmfile" value="MADE1.hmm"/>
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57 <param name="seqfile" value="dna_target.fa"/>
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58 <expand macro="oformat_test" />
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59 <expand macro="seed_test" />
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60 <output name="output" file="MADE1.out" lines_diff="24"/>
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61 <output name="tblout" file="MADE1.out.tblout" lines_diff="20"/>
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62 <output name="domtblout" file="MADE1.out.domtblout" lines_diff="20"/>
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63 <output name="pfamtblout" file="MADE1.out.pfamtblout" lines_diff="20"/>
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64 </test>
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65 </tests>
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66 <help><![CDATA[
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67 @HELP_PRE@
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68
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69 hmmscan is used to search protein sequences against collections of protein
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70 profiles. For each sequence in <seqfile>, use that query sequence to search the
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71 target database of profiles in <hmmfile>, and output ranked lists of the profiles
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72 with the most significant matches to the sequence.
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73
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74 @HELP_PRE_OTH@
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75
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76 @OFORMAT_WITH_OPTS_HELP@
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77 @THRESHOLDS_HELP@
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78 @CUT_HELP@
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79 @ACCEL_HEUR_HELP@
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80 @ADV_OPTS_HELP@
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81 @SEED_HELP@
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82
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83 @ATTRIBUTION@
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84 ]]></help>
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85 <expand macro="citation"/>
8a93368dd5a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 76281ba139c693f75a900a42c314e74d9649b0ef-dirty
lecorguille
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86 </tool>