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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit 7e41142050e4afb3d32570444c904a11b9d0c913
author jvolkening
date Fri, 23 Aug 2019 16:58:38 -0400
parents aa75dcf4cd74
children
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aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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1 <tool id="mira3" name="MIRA Assembler v3" version="3.4.1.1">
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2
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3 <description>Assemble short/long/hybrid reads using MIRA 3.4</description>
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5 <!-- ***************************************************************** -->
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7 <requirements>
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8 <requirement type="package" version="3.4.1.1">mira</requirement>
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9 </requirements>
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11 <!-- ***************************************************************** -->
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aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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13 <version_command>mira --version | perl -wnE'print "$1\n" for /This is MIRA V([\d\.]+)/g'</version_command>
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aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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15 <!-- ***************************************************************** -->
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17 <command detect_errors="aggressive">
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18 <![CDATA[
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aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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20 mira
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21 --project=mira
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22 --job=$job_method,$job_type,$job_quality
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23 -GE:not="\${GALAXY_SLOTS:-1}"
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24 #if $condBackbone.use == "true":
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25 ## Can this be linked to job_method as well? If mapping we need the backbone...
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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26 -SB:lb=1:bft=fasta -FN:bbin=${condBackbone.filename}
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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27 #end if
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28 #if $condSanger.use == "true":
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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29 SANGER_SETTINGS
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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30 ## Not easy in Galaxy to add sanger to --job, so use load_sequence_data(lsd) instead
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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31 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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32 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condSanger.filename}
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33 ${condSanger.sanger_extra}
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34 #end if
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35 #if $condRoche.use == "true":
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36 454_SETTINGS
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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37 ## Not easy in Galaxy to add 454 to --job, so use load_sequence_data(lsd) instead
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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38 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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39 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condRoche.filename}
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40 ${condRoche.roche_extra}
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41 #end if
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42 #if $condIllumina.use == "true":
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43 SOLEXA_SETTINGS
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44 ## Not easy in Galaxy to add solexa to --job, so use load_sequence_data(lsd) instead
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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45 -LR:lsd=1:ft=fastq -FN:fqi=${condIllumina.filename}
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46 ${condIllumina.solexa_extra}
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47 ##TODO - Look at -LR FASTQ qual offset (fqqo)
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48 #end if
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49 #if $condIonTorrent.use == "true":
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50 IONTOR_SETTINGS
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51 ## Not easy in Galaxy to add iontor to --job, so use load_sequence_data(lsd) instead
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52 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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53 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condIonTorrent.filename}
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54 ${condIonTorrent.torrent_extra}
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55 #end if
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56
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57 COMMON_SETTINGS
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58 $common_extra
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59
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60 ##ignore warnings about long read names
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61 -MI:somrnl=0
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62
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63 ##Explicitly request the FASTA (+QUAL), CAF, ACE, WIG output
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64 ##Explicitly disable formats we won't use like MAF (reduce IO)
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65 -OUT:orf=$output_fasta:orc=$output_caf:ora=$output_ace:orw=$output_wig:orm=0:org=0:ors=0
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66
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67 ##remove_rollover_tmps, remove_tmp_directory
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68 -OUT:rrot=1:rtd=1
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69
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70 ##put mira temp directory on local storage
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71 ##NO, must run from NFS or problems with multiple jobs/same name can arise
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72 ##-DI:trt=/tmp
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73 -MI:sonfs=no
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74 ]]>
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75 </command>
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76
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77 <!-- ***************************************************************** -->
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78
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79 <inputs>
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80 <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)">
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81 <option value="denovo">De novo</option>
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82 <option value="mapping">Mapping</option>
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83 </param>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
84 <param name="job_type" type="select" label="Assembly type">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
85 <option value="genome">Genome</option>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
86 <option value="est">EST (transcriptome)</option>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
87 </param>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
88 <param name="job_quality" type="select" label="Assembly quality grade">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
89 <option value="accurate">Accurate</option>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
90 <option value="normal">Normal (deprecated)</option>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
91 <option value="draft">Draft</option>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
92 </param>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
93 <!-- Backbone -->
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
94 <conditional name="condBackbone">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
95 <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly.">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
96 <option value="false">No</option>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
97 <option value="true">Yes</option>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
98 </param>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
99 <when value="false" />
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
100 <when value="true">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
101 <!-- MIRA also allows CAF and GenBank, but Galaxy doesn't define those (yet) -->
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
102 <param name="filename" type="data" format="fasta" label="Backbone/reference sequences" help="FASTA format" />
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
103 </when>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
104 </conditional>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
105 <!-- Sanger -->
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
106 <conditional name="condSanger">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
107 <param name="use" type="select" label="Sanger/Capillary reads?">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
108 <option value="false">No</option>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
109 <option value="true">Yes</option>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
110 </param>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
111 <when value="false" />
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
112 <when value="true">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
113 <param name="filename" type="data" format="fastq" label="Sanger/Capillary reads file" help="FASTQ format" />
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
114 <param name="sanger_extra" type="text" size="100" value="" label="extra Sanger parameters for MIRA">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
115 <sanitizer invalid_char="">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
116 <valid initial=",string.letters,string.digits">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
117 <add value=" " />
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
118 <add value="-" />
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
119 <add value=":" />
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
120 <add value="=" />
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
121 </valid>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
122 </sanitizer>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
123 </param>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
124 </when>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
125 </conditional>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
126 <!-- Roche 454 -->
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
127 <conditional name="condRoche">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
128 <param name="use" type="select" label="454 reads?">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
129 <option value="false">No</option>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
130 <option value="true">Yes</option>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
131 </param>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
132 <when value="false" />
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
133 <when value="true">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
134 <!-- TODO? Support SFF files directly, e.g. with sff_extract, but will need linker sequences -->
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
135 <param name="filename" type="data" format="fastq" label="Roche 454 reads file" help="FASTQ format" />
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
136 <param name="roche_extra" type="text" size="100" value="" label="extra 454 parameters for MIRA">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
137 <sanitizer invalid_char="">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
138 <valid initial=",string.letters,string.digits">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
139 <add value=" " />
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
140 <add value="-" />
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
141 <add value=":" />
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
142 <add value="=" />
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
143 </valid>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
144 </sanitizer>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
145 </param>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
146 </when>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
147 </conditional>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
148 <!-- Illumina -->
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
149 <conditional name="condIllumina">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
150 <param name="use" type="select" label="Solexa/Illumina reads?">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
151 <option value="false">No</option>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
152 <option value="true">Yes</option>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
153 </param>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
154 <when value="false" />
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
155 <when value="true">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
156 <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" />
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
157 <param name="solexa_extra" type="text" size="100" value="-DP:ure=yes -AS:mrpc=100 -AL:mo=16" label="extra Illumina parameters for MIRA">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
158 <sanitizer invalid_char="">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
159 <valid initial=",string.letters,string.digits">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
160 <add value=" " />
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
161 <add value="-" />
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
162 <add value=":" />
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
163 <add value="=" />
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
164 </valid>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
165 </sanitizer>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
166 </param>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
167 </when>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
168 </conditional>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
jvolkening
parents:
diff changeset
169 <!-- Ion Torrent -->
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170 <conditional name="condIonTorrent">
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171 <param name="use" type="select" label="Ion Torrent reads?">
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172 <option value="false">No</option>
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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173 <option value="true">Yes</option>
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174 </param>
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175 <when value="false" />
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176 <when value="true">
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177 <!-- TODO? Support SFF files directly, e.g. with sff_extract -->
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178 <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" />
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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179 <param name="torrent_extra" type="text" size="100" value="" label="extra IonTorrent parameters for MIRA">
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180 <sanitizer invalid_char="">
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181 <valid initial=",string.letters,string.digits">
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182 <add value=" " />
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183 <add value="-" />
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184 <add value=":" />
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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185 <add value="=" />
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186 </valid>
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187 </sanitizer>
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188 </param>
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189 </when>
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190 </conditional>
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191 <param name="common_extra" type="text" size="100" value="-CO:mr=yes:mroir=no:asir=yes -SK:mnr=no:mmhr=.2 -AS:urd=no:ard=no:sd=yes:sdlpo=no" label="extra common parameters for MIRA">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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192 <sanitizer invalid_char="">
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193 <valid initial=",string.letters,string.digits">
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194 <add value=" " />
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195 <add value="-" />
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196 <add value=":" />
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197 <add value="=" />
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198 </valid>
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199 </sanitizer>
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200 </param>
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201 <param name="output_fasta" type="boolean" truevalue="1" falsevalue="0" checked="yes" label="Output FASTA" />
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202 <param name="output_caf" type="boolean" truevalue="1" falsevalue="0" checked="0" label="Output CAF" />
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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203 <param name="output_ace" type="boolean" truevalue="1" falsevalue="0" checked="0" label="Output ACE" />
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204 <param name="output_wig" type="boolean" truevalue="1" falsevalue="0" checked="0" label="Output WIG" />
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205 </inputs>
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206
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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207 <!-- ***************************************************************** -->
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208
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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209 <outputs>
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210 <data name="out_log" format="txt" label="MIRA log" from_work_dir="mira_assembly/mira_d_info/mira_info_assembly.txt" />
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211 <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" from_work_dir="mira_assembly/mira_d_results/mira_out.unpadded.fasta">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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212 <filter>output_fasta is True</filter>
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213 </data>
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214 <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" from_work_dir="mira_assembly/mira_d_results/mira_out.unpadded.fasta.qual">
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215 <filter>output_fasta is True</filter>
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216 </data>
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217 <data name="out_caf" format="txt" label="MIRA contigs (CAF)" from_work_dir="mira_assembly/mira_d_results/mira_out.caf" >
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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218 <filter>output_caf is True</filter>
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219 </data>
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220 <data name="out_ace" format="txt" label="MIRA contigs (ACE)" from_work_dir="mira_assembly/mira_d_results/mira_out.ace">
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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221 <filter>output_ace is True</filter>
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222 </data>
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223 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" from_work_dir="mira_assembly/mira_d_results/mira_out.wig">
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224 <filter>output_wig is True</filter>
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225 </data>
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226 </outputs>
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227
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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228 <!-- ***************************************************************** -->
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229
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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230 <tests>
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231 <test>
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232 <param name="job_method" value="denovo" />
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233 <param name="job_type" value="est" />
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234 <param name="job_qual" value="accurate" />
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235 <param name="condBackbone|use" value="false" />
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236 <param name="condSanger|use" value="true" />
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237 <param name="condSanger|filename" value="tvc_mini.fastq" ftype="fastq" />
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238 <param name="condRoche|use" value="false" />
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239 <param name="condIllumina|use" value="false" />
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240 <param name="condIonTorrent|use" value="false" />
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241 <param name="output_fasta" value="true" />
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242 <param name="output_caf" value="false" />
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243 <param name="output_ace" value="false" />
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244 <param name="output_wig" value="false" />
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245 <param name="common_extra" value="" />
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246 <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" />
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247 </test>
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248 </tests>
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249
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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250 <!-- ***************************************************************** -->
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251
aa75dcf4cd74 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
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252 <help>
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253
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254 **What it does**
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255
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256 Runs MIRA v3.4, collects the output, and throws away all the temporary files.
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257
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258 MIRA is an open source assembly tool capable of handling sequence data from
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259 a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454 and also
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260 Ion Torrent).
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261
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262 It is particularly suited to small genomes such as bacteria.
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263
1
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264 **Citation**
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265
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266 This tool was forked from the original by Peter J. Cock:
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267
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268 http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
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269
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270 https://github.com/peterjc/galaxy_mira/tree/master/tools/mira3
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271
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272
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273 If you use this Galaxy tool in work leading to a scientific publication please
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274 cite the following papers:
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275
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276 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
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277 Galaxy tools and workflows for sequence analysis with applications
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278 in molecular plant pathology. PeerJ 1:e167
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279 https://doi.org/10.7717/peerj.167
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280
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281 Bastien Chevreux, Thomas Wetter and Sándor Suhai (1999).
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282 Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.
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283 Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
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284 http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html
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285
0
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286 </help>
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287
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288 <!-- ***************************************************************** -->
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289
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290 <citations>
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291 <citation type="doi">10.7717/peerj.167</citation>
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292 <citation type="bibtex">@ARTICLE{Chevreux1999-mira3,
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293 author = {B. Chevreux and T. Wetter and S. Suhai},
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294 year = {1999},
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295 title = {Genome Sequence Assembly Using Trace Signals and Additional Sequence Information},
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296 journal = {Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB)}
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297 volume = {99},
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298 pages = {45-56},
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299 url = {http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html}
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300 }</citation>
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301 </citations>
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302
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303 </tool>