Mercurial > repos > peterjc > mira_assembler
annotate tools/mira_3_4/mira.xml @ 9:5573d802e431 draft
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| author | peterjc |
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| date | Wed, 18 Sep 2013 06:22:19 -0400 |
| parents | 4266cccbb45a |
| children |
| rev | line source |
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1 <tool id="mira_assembler" name="Assemble with MIRA v3.4" version="0.0.8"> |
| 8 | 2 <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description> |
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3 <requirements> |
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4 <requirement type="python-module">Bio</requirement> |
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5 <requirement type="binary">mira</requirement> |
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6 <requirement type="package" version="3.4.1.1">MIRA</requirement> |
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7 </requirements> |
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8 <version_command interpreter="python">mira.py -v</version_command> |
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9 <command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log |
| 8 | 10 ##Give the wrapper script list of output filenames, then the mira command... |
| 11 mira --job=$job_method,$job_type,$job_quality | |
| 12 | |
| 13 ##Input files | |
| 14 #if $condBackbone.use == "true": | |
| 15 ## Can this be linked to job_method as well? If mapping we need the backbone... | |
| 16 -SB:lb=1:bft=fasta -FN:bbin=${condBackbone.filename} | |
| 17 #end if | |
| 18 #if $condSanger.use == "true": | |
| 19 SANGER_SETTINGS | |
| 20 ## Not easy in Galaxy to add sanger to --job, so use load_sequence_data(lsd) instead | |
| 21 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file | |
| 22 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condSanger.filename} | |
| 23 #end if | |
| 24 #if $condRoche.use == "true": | |
| 25 454_SETTINGS | |
| 26 ## Not easy in Galaxy to add 454 to --job, so use load_sequence_data(lsd) instead | |
| 27 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file | |
| 28 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condRoche.filename} | |
| 29 #end if | |
| 30 #if $condIllumina.use == "true": | |
| 31 SOLEXA_SETTINGS | |
| 32 ## Not easy in Galaxy to add solexa to --job, so use load_sequence_data(lsd) instead | |
| 33 -LR:lsd=1:ft=fastq -FN:fqi=${condIllumina.filename} | |
| 34 ##TODO - Look at -LR FASTQ qual offset (fqqo) | |
| 35 #end if | |
| 36 #if $condIonTorrent.use == "true": | |
| 37 IONTOR_SETTINGS | |
| 38 ## Not easy in Galaxy to add iontor to --job, so use load_sequence_data(lsd) instead | |
| 39 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file | |
| 40 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condIonTorrent.filename} | |
| 41 #end if | |
| 42 | |
| 43 ##Output files | |
| 44 COMMON_SETTINGS | |
| 45 | |
| 46 ##ignore warnings about long read names | |
| 47 -MI:somrnl=0 | |
| 48 | |
| 49 ##Explicitly request the FASTA (+QUAL), CAF, ACE, WIG output | |
| 50 ##Explicitly disable formats we won't use like MAF (reduce IO) | |
| 51 -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0 | |
| 52 | |
| 53 ##remove_rollover_tmps, remove_tmp_directory | |
| 54 -OUT:rrot=1:rtd=1 | |
| 55 | |
| 56 ##put mira temp directory on local storage | |
| 57 -DI:trt=/tmp | |
| 58 | |
| 59 </command> | |
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60 <inputs> |
| 8 | 61 <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)"> |
| 62 <option value="denovo">De novo</option> | |
| 63 <option value="mapping">Mapping</option> | |
| 64 </param> | |
| 65 <param name="job_type" type="select" label="Assembly type"> | |
| 66 <option value="genome">Genome</option> | |
| 67 <option value="est">EST (transcriptome)</option> | |
| 68 </param> | |
| 69 <param name="job_quality" type="select" label="Assembly quality grade"> | |
| 70 <option value="accurate">Accurate</option> | |
| 71 <option value="normal">Normal (deprecated)</option> | |
| 72 <option value="draft">Draft</option> | |
| 73 </param> | |
| 74 <!-- Backbone --> | |
| 75 <conditional name="condBackbone"> | |
| 76 <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly."> | |
| 77 <option value="false">No</option> | |
| 78 <option value="true">Yes</option> | |
| 79 </param> | |
| 80 <when value="false" /> | |
| 81 <when value="true"> | |
| 82 <!-- MIRA also allows CAF and GenBank, but Galaxy doesn't define those (yet) --> | |
| 83 <param name="filename" type="data" format="fasta" label="Backbone/reference sequences" help="FASTA format" /> | |
| 84 </when> | |
| 85 </conditional> | |
| 86 <!-- Sanger --> | |
| 87 <conditional name="condSanger"> | |
| 88 <param name="use" type="select" label="Sanger/Capillary reads?"> | |
| 89 <option value="false">No</option> | |
| 90 <option value="true">Yes</option> | |
| 91 </param> | |
| 92 <when value="false" /> | |
| 93 <when value="true"> | |
| 94 <param name="filename" type="data" format="fastq" label="Sanger/Capillary reads file" help="FASTQ format" /> | |
| 95 </when> | |
| 96 </conditional> | |
| 97 <!-- Roche 454 --> | |
| 98 <conditional name="condRoche"> | |
| 99 <param name="use" type="select" label="454 reads?"> | |
| 100 <option value="false">No</option> | |
| 101 <option value="true">Yes</option> | |
| 102 </param> | |
| 103 <when value="false" /> | |
| 104 <when value="true"> | |
| 105 <!-- TODO? Support SFF files directly, e.g. with sff_extract, but will need linker sequences --> | |
| 106 <param name="filename" type="data" format="fastq" label="Roche 454 reads file" help="FASTQ format" /> | |
| 107 </when> | |
| 108 </conditional> | |
| 109 <!-- Illumina --> | |
| 110 <conditional name="condIllumina"> | |
| 111 <param name="use" type="select" label="Solexa/Illumina reads?"> | |
| 112 <option value="false">No</option> | |
| 113 <option value="true">Yes</option> | |
| 114 </param> | |
| 115 <when value="false" /> | |
| 116 <when value="true"> | |
| 117 <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" /> | |
| 118 </when> | |
| 119 </conditional> | |
| 120 <!-- Ion Torrent --> | |
| 121 <conditional name="condIonTorrent"> | |
| 122 <param name="use" type="select" label="Ion Torrent reads?"> | |
| 123 <option value="false">No</option> | |
| 124 <option value="true">Yes</option> | |
| 125 </param> | |
| 126 <when value="false" /> | |
| 127 <when value="true"> | |
| 128 <!-- TODO? Support SFF files directly, e.g. with sff_extract --> | |
| 129 <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" /> | |
| 130 </when> | |
| 131 </conditional> | |
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132 </inputs> |
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133 <outputs> |
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134 <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" /> |
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135 <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" /> |
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136 <data name="out_caf" format="txt" label="MIRA contigs (CAF)" /> |
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137 <data name="out_ace" format="txt" label="MIRA contigs (ACE)" /> |
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138 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" /> |
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139 <data name="out_log" format="txt" label="MIRA log" /> |
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140 </outputs> |
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141 <tests> |
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142 <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses |
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143 strain data and miraSearchESTSNPs. Here we just assemble it. --> |
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144 <!-- |
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145 Commenting out test until Galaxy framework is fixed, |
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146 https://trello.com/c/zSTrfDOB/820-disambiguated-conditional-parameters-not-supported-in-unit-tests |
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147 <test> |
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148 <param name="job_method" value="denovo" /> |
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149 <param name="job_type" value="est" /> |
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150 <param name="job_qual" value="accurate" /> |
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151 <param name="condBackbone.use" value="false" /> |
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152 <param name="condSanger.use" value="true" /> |
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153 <param name="condSanger.filename" value="tvc_mini.fastq" ftype="fastq" /> |
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154 <param name="condRoche.use" value="false" /> |
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155 <param name="condIllumina.use" value="false" /> |
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156 <param name="condIonTorrent.use" value="false" /> |
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157 <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" /> |
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158 </test> |
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159 --> |
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160 </tests> |
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161 <help> |
| 8 | 162 |
| 163 **What it does** | |
| 164 | |
| 165 Runs MIRA v3.4, collects the output, and throws away all the temporary files. | |
| 166 | |
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167 MIRA is an open source assembly tool capable of handling sequence data from |
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168 a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454 and also |
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169 Ion Torrent). |
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170 |
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171 It is particularly suited to small genomes such as bacteria. |
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172 |
| 8 | 173 **Citation** |
| 174 | |
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175 If you use this Galaxy tool in work leading to a scientific publication please |
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176 cite the following papers: |
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177 |
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178 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). |
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179 Galaxy tools and workflows for sequence analysis with applications |
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180 in molecular plant pathology. PeerJ 1:e167 |
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181 http://dx.doi.org/10.7717/peerj.167 |
| 8 | 182 |
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183 Chevreux et al. (1999). |
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184 Genome Sequence Assembly Using Trace Signals and Additional Sequence Information. |
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185 Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56. |
| 8 | 186 |
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187 This wrapper is available to install into other Galaxy Instances via the Galaxy |
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188 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler |
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189 |
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190 </help> |
| 8 | 191 </tool> |