Mercurial > repos > peterjc > mira4_assembler
annotate tools/mira4/mira4_mapping.xml @ 4:df86ed992a1b draft
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| author | peterjc |
|---|---|
| date | Fri, 11 Oct 2013 04:28:45 -0400 |
| parents | 32f693f6e741 |
| children | ffefb87bd414 |
| rev | line source |
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1 <tool id="mira_4_0_mapping" name="MIRA v4.0 mapping" version="0.0.1"> |
| 4 | 2 <description>Maps Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</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="4.0">MIRA</requirement> |
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7 </requirements> |
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8 <version_command interpreter="python">mira4.py -v</version_command> |
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9 <command interpreter="python"> |
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10 mira4.py $manifest $out_maf $out_fasta $out_log |
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11 </command> |
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12 <inputs> |
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13 <param name="job_type" type="select" label="Assembly type"> |
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14 <option value="genome">Genome</option> |
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15 <option value="est">EST (transcriptome)</option> |
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16 </param> |
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17 <param name="job_quality" type="select" label="Assembly quality grade"> |
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18 <option value="accurate">Accurate</option> |
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19 <option value="draft">Draft</option> |
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20 </param> |
| 4 | 21 <!-- TODO? Allow technology type for references? --> |
| 22 <!-- TODO? Allow strain settings for reference(s) and reads? --> | |
| 23 <!-- TODO? Use a repeat to allow for multi-strain references? --> | |
| 24 <!-- TODO? Add strain to the mapping read groups? --> | |
| 25 <param name="references" type="data" format="fasta,fastq,mira" multiple="true" required="true" label="Backbone reference file(s)" | |
| 26 help="Multiple files allowed, for example one FASTA file per chromosome or plasmid." /> | |
| 27 <param name="strain_setup" type="select" label="Strain configuration (reference vs reads)"> | |
| 28 <option value="default">Different strains - mapping reads onto a related reference ('StrainX' vs 'ReferenceStrain')</option> | |
| 29 <option value="same">Same strain - mapping reads from same reference (all 'StrainX')</option> | |
| 30 </param> | |
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31 <repeat name="read_group" title="Read Group" min="1"> |
| 4 | 32 <param name="technology" type="select" label="Read technology"> |
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33 <option value="solexa">Solexa/Illumina</option> |
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34 <option value="sanger">Sanger cappillary sequencing</option> |
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35 <option value="454">Roche 454</option> |
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36 <option value="iontor">Ion Torrent</option> |
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37 <option value="pcbiolq">PacBio low quality (raw)</option> |
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38 <option value="pcbiohq">PacBio high quality (corrected)</option> |
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39 <option value="text">Synthetic reads (database entries, consensus sequences, artifical reads, etc)</option> |
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40 </param> |
| 4 | 41 <param name="filenames" type="data" format="fastq,mira" multiple="true" required="true" label="Read file(s)" |
| 42 help="Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs)." /> | |
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43 </repeat> |
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44 </inputs> |
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45 <outputs> |
| 4 | 46 <data name="out_fasta" format="fasta" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping contigs (FASTA)" /> |
| 47 <data name="out_maf" format="mira" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping assembly" /> | |
| 48 <data name="out_log" format="txt" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping log" /> | |
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49 </outputs> |
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50 <configfiles> |
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51 <configfile name="manifest"> |
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52 project = MIRA |
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53 job = mapping,${job_type},${job_quality} |
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54 parameters = -GE:not=1 -NW:cmrnl -DI:trt=/tmp |
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55 ## -GE:not is short for -GENERAL:number_of_threads and using one (1) |
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56 ## can be useful for repeatability of assemblies and bug hunting. |
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57 ## |
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58 ## -NW:cmrnl is short for -NAG_AND_WARN:check_maxreadnamelength |
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59 ## and without this MIRA aborts with read names over 40 characters |
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60 ## due to limitations of some downstream tools. |
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61 ## |
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62 ## -DI:trt is short for -DIRECTORY:tmp_redirected_to and should |
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63 ## point to a local hard drive (not something like NFS on network). |
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64 |
| 4 | 65 ##This bar goes into the manifest as a comment line |
| 66 #------------------------------------------------------------------------------ | |
| 67 | |
| 68 readgroup | |
| 69 is_reference | |
| 70 #if str($strain_setup)=="same" | |
| 71 strain = StrainX | |
| 72 #end if | |
| 73 #for $f in $references | |
| 74 ##Must now map Galaxy datatypes to MIRA file types... | |
| 75 #if $f.ext.startswith("fastq") | |
| 76 ##MIRA doesn't like fastqsanger etc, just plain old fastq: | |
| 77 data = fastq::$f | |
| 78 #elif $f.ext == "mira" | |
| 79 ##We're calling *.maf the "mira" format in Galaxy (name space collision) | |
| 80 data = maf::$f | |
| 81 #elif $f.ext == "fasta" | |
| 82 ##We're calling MIRA with the file type as "fna" as otherwise it wants quals | |
| 83 data = fna::$f | |
| 84 #else | |
| 85 ##Currently don't expect anything else... | |
| 86 data = ${f.ext}::$f | |
| 87 #end if | |
| 88 #end for | |
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89 #for $rg in $read_group |
| 4 | 90 |
| 91 ##This bar goes into the manifest as a comment line | |
| 92 #------------------------------------------------------------------------------ | |
| 93 | |
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94 readgroup |
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95 technology = ${rg.technology} |
| 4 | 96 #if str($strain_setup)=="same" |
| 97 ##This is perhaps redundant as MIRA defaults to StrainX for the reads: | |
| 98 strain = StrainX | |
| 99 #end if | |
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100 ##MIRA will accept multiple filenames on one data line, or multiple data lines |
| 4 | 101 #for $f in $rg.filenames |
| 102 ##Must now map Galaxy datatypes to MIRA file types... | |
| 103 #if $f.ext.startswith("fastq") | |
| 104 ##MIRA doesn't like fastqsanger etc, just plain old fastq: | |
| 105 data = fastq::$f | |
| 106 #elif $f.ext == "mira" | |
| 107 ##We're calling *.maf the "mira" format in Galaxy (name space collision) | |
| 108 data = maf::$f | |
| 109 #else | |
| 110 ##Currently don't expect anything else... | |
| 111 data = ${f.ext}::$f | |
| 112 #end if | |
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113 #end for |
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114 #end for |
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115 </configfile> |
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116 </configfiles> |
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117 <tests> |
| 4 | 118 <!-- Deliberately using default read_group.technology value "solexa" |
| 119 as then Galaxy's broken <repeat> handling in tests should work... --> | |
| 120 <!-- Tests currently failing, | |
| 121 TwillException: more than one form; you must select one (use 'fv') before submitting | |
| 122 <test> | |
| 123 <param name="job_type" value="genome" /> | |
| 124 <param name="job_quality" value="accurate" /> | |
| 125 <param name="references" value="tvc_contigs.fasta" ftype="fasta" /> | |
| 126 <param name="strain_setup" value="default" /> | |
| 127 <param name="filenames" value="tvc_mini.fastq" ftype="fastqsanger" /> | |
| 128 <output name="out_fasta" file="tvc_map_same_strain.fasta" ftype="fasta" /> | |
| 129 </test> | |
| 130 <test> | |
| 131 <param name="job_type" value="genome" /> | |
| 132 <param name="job_quality" value="accurate" /> | |
| 133 <param name="references" value="tvc_contigs.fasta" ftype="fasta" /> | |
| 134 <param name="strain_setup" value="same" /> | |
| 135 <param name="filenames" value="tvc_mini.fastq" ftype="fastqsanger" /> | |
| 136 <output name="out_fasta" file="tvc_map_ref_strain.fasta" ftype="fasta" /> | |
| 137 </test> | |
| 138 --> | |
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139 </tests> |
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140 <help> |
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141 |
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142 **What it does** |
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143 |
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144 Runs MIRA v4.0 in mapping mode, collects the output, and throws away all the temporary files. |
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145 |
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146 MIRA is an open source assembly tool capable of handling sequence data from |
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147 a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454, Ion Torrent |
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148 and also PacBio). |
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149 |
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150 It is particularly suited to small genomes such as bacteria. |
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151 |
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152 **Citation** |
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153 |
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154 If you use this Galaxy tool in work leading to a scientific publication please |
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155 cite the following papers: |
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156 |
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157 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). |
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158 Galaxy tools and workflows for sequence analysis with applications |
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159 in molecular plant pathology. PeerJ 1:e167 |
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160 http://dx.doi.org/10.7717/peerj.167 |
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161 |
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162 Bastien Chevreux, Thomas Wetter and Sándor Suhai (1999). |
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163 Genome Sequence Assembly Using Trace Signals and Additional Sequence Information. |
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164 Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56. |
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165 http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html |
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166 |
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167 This wrapper is available to install into other Galaxy Instances via the Galaxy |
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168 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler |
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169 </help> |
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170 </tool> |