Mercurial > repos > peterjc > mira4_assembler
annotate tools/mira4_0/mira4_mapping.xml @ 37:eeeb21870a73 draft
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit ee574302295ee1e835b8f7315f6634d6f41ab461
| author | peterjc |
|---|---|
| date | Thu, 31 May 2018 04:30:47 -0400 |
| parents | 259891fce7fd |
| children |
| rev | line source |
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259891fce7fd
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
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1 <tool id="mira_4_0_mapping" name="MIRA v4.0 mapping" version="0.0.11"> |
| 25 | 2 <description>Maps Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description> |
| 3 <requirements> | |
| 4 <requirement type="package" version="4.0.2">MIRA</requirement> | |
| 5 <requirement type="package" version="0.1.19">samtools</requirement> | |
| 6 </requirements> | |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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7 <version_command> |
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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8 python $__tool_directory__/mira4.py --version |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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9 </version_command> |
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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10 <command detect_errors="aggressive"> |
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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11 python $__tool_directory__/mira4.py |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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12 --manifest '$manifest' |
| 25 | 13 #if str($maf_wanted) == "true": |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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14 --maf '$out_maf' |
| 25 | 15 #end if |
| 16 #if str($bam_wanted) == "true": | |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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17 --bam '$out_bam' |
| 25 | 18 #end if |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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19 --fasta '$out_fasta' |
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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20 --log '$out_log' |
| 25 | 21 </command> |
| 22 <configfiles> | |
| 23 <configfile name="manifest"> | |
| 24 project = MIRA | |
| 25 job = mapping,${job_type},${job_quality} | |
| 26 parameters = -NW:cmrnl=no -DI:trt=/tmp -OUT:orc=no | |
| 27 ## -GE:not is short for -GENERAL:number_of_threads and using one (1) | |
| 28 ## can be useful for repeatability of assemblies and bug hunting. | |
| 29 ## This is overriden by the command line -t switch which is easier | |
| 30 ## to set from within Galaxy. | |
| 31 ## | |
| 32 ## -NW:cmrnl is short for -NAG_AND_WARN:check_maxreadnamelength | |
| 33 ## and without this MIRA aborts with read names over 40 characters | |
| 34 ## due to limitations of some downstream tools. | |
| 35 ## | |
| 36 ## -DI:trt is short for -DIRECTORY:tmp_redirected_to and should | |
| 37 ## point to a local hard drive (not something like NFS on network). | |
| 38 ## We replace /tmp with an environment variable via mira4.py | |
| 39 ## | |
| 40 ## -OUT:orc=no is short for -OUTPUT:output_result_caf=no | |
| 41 ## which turns off an output file we don't want anyway. | |
| 42 | |
| 43 ##This bar goes into the manifest as a comment line | |
| 44 #------------------------------------------------------------------------------ | |
| 45 | |
| 46 readgroup | |
| 47 is_reference | |
| 48 #if str($strain_setup)=="same" | |
| 49 strain = StrainX | |
| 50 #end if | |
| 51 #for $f in $references | |
| 52 ##Must now map Galaxy datatypes to MIRA file types... | |
| 53 #if $f.ext.startswith("fastq") | |
| 54 ##MIRA doesn't like fastqsanger etc, just plain old fastq: | |
| 55 data = fastq::$f | |
| 56 #elif $f.ext == "mira" | |
| 57 ##We're calling *.maf the "mira" format in Galaxy (name space collision) | |
| 58 data = maf::$f | |
| 59 #elif $f.ext == "fasta" | |
| 60 ##We're calling MIRA with the file type as "fna" as otherwise it wants quals | |
| 61 data = fna::$f | |
| 62 #else | |
| 63 ##Currently don't expect anything else... | |
| 64 data = ${f.ext}::$f | |
| 65 #end if | |
| 66 #end for | |
| 67 #for $rg in $read_group | |
| 68 | |
| 69 ##This bar goes into the manifest as a comment line | |
| 70 #------------------------------------------------------------------------------ | |
| 71 | |
| 72 readgroup | |
| 73 technology = ${rg.technology} | |
| 74 #if str($strain_setup)=="same" | |
| 75 ##This is perhaps redundant as MIRA defaults to StrainX for the reads: | |
| 76 strain = StrainX | |
| 77 #end if | |
| 78 ##Record the segment placement (if any) | |
| 79 #if str($rg.segments.type) == "paired" | |
| 80 segment_placement = ${rg.segments.placement} | |
| 81 segment_naming = ${rg.segments.naming} | |
| 82 #end if | |
| 83 ##if str($rg.segments.type) == "none" | |
| 84 ##MIRA4 manual says use segment_placement = unknown or ? for unpaired data | |
| 85 ##but this stopped working in MIRA 4.0 RC5 and 4.0 (final). See: | |
| 86 ##http://www.freelists.org/post/mira_talk/Unpaired-reads-and-segment-placement--or-unknown | |
| 87 ##segment_placement = ? | |
| 88 ##end if | |
| 89 ##MIRA will accept multiple filenames on one data line, or multiple data lines | |
| 90 #for $f in $rg.filenames | |
| 91 ##Must now map Galaxy datatypes to MIRA file types... | |
| 92 #if $f.ext.startswith("fastq") | |
| 93 ##MIRA doesn't like fastqsanger etc, just plain old fastq: | |
| 94 data = fastq::$f | |
| 95 #elif $f.ext == "mira" | |
| 96 ##We're calling *.maf the "mira" format in Galaxy (name space collision) | |
| 97 data = maf::$f | |
| 98 #else | |
| 99 ##Currently don't expect anything else... | |
| 100 data = ${f.ext}::$f | |
| 101 #end if | |
| 102 #end for | |
| 103 #end for | |
| 104 </configfile> | |
| 105 </configfiles> | |
| 106 <inputs> | |
| 107 <param name="job_type" type="select" label="Assembly type"> | |
| 108 <option value="genome">Genome</option> | |
| 109 <option value="est">EST (transcriptome)</option> | |
| 110 </param> | |
| 111 <param name="job_quality" type="select" label="Assembly quality grade"> | |
| 112 <option value="accurate">Accurate</option> | |
| 113 <option value="draft">Draft</option> | |
| 114 </param> | |
| 115 <!-- TODO? Allow technology type for references? --> | |
| 116 <!-- TODO? Allow strain settings for reference(s) and reads? --> | |
| 117 <!-- TODO? Use a repeat to allow for multi-strain references? --> | |
| 118 <!-- TODO? Add strain to the mapping read groups? --> | |
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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119 <param name="references" type="data" format="fasta,fastq,mira" multiple="true" optional="false" label="Backbone reference file(s)" |
| 25 | 120 help="Multiple files allowed, for example one FASTA file per chromosome or plasmid." /> |
| 121 <param name="strain_setup" type="select" label="Strain configuration (reference vs reads)"> | |
| 122 <option value="default">Different strains - mapping reads onto a related reference ('StrainX' vs 'ReferenceStrain')</option> | |
| 123 <option value="same">Same strain - mapping reads from same reference (all 'StrainX')</option> | |
| 124 </param> | |
| 125 <repeat name="read_group" title="Read Group" min="1"> | |
| 126 <param name="technology" type="select" label="Read technology"> | |
| 127 <option value="solexa">Solexa/Illumina</option> | |
| 128 <option value="sanger">Sanger cappillary sequencing</option> | |
| 129 <option value="454">Roche 454</option> | |
| 130 <option value="iontor">Ion Torrent</option> | |
| 131 <option value="pcbiolq">PacBio low quality (raw)</option> | |
| 132 <option value="pcbiohq">PacBio high quality (corrected)</option> | |
| 133 <option value="text">Synthetic reads (database entries, consensus sequences, artifical reads, etc)</option> | |
| 134 </param> | |
| 135 <conditional name="segments"> | |
| 136 <param name="type" type="select" label="Are these paired reads?"> | |
| 137 <option value="paired">Paired reads</option> | |
| 138 <option value="none">Single reads or not relevant (e.g. primer walking with Sanger capillary sequencing)</option> | |
| 139 </param> | |
| 140 <when value="paired"> | |
| 141 <param name="placement" type="select" label="Pairing type (segment placing)"> | |
| 142 <option value="FR">---> <--- (e.g. Sanger capillary or Solexa/Illumina paired-end library)</option> | |
| 143 <option value="RF"><--- ---> (e.g. Solexa/Illumina mate-pair library)</option> | |
| 144 <option value="SB">2---> 1---> (e.g. Roche 454 paired-end libraries or IonTorrent long-mate; see note)</option> | |
| 145 </param> | |
| 146 <param name="naming" type="select" label="Pair naming convention"> | |
| 147 <option value="solexa">Solexa/Illumina (using '/1' and '/2' suffixes, or later Illumina colon system)</option> | |
| 148 <option value="FR">Forward/Reverse scheme (using '.f*' and '.r*' suffixes)</option> | |
| 149 <option value="tigr">TIGR scheme (using 'TF*' and 'TR*' suffixes)</option> | |
| 150 <option value="sanger">Sanger scheme (see notes)</option> | |
| 151 <option value="stlouis">St. Louis scheme (see notes)</option> | |
| 152 </param> | |
| 153 </when> | |
| 154 <when value="none" /><!-- no further questions --> | |
| 155 </conditional> | |
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56b421d59805
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6
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156 <param name="filenames" type="data" format="fastq,mira" multiple="true" optional="false" label="Read file(s)" |
| 25 | 157 help="Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs)." /> |
| 158 </repeat> | |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 1d7d466d01b23d03d214e93f1f8efa19cfa18268
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159 <param name="maf_wanted" type="boolean" label="Output mapping in MIRA's own format?" checked="false" /> |
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1291ed21789f
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 1d7d466d01b23d03d214e93f1f8efa19cfa18268
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160 <param name="bam_wanted" type="boolean" label="Convert mapping into BAM format?" checked="true" /> |
| 25 | 161 </inputs> |
| 162 <outputs> | |
| 163 <data name="out_fasta" format="fasta" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping contigs (FASTA)" /> | |
| 164 <data name="out_bam" format="bam" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping assembly (BAM)"> | |
| 165 <filter>bam_wanted is True</filter> | |
| 166 </data> | |
| 167 <data name="out_maf" format="mira" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping assembly"> | |
| 168 <filter>maf_wanted is True</filter> | |
| 169 </data> | |
| 170 <data name="out_log" format="txt" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping log" /> | |
| 171 </outputs> | |
| 172 <tests> | |
| 173 <test> | |
| 174 <param name="job_type" value="genome" /> | |
| 175 <param name="job_quality" value="accurate" /> | |
| 176 <param name="references" value="tvc_contigs.fasta" ftype="fasta" /> | |
| 177 <param name="strain_setup" value="default" /> | |
| 178 <param name="type" value="none" /> | |
| 179 <param name="filenames" value="tvc_mini.fastq" ftype="fastqsanger" /> | |
| 180 <param name="maf_wanted" value="true"/> | |
| 181 <param name="bam_wanted" value="true"/> | |
| 182 <output name="out_fasta" file="tvc_map_ref_strain.fasta" ftype="fasta" /> | |
| 183 <output name="out_bam" file="empty_file.dat" compare="contains" /> | |
| 184 <!-- TODO: Suggest startswith as a compare method? --> | |
| 185 <output name="out_maf" file="header.mira" compare="contains" /> | |
| 186 <output name="out_log" file="empty_file.dat" compare="contains" /> | |
| 187 </test> | |
| 188 <test> | |
| 189 <param name="job_type" value="genome" /> | |
| 190 <param name="job_quality" value="accurate" /> | |
| 191 <param name="references" value="tvc_contigs.fasta" ftype="fasta" /> | |
| 192 <param name="strain_setup" value="same" /> | |
| 193 <param name="type" value="none" /> | |
| 194 <param name="filenames" value="tvc_mini.fastq" ftype="fastqsanger" /> | |
| 195 <param name="maf_wanted" value="false"/> | |
| 196 <param name="bam_wanted" value="false"/> | |
| 197 <output name="out_fasta" file="tvc_map_same_strain.fasta" ftype="fasta" /> | |
| 198 <output name="out_log" file="empty_file.dat" compare="contains" /> | |
| 199 </test> | |
| 200 </tests> | |
| 201 <help> | |
| 202 | |
| 203 **What it does** | |
| 204 | |
| 205 Runs MIRA v4.0 in mapping mode, collects the output, generates a sorted BAM | |
| 206 file, and throws away all the temporary files. | |
| 207 | |
| 208 MIRA is an open source assembly tool capable of handling sequence data from | |
| 209 a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454, Ion Torrent | |
| 210 and also PacBio). | |
| 211 | |
| 212 It is particularly suited to small genomes such as bacteria. | |
| 213 | |
| 214 | |
| 215 **Notes on paired reads** | |
| 216 | |
| 217 .. class:: warningmark | |
| 218 | |
| 219 MIRA uses read naming conventions to identify paired read partners | |
| 220 (and does not care about their order in the input files). In most cases, | |
| 221 the Solexa/Illumina setting is fine. For Sanger capillary sequencing, | |
| 222 you may need to rename your reads to match one of the standard conventions | |
| 223 supported by MIRA. For Roche 454 or Ion Torrent the appropriate settings | |
| 224 depend on how the FASTQ file was produced: | |
| 225 | |
| 226 * If using Roche's ``sffinfo`` or older versions of ``sff_extract`` | |
| 227 to convert SFF files to FASTQ, your reads will probably have the | |
| 228 ``---> <---`` orientation and use the ``.f`` and ``.r`` | |
| 229 suffixes (FR naming). | |
| 230 | |
| 231 * If using a recent version of ``sff_extract``, then the ``/1`` and ``/2`` | |
| 232 suffixes are used (Solexa/Illumina style naming) and the original | |
| 233 ``2---> 1--->`` orientation is preserved. | |
| 234 | |
| 235 The reason for this is the raw data for Roche 454 and Ion Torrent paired-end | |
| 236 libraries sequences a circularised fragment such that the raw data begins | |
| 237 with the end of the fragment, a linker, then the start of the fragment. | |
| 238 This means both the start and end are sequenced from the same strand, and | |
| 239 have the orientation ``2---> 1--->``. However, in order to use the data | |
| 240 with traditional tools expecting Sanger capillary style ``---> <---`` | |
| 241 orientation it was common to reverse complement one of the pair to mimic this. | |
| 242 | |
| 243 | |
| 244 **Citation** | |
| 245 | |
| 246 If you use this Galaxy tool in work leading to a scientific publication please | |
| 247 cite the following papers: | |
| 248 | |
| 249 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). | |
| 250 Galaxy tools and workflows for sequence analysis with applications | |
| 251 in molecular plant pathology. PeerJ 1:e167 | |
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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit ee574302295ee1e835b8f7315f6634d6f41ab461
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252 https://doi.org/10.7717/peerj.167 |
| 25 | 253 |
| 254 Bastien Chevreux, Thomas Wetter and Sándor Suhai (1999). | |
| 255 Genome Sequence Assembly Using Trace Signals and Additional Sequence Information. | |
| 256 Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56. | |
| 257 http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html | |
| 258 | |
| 259 This wrapper is available to install into other Galaxy Instances via the Galaxy | |
| 260 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler | |
| 261 </help> | |
| 262 <citations> | |
| 263 <citation type="doi">10.7717/peerj.167</citation> | |
| 264 <citation type="bibtex">@ARTICLE{Chevreux1999-mira3, | |
| 265 author = {B. Chevreux and T. Wetter and S. Suhai}, | |
| 266 year = {1999}, | |
| 267 title = {Genome Sequence Assembly Using Trace Signals and Additional Sequence Information}, | |
| 268 journal = {Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB)} | |
| 269 volume = {99}, | |
| 270 pages = {45-56}, | |
| 271 url = {http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html} | |
| 272 }</citation> | |
| 273 </citations> | |
| 274 </tool> |