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1 <tool id="mira_4_0_convert" name="MIRA v4.0 miraconvert" version="0.0.5">
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2 <description>Convert MIRA assembly to FASTA/SAM/BAM</description>
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3 <requirements>
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4 <requirement type="binary">miraconvert</requirement>
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5 <requirement type="package" version="4.0">MIRA</requirement>
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6 </requirements>
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7 <version_command interpreter="python">mira4_convert.py --version</version_command>
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8 <command interpreter="python">
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9 mira4_convert.py
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10 --input "$mira_file"
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11 --min_length $min_length
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12 --min_cover $min_cover
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13 --min_reads $min_reads
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14 #if str($maf_wanted)=="true":
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15 --maf "$out_maf"
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16 #end if
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17 #if str($fasta_wanted)=="true":
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18 --fasta "$out_fasta"
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19 #end if
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20 #if str($bam_wanted)=="true":
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21 --bam "$out_bam"
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22 #end if
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23 ##Don't yet have a Galaxy datatype defined for ace:
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24 ## #if str($ace_wanted)=="true":
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25 ## --ace "$out_ace"
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26 ## #end if
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27 #if str($cstats_wanted)=="true":
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28 --cstats "$out_cstats"
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29 #end if
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30 </command>
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31 <stdio>
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32 <!-- Assume anything other than zero is an error -->
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33 <exit_code range="1:" />
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34 <exit_code range=":-1" />
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35 </stdio>
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36 <inputs>
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37 <param name="mira_file" type="data" format="mira" required="true" label="MIRA Assembly Format input" />
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38 <!-- TODO - top level select for contig versus read output? Or two Galaxy tools in different XML files? -->
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39 <param name="min_length" type="integer" required="false" value="0" min="0"
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40 label="Minimum contig length"
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41 help="e.g. Set to 1000 to exclude small contigs. Default is to keep all contigs (minimum zero)" />
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42 <param name="min_cover" type="integer" required="false" value="0" min="0"
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43 label="Minimum average contig coverage"
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44 help="e.g. Set to 10 to exclude low coverage contigs. Default is to keep all contigs (minimum zero)" />
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45 <param name="min_reads" type="integer" required="false" value="0" min="0"
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46 label="Minimum reads per contig"
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47 help="e.g. Set to 5 to exclude low coverage contigs with only a few reads. Default is to keep all contigs (minimum zero)." />
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48 <param name="maf_wanted" type="boolean" label="Output assembly in MIRA's own format? (useful if filtering)" checked="False" />
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49 <param name="fasta_wanted" type="boolean" label="Convert assembly into (unpadded) FASTA?" checked="True" />
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50 <param name="bam_wanted" type="boolean" label="Convert assembly into (upadded) BAM format?" checked="False" />
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51 <!-- Don't yet have a Galaxy datatype defined for ace:
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52 <param name="ace_wanted" type="boolean" label="Convert assembly in ACE format?" checked="False" />
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53 -->
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54 <param name="cstats_wanted" type="boolean" label="Assembly statistics file?" checked="False" />
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55 </inputs>
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56 <outputs>
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57 <data name="out_maf" format="mira" label="$mira_file.name (filtered)">
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58 <filter>maf_wanted is True</filter>
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59 </data>
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60 <data name="out_fasta" format="fasta" label="$mira_file.name (as FASTA)">
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61 <filter>fasta_wanted is True</filter>
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62 </data>
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63 <data name="out_bam" format="bam" label="$mira_file.name (as BAM)">
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64 <filter>bam_wanted is True</filter>
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65 </data>
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66 <!--
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67 <data name="out_ace" format="ace" label="$mira_file.name (as ACE)">
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68 <filter>ace_wanted is True</filter>
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69 </data>
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70 -->
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71 <data name="out_cstats" format="tabular" label="$mira_file.name (filtered stats)">
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72 <filter>cstats_wanted is True</filter>
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73 </data>
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74 </outputs>
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75 <tests>
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76 <!-- TODO -->
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77 </tests>
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78 <help>
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79 **What it does**
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80
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81 Runs the ``miraconvert`` utility from MIRA v4.0 to filter and/or convert
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82 a MIRA Assembly Format file produced by a *mapping* or *de novo* assembly.
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83
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84 **Example Usage**
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85
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86 You want to remove all the low coverage contigs from a transcriptome
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87 assembly to focus on those with higher coverage.
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88
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89 You want to convert your MIRA assembly into SAM/BAM to run a standard
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90 SNP finding tool.
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91
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92 You've lost the FASTA consensus from your MIRA assembly and need to
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93 regenerate it.
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94
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95
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96 **Citation**
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97
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98 If you use this Galaxy tool in work leading to a scientific publication please
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99 cite the following papers:
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100
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101 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
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102 Galaxy tools and workflows for sequence analysis with applications
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103 in molecular plant pathology. PeerJ 1:e167
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104 http://dx.doi.org/10.7717/peerj.167
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105
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106 Bastien Chevreux, Thomas Wetter and Sándor Suhai (1999).
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107 Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.
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108 Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
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109 http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html
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110
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111 This wrapper is available to install into other Galaxy Instances via the Galaxy
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112 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
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113 </help>
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114 </tool>
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