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1 <tool id="cloudmap_prepare" name="Prepare variant data for mapping">
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2 <description>with the CloudMap series of tools.</description>
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3 <requirements>
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4 <requirement type="package" version="0.1.5">mimodd</requirement>
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5 </requirements>
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6 <version_command>mimodd version -q</version_command>
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7 <command>
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8 mimodd cloudmap "$ifile" ${run.mode}
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9
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10 #if $str($run.mode) != "EMS":
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11 "${run.refsample}"
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12 #end if
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13
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14 "$sample" -o $ofile
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15
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16 #if $seqdict:
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17 -s $dictfile
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18 #end if
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19 </command>
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20
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21 <inputs>
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22 <param name="ifile" type="data" format="vcf" label="vcf input file" />
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23 <conditional name="run">
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24 <param name="mode" type="select" label="CloudMap analysis to prepare data for">
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25 <option value="EMS">EMS Variant Density Mapping</option>
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26 <option value="VARIANT">Variant Discovery Mapping</option>
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27 <option value="HAWAIIAN">Hawaiian Variant Mapping</option>
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28 </param>
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29 <when value="EMS">
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30 <param name="refsample" type="hidden" value="None" />
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31 </when>
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32 <when value="VARIANT">
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33 <param name="refsample" type="text" label="name of the reference sample" help="the sample that provides crossing strain variants to be EXCLUDED from the analysis" />
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34 </when>
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35 <when value="HAWAIIAN">
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36 <param name="refsample" type="text" label="name of the reference sample" help="the sample that provides crossing strain variants to be INCLUDED in the analysis" />
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37 </when>
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38 </conditional>
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39 <param name="sample" type="text" label="subject sample name" help="the sample to perform CloudMap mapping for" />
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40 <param name="seqdict" type="boolean" checked="true" label="Generate species configuration file for CloudMap" />
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41
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42 </inputs>
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43
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44 <outputs>
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45 <data name="ofile" format="vcf" label="CloudMap ${run.mode} Mapping-ready VCF File from ${on_string}" />
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46 <data name="dictfile" format="tabular" label="Species Configuration File for CloudMap from ${on_string}">
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47 <filter>seqdict</filter>
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48 </data>
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49 </outputs>
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50
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51 <help>
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52 .. class:: infomark
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53
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54 **What it does**
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55
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56 The purpose of this tool is to provide compatibility of the MiModD analysis workflow with the external `CloudMap`_ *EMS Variant Density Mapping*, *Variant Discovery Mapping* and *Hawaiian Variant Mapping* tools.
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57
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58 These tools complement MiModD by providing easily interpreted visualizations of mapping-by-sequencing analysis workflows.
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59
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60 The tool converts a VCF file as generated by the *Extract Variant Sites* or *VCF Filter* tools to the format expected by the *CloudMap* series of tools.
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61
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62 Optionally, it also extracts the chromosome names and sizes and reports them in the *CloudMap* *species configuration file* format.
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63 Such a file is required as input to the current versions of the *CloudMap* *Hawaiian* and *Variant Density* mapping tools, if you are working with a species other than the natively supported ones (i.e., other than *C. elegans* or *A. thaliana*).
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64
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65 To use the output datasets of the tool with *CloudMap*, you only have to upload them to any public Galaxy server that hosts *CloudMap* like, e.g., the main Galaxy server at https://usegalaxy.org .
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66
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67 .. class:: warningmark
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68
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69 EMS Variant Density Mapping is currently limited to *C. elegans* and other species with six chromosomes on the *CloudMap* side.
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70
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71 .. _CloudMap: https://usegalaxy.org/u/gm2123/p/cloudmap
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72
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73 </help>
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74 </tool>
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