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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 <version_command>mimodd version -q</version_command>
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4 <command>
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5 mimodd cloudmap "$ifile" ${run.mode}
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6
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7 #if $str($run.mode) != "SVD":
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8 "${run.refsample}"
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9 #end if
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10
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11 "$sample" -o "$ofile"
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12
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13 #if $seqdict:
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14 -s "$dictfile"
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15 #end if
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16 </command>
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17
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18 <inputs>
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19 <param name="ifile" type="data" format="vcf" label="vcf input file" />
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20 <conditional name="run">
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21 <param name="mode" type="select" label="CloudMap analysis to prepare data for">
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22 <option value="SVD">EMS Variant Density Mapping</option>
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23 <option value="VAF">Variant Discovery / Hawaiian Variant Mapping</option>
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24 </param>
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25 <when value="SVD">
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26 <param name="refsample" type="hidden" value="None" />
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27 </when>
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28 <when value="VAF">
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29 <param name="refsample" type="text" label="name of the reference sample" help="the sample that provides mapping strain variants" />
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30 </when>
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31 </conditional>
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32 <param name="sample" type="text" label="subject sample name" help="the sample to perform CloudMap mapping for" />
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33 <param name="seqdict" type="boolean" checked="true" label="Generate species configuration file for CloudMap" />
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34
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35 </inputs>
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36
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37 <outputs>
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38 <data name="ofile" format="vcf" label="CloudMap-ready ${run.mode} File from ${on_string}" />
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39 <data name="dictfile" format="tabular" label="Species Configuration File for CloudMap from ${on_string}">
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40 <filter>seqdict</filter>
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41 </data>
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42 </outputs>
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43
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44 <help>
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45 .. class:: infomark
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46
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47 **What it does**
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48
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49 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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50
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51 These tools complement MiModD by providing easily interpreted visualizations of mapping-by-sequencing analysis workflows.
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52
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53 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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54
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55 Optionally, it also extracts the chromosome names and sizes and reports them in the *CloudMap* *species configuration file* format.
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56 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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57
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58 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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59
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60 .. class:: warningmark
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61
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62 EMS Variant Density Mapping is currently limited to *C. elegans* and other species with six chromosomes on the *CloudMap* side.
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63
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64 More information on combining MiModD and CloudMap in mapping-by-sequencing analyses can be found in the `corresponding section of the MiModD User Guide`_.
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65
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66 .. _CloudMap: https://usegalaxy.org/u/gm2123/p/cloudmap
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67 .. _corresponding section of the MiModD User Guide: http://mimodd.readthedocs.org/en/latest/cloudmap.html
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68
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69 </help>
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70 </tool>
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