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1 <tool id="crossmap" name="crossmap" version="0.1.8">
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2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
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3
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4 <requirements>
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5 <requirement type="package" version="0.1.8">crossmap</requirement>
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6 </requirements>
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7
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8 <stdio></stdio>
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9
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10 <command>
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11 CrossMap.py --help > $output
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12 </command>
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13
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14 <inputs>
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15 <param format="interval,gff,gtf,vcf" name="input" type="data" label="Convert coordinates of" />
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16 <!--
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17 <param format="interval,gff,gtf,vcf" name="input" type="data" label="Convert coordinates of">
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18 <validator type="unspecified_build" />
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19 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="Liftover mappings are currently not available for the specified build." />
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20 </param>
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21 <param name="to_dbkey" type="select" label="To">
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22 <options from_file="liftOver.loc">
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23 <column name="name" index="1"/>
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24 <column name="value" index="2"/>
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25 <column name="dbkey" index="0"/>
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26 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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27 </options>
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28 </param>
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29 <param name="minMatch" size="10" type="float" value="0.95" label="Minimum ratio of bases that must remap" help="Recommended values: same species = 0.95, different species = 0.10" />
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30 <conditional name="multiple">
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31 <param name="choice" type="select" label="Allow multiple output regions?" help="Recommended values: same species = No, different species = Yes">
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32 <option value="0" selected="true">No</option>
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33 <option value="1">Yes</option>
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34 </param>
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35 <when value="0">
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36 <param name="minSizeQ" type="hidden" value="0" />
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37 <param name="minChainQ" type="hidden" value="0" />
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38 <param name="minChainT" type="hidden" value="0" />
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39 </when>
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40 <when value="1">
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41 <param name="minSizeQ" size="10" type="integer" value="0" label="Minimum matching region size in dataset" help="Recommended value: set to >= 300 bases for complete transcripts"/>
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42 <param name="minChainQ" size="10" type="integer" value="500" label="Minimum chain size in dataset"/>
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43 <param name="minChainT" size="10" type="integer" value="500" label="Minimum chain size in target"/>
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44 </when>
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45 </conditional>
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46 -->
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47 </inputs>
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48
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49 <outputs>
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50 <data format="text" name="output" label="Output file">
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51 </data>
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52 </outputs>
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53
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54 <tests>
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55 <test>
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56 <param name="input" value="test1.hg19.txt"/>
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57 <output name="output" file="test1.hg18.txt"/>
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58 </test>
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59 </tests>
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60
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61 <help>
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62 CrossMap is versatile tool to convert genome coordinates or annotation files between genome
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63 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
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64 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
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65 and VCF, reading from remote servers and file compression are supported.
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66 </help>
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67
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68 <citations>
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69 <citation type="doi">10.1093/bioinformatics/btt730</citation>
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70 </citations>
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71 </tool>
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