Mercurial > repos > iuc > crossmap_region

annotate crossmap_region.xml @ 1:eb66d7a04bf8 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e10d34b547557b2bd4f0be69e31204bd5703e422"
author iuc
date Thu, 20 Jan 2022 04:31:00 +0000
parents 8635b6b8a8f2
children a50ef4d58c90
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8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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1 <tool id="crossmap_region" name="CrossMap region" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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3 <macros>
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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4 <import>macros.xml</import>
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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5 </macros>
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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10 CrossMap.py region
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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11 '${chain_source.input_chain}'
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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12 '${input}'
1
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13 $output
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14 --chromid $chromid
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15 --ratio $ratio
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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16 ]]></command>
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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17 <inputs>
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18 <param name="input" type="data" format="bed" label="BED file"
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19 help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/>
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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20 <expand macro="chain" />
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21 <param argument="--ratio" type="float" min="0" max="1" value="0.85" label="Minimum ratio of bases that must remap."/>
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22 <param argument="--chromid" type="select" label="Chromid" help="The style of chromosome IDs">
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23 <option value="a" selected="true">Default (a)</option>
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24 <option value="s">Short style (s)</option>
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25 <option value="l">Long stype (l)</option>
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26 </param>
0
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27 </inputs>
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28 <outputs>
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29 <data name="output" format="bed"/>
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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30 </outputs>
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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31 <tests>
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32 <test>
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33 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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34 <param name="index_source" value="history"/>
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35 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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36 <output name="output" file="test_region.bed"/>
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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37 </test>
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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38 </tests>
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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39 <help><![CDATA[
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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40 @HELP_GENERAL@
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41
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42 CrossMap region
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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43 ---------------
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44
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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45 Unlike the "CrossMap bed" function which splits big genomic regions, "CrossMap region" tries to convert the big genomic region as a whole.
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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46
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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47 BED
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48 ---
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49
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50 BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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51 BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
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52
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53 A BED (Browser Extensible Data) file is a tab-delimited text file
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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54 describing genome regions or gene annotations. It is the standard file
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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55 format used by UCSC. It consists of one line per feature, each containing
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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56 3-12 columns. CrossMap converts BED files with less than 12 columns to a
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57 different assembly by updating the chromosome and genome coordinates only;
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58 all other columns remain unchanged. Regions from old assembly mapping to
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59 multiple locations to the new assembly will be split. For 12-columns BED
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60 files, all columns will be updated accordingly except the 4th column (name
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61 of bed line), 5th column (score value) and 9th column (RGB value describing
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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62 the display color). 12-column BED files usually define multiple blocks (eg.
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63 exon); if any of the exons fails to map to a new assembly, the whole BED
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64 line is skipped.
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65
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66 Notes:
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67
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68 1. For BED-like formats mentioned above, CrossMap only updates “chrom (1st
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69 column)”, “start (2nd column) ”, “end (3rd column) ” and “strand” (if
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70 any). All other columns will keep AS-IS.
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71 2. Lines starting with ‘#’, ‘browser’, ‘track’ will be skipped.
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72 3. Lines will less than 3 columns will be skipped.
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73 4. 2nd-column and 3-column must be integer, otherwise skipped.
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74 5. “+” strand is assumed if no strand information was found.
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75 6. For standard BED format (12 columns). If any of the defined exon blocks
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76 cannot be uniquely mapped to target assembly, the whole entry will be
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77 skipped.
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78 7. If input region cannot be consecutively mapped target assembly, it will be split.
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79 8. \*.unmap file contains regions that cannot be unambiguously converted.
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80 ]]></help>
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81
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82 <citations>
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83 <citation type="doi">10.1093/bioinformatics/btt730</citation>
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84 </citations>
8635b6b8a8f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
iuc
parents:
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85 </tool>