Mercurial > repos > iuc > crossmap_bed

annotate crossmap_bed.xml @ 0:235ab3277db1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
author iuc
date Sat, 01 Jul 2017 17:44:51 -0400
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children b0d8635e0161
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235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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1 <tool id="crossmap_bed" name="CrossMap BED" version="@WRAPPER_VERSION@-0">
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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3 <macros>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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4 <import>macros.xml</import>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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5 </macros>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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6 <expand macro="requirements"/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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7 <expand macro="stdio"/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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8 <expand macro="version_command"/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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9
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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10 <command><![CDATA[
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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11 #set $input_file = str($seq_source.input)
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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13 CrossMap.py bed
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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14 '${chain_source.input_chain}'
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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16 '${input_file}'
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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18 #if str($include_fails) == "True"
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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19 >
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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20 #end if
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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22 '${output}'
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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23 ]]></command>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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26 <inputs>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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27 <conditional name="seq_source">
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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28 <expand macro="source" />
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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30 <when value="cached">
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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31 <param format="bed" name="input" type="data" label="BED file"
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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32 help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.">
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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33 <validator type="unspecified_build"/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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34 <!-- Gives error in tests
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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35 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build."/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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36 -->
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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37 </param>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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38 </when>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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39 <when value="history">
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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40 <param type="data" format="bed" name="input" label="BED file"
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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41 help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns."/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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42 </when>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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43 </conditional>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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44 <expand macro="chain" />
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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45
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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46 <param name="include_fails" type="boolean" truevalue="True" checked="false" falsevalue="False" label="Include failed liftovers"
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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47 help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')"/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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48 </inputs>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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49
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50 <outputs>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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51 <data format="bed" name="output" label="${tool.name} on ${on_string}" />
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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52 <data format="text" name="output2" label="${tool.name} (bedgraph) on ${on_string}" />
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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53 </outputs>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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54
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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55 <tests>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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56 <!-- BED -->
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57 <test>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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58 <param name="index_source" value="history"/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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59 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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60 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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61 <param name="include_fails" value="False"/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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62
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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63 <output name="output" file="test_bed_01_output_a__only-matches.bed"/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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64 </test>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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65 <test>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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66 <param name="index_source" value="history"/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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67 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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68 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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69 <param name="include_fails" value="True"/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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70
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71 <output name="output" file="test_bed_01_output_a__all.bed"/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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72 </test>
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73 <test>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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74 <param name="index_source" value="history"/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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75 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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76 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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77 <param name="include_fails" value="False"/>
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78
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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79 <output name="output" file="test_bed_02_output_a__only-matches.bed"/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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80 </test>
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81 <test>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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82 <param name="index_source" value="history"/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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83 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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84 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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85 <param name="include_fails" value="True"/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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86
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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87 <output name="output" file="test_bed_02_output_a__all.bed"/>
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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88 </test>
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89 </tests>
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90 <help><![CDATA[
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91 @HELP_GENERAL@
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92
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93 BED
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94 ---
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95
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96 BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.
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97 BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
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98
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99 A BED (Browser Extensible Data) file is a tab-delimited text file
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100 describing genome regions or gene annotations. It is the standard file
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101 format used by UCSC. It consists of one line per feature, each containing
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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102 3-12 columns. CrossMap converts BED files with less than 12 columns to a
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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103 different assembly by updating the chromosome and genome coordinates only;
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104 all other columns remain unchanged. Regions from old assembly mapping to
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105 multiple locations to the new assembly will be split. For 12-columns BED
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106 files, all columns will be updated accordingly except the 4th column (name
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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107 of bed line), 5th column (score value) and 9th column (RGB value describing
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108 the display color). 12-column BED files usually define multiple blocks (eg.
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109 exon); if any of the exons fails to map to a new assembly, the whole BED
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110 line is skipped.
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111
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112 NOTE:
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113
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114 1. For BED-like formats mentioned above, CrossMap only updates “chrom (1st
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115 column)”, “start (2nd column) ”, “end (3rd column) ” and “strand” (if
235ab3277db1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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116 any). All other columns will keep AS-IS.
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117 2. Lines starting with ‘#’, ‘browser’, ‘track’ will be skipped.
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118 3. Lines will less than 3 columns will be skipped.
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119 4. 2nd-column and 3-column must be integer, otherwise skipped.
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120 5. “+” strand is assumed if no strand information was found.
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121 6. For standard BED format (12 columns). If any of the defined exon blocks
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122 cannot be uniquely mapped to target assembly, the whole entry will be
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123 skipped.
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124 7. If input region cannot be consecutively mapped target assembly, it will be split.
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125 8. *.unmap file contains regions that cannot be unambiguously converted.
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126
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127 Please see `the manual <http://crossmap.sourceforge.net/#convert-bed-format-files>`__ for more details.
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128 ]]></help>
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129
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130 <citations>
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131 <citation type="doi">10.1093/bioinformatics/btt730</citation>
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132 </citations>
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133 </tool>