Mercurial > repos > iuc > crossmap_gff

annotate crossmap_gff.xml @ 2:aeecd2650942 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
author iuc
date Thu, 19 Oct 2017 12:39:42 -0400
parents de420379eb28
children abd0775e221f
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1 <tool id="crossmap_gff" name="CrossMap GFF" version="@WRAPPER_VERSION@-0">
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2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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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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10 <command><![CDATA[
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11 CrossMap.py gff
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12 '${chain_source.input_chain}'
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13 '${input}'
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15 #if str($include_fails) == "True"
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16 >
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17 #end if
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19 '${output}'
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20 ]]></command>
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22 <inputs>
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23 <param name="input" type="data" format="gtf,gff,gff3" label="GTF/GFF file"/>
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25 <expand macro="chain" />
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27 <param name="include_fails" type="boolean" truevalue="True" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')"/>
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28 </inputs>
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30 <outputs>
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31 <data name="output" format="gff" label="${tool.name} on ${on_string}" />
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32 </outputs>
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34 <tests>
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35 <test>
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36 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
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37 <param name="index_source" value="history"/>
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38 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
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39 <param name="include_fails" value="False"/>
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41 <output name="output" file="test_gff_01_output_a__only-matches.gtf"/>
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42 </test>
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43 <test>
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44 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
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45 <param name="index_source" value="history"/>
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46 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
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47 <param name="include_fails" value="True"/>
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49 <output name="output" file="test_gff_01_output_a__all.gtf"/>
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50 </test>
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51 <test><!-- cached chain file -->
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52 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
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53 <param name="index_source" value="cached"/>
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54 <param name="include_fails" value="True"/>
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56 <output name="output" file="test_gff_01_output_a__all.gtf"/>
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57 </test>
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58 </tests>
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59 <help><![CDATA[
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60 @HELP_GENERAL@
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62 GFF / GTF
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63 ---------
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64 Your input data should be either GTF/GFF2.5 or GFF3 format.
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65
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66 GFF (General Feature Format) is another plain text file used to describe
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67 gene structure. GTF (Gene Transfer Format) is a refined version of GTF. The
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68 first eight fields are the same as GFF. Only chromosome and genome
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69 coordinates are updated. The format of output is determined from the input.
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70
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71 Notes:
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72
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73 - Each feature (exon, intron, UTR, etc) is processed separately and
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74 independently, and we do NOT check if features originally belonging to
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75 the same gene were converted into the same gene.
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76 - If user want to liftover gene annotation files, use BED12 format.
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77
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78 ]]></help>
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80 <citations>
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81 <citation type="doi">10.1093/bioinformatics/btt730</citation>
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82 </citations>
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83 </tool>