Mercurial > repos > iuc > crossmap_gff

annotate crossmap_gff.xml @ 0:de420379eb28 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 17:45:21 -0400
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de420379eb28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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1 <tool id="crossmap_gff" name="CrossMap GFF" version="@WRAPPER_VERSION@-0">
de420379eb28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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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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9
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10 <command><![CDATA[
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11 CrossMap.py gff
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12 '${chain_source.input_chain}'
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13 '${seq_source.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 <conditional name="seq_source">
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24 <expand macro="source" />
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26 <when value="cached">
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27 <param format="gtf,gff,gff3" name="input" type="data" label="GTF/GFF file">
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28 <validator type="unspecified_build"/>
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29 <!-- Gives error in tests
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30 <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."/>
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31 -->
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32 </param>
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33 </when>
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34 <when value="history">
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35 <param type="data" format="gtf,gff,gff3" name="input" label="GTF/GFF file"/>
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36 </when>
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37 </conditional>
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38 <expand macro="chain" />
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39
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40 <param name="include_fails" type="boolean" truevalue="True" checked="false" 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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41 </inputs>
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43 <outputs>
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44 <!-- GTF/GFF3? test... -->
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45 <data format="gff" name="output" label="${tool.name} on ${on_string}" />
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46 </outputs>
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47
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48 <tests>
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49 <!-- GFF -->
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50 <test>
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51 <param name="input_format" value="gff"/>
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52 <param name="index_source" value="history"/>
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53 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
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54 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
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55 <param name="include_fails" value="False"/>
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56
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57 <output name="output" file="test_gff_01_output_a__only-matches.gtf"/>
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58 </test>
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59 <test>
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60 <param name="input_format" value="gff"/>
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61 <param name="index_source" value="history"/>
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62 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
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63 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
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64 <param name="include_fails" value="True"/>
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65
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66 <output name="output" file="test_gff_01_output_a__all.gtf"/>
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67 </test>
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68 </tests>
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69 <help><![CDATA[
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70 @HELP_GENERAL@
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71
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72 GFF / GTF
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73 ---------
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74 Your input data should be either GTF/GFF2.5 or GFF3 format.
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75
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76 GFF (General Feature Format) is another plain text file used to describe
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77 gene structure. GTF (Gene Transfer Format) is a refined version of GTF. The
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78 first eight fields are the same as GFF. Only chromosome and genome
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79 coordinates are updated. The format of output is determined from the input.
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80
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81 NOTE:
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82
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83 - Each feature (exon, intron, UTR, etc) is processed separately and
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84 independently, and we do NOT check if features originally belonging to
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85 the same gene were converted into the same gene.
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86 - If user want to liftover gene annotation files, use BED12 format.
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87
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88 Please see `the manual <http://crossmap.sourceforge.net/#convert-gff-gtf-format-files>`__ for more details
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89 ]]></help>
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90
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91 <citations>
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92 <citation type="doi">10.1093/bioinformatics/btt730</citation>
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93 </citations>
de420379eb28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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94 </tool>