Mercurial > repos > iuc > crossmap_gff

annotate crossmap_gff.xml @ 10:8dd8edcd3970 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
author iuc
date Mon, 02 Sep 2024 12:00:25 +0000
parents bb8290b7d207
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bb8290b7d207 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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1 <tool id="crossmap_gff" name="CrossMap GFF" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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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 <command><![CDATA[
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10 CrossMap gff
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11 '${chain_source.input_chain}'
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12 '${input}'
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13
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14 #if str($include_fails) == "True"
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15 >
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16 #end if
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18 output
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19 ]]></command>
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20 <inputs>
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21 <param name="input" type="data" format="gtf,gff,gff3" label="GTF/GFF file"/>
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22 <expand macro="chain"/>
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23 <param name="include_fails" type="boolean" truevalue="True" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')"/>
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24 </inputs>
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25 <outputs>
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26 <data name="output" format="gff" label="${tool.name} on ${on_string}" from_work_dir="output"/>
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
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31 <param name="index_source" value="history"/>
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32 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
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33 <param name="include_fails" value="False"/>
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34 <output name="output" file="test_gff_01_output_a__only-matches.gtf"/>
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35 </test>
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36 <test>
2
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37 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
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38 <param name="index_source" value="history"/>
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39 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
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40 <param name="include_fails" value="True"/>
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41 <output name="output" file="test_gff_01_output_a__all.gtf"/>
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42 </test>
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43 <test>
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44 <!-- cached chain file -->
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45 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf" dbkey="hg18"/>
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46 <param name="index_source" value="cached"/>
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47 <param name="include_fails" value="True"/>
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48 <output name="output" file="test_gff_01_output_a__all.gtf"/>
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49 </test>
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50 </tests>
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51 <help><![CDATA[
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52 @HELP_GENERAL@
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53
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54 GFF / GTF
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55 ---------
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56 Your input data should be either GTF/GFF2.5 or GFF3 format.
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57
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58 GFF (General Feature Format) is another plain text file used to describe
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59 gene structure. GTF (Gene Transfer Format) is a refined version of GTF. The
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60 first eight fields are the same as GFF. Only chromosome and genome
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61 coordinates are updated. The format of output is determined from the input.
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62
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63 Notes:
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64
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65 - Each feature (exon, intron, UTR, etc) is processed separately and
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66 independently, and we do NOT check if features originally belonging to
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67 the same gene were converted into the same gene.
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68 - If user want to liftover gene annotation files, use BED12 format.
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69 ]]></help>
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70 <citations>
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71 <citation type="doi">10.1093/bioinformatics/btt730</citation>
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72 </citations>
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73 </tool>