Mercurial > repos > galaxyp > gffcompare_to_bed

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 98ac160e172e3a404163c1af8e2d5ae42a2b425d"
author galaxyp
date Wed, 13 Jan 2021 20:59:52 +0000
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9a4cfc910674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
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1 <tool id="gffcompare_to_bed" name="Convert gffCompare annotated GTF to BED" version="0.2.1">
0
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2 <description>for StringTie results</description>
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9a4cfc910674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
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3 <requirements>
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4 <requirement type="package" version="3.7">python</requirement>
9a4cfc910674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
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5 </requirements>
0
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6 <command detect_errors="exit_code"><![CDATA[
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7 python '$__tool_directory__/gffcompare_to_bed.py'
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8 #if $class_codes:
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9 --class_code='$class_codes'
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10 #end if
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11 $input $output
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12 ]]></command>
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13 <inputs>
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14 <param name="input" type="data" format="gtf" label="GTF annotated by gffCompare"/>
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15 <param name="class_codes" type="select" display="checkboxes" multiple="true" optional="true"
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16 label="filter gffCompare class_codes to convert" help="No selection implies no filtering">
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17 <option value="=">= : Complete match of intron chain</option>
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18 <option value="~">~ : Intron chain match or single-exon (gffcompare strict-match)</option>
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19 <option value="c">c : Contained</option>
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20 <option value="j">j : Potentially novel isoform (fragment): at least one splice junction is shared with a reference transcript</option>
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21 <option value="e">e : Single exon transfrag overlapping a reference exon and at least 10 bp of a reference intron, indicating a possible pre-mRNA fragment.</option>
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22 <option value="i">i : A transfrag falling entirely within a reference intron</option>
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23 <option value="o">o : Generic exonic overlap with a reference transcript</option>
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24 <option value="p">p : Possible polymerase run-on fragment (within 2Kbases of a reference transcript)</option>
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25 <option value="r">r : Repeat. Currently determined by looking at the soft-masked reference sequence and applied to transcripts where at least 50% of the bases are lower case</option>
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26 <option value="u">u : Unknown, intergenic transcript</option>
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27 <option value="x">x : Exonic overlap with reference on the opposite strand</option>
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28 <option value="s">s : An intron of the transfrag overlaps a reference intron on the opposite strand (likely due to read mapping errors)</option>
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29 </param>
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30 </inputs>
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31 <outputs>
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32 <data name="output" format="bed" />
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="input" value="gffcompare_annotated.gtf" ftype="gtf"/>
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37 <output name="output" file="gffcompare_output.bed"/>
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38 </test>
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39 <test>
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40 <param name="input" value="gffcompare_annotated.gtf" ftype="gtf"/>
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41 <param name="class_codes" value="j"/>
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42 <output name="output" file="gffcompare_output_j.bed"/>
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43 </test>
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44 <test>
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45 <param name="input" value="gffcompare_annotated.gtf" ftype="gtf"/>
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46 <param name="class_codes" value="j,e,i,p,u,x"/>
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47 <output name="output" file="gffcompare_output_jeipux.bed"/>
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48 </test>
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49
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50 </tests>
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51 <help><![CDATA[
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52 Convert a GFFCompare annotated GTF file to BED format.
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53
1
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54 A typical workflow:
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55
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56 .. image:: GTF2Bed_workflow.png
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57 :height: 308
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58 :width: 750
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59
0
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60 usage: gffcompare_to_bed.py [-h] [-C CLASS_CODE] [-v] [-d] input output
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61
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62 positional arguments:
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63 input GFFCompare annotated GTF file, (-) for stdin
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64 output BED file, (-) for stdout
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65
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66 optional arguments:
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67 -h, --help show this help message and exit
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68 -C CLASS_CODE, --class_code CLASS_CODE
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69 Restrict output to gffcompare class codes
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70 -d, --debug Debug
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71
1
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72 For class_code definitions see gffcompare documentation:
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73 http://ccb.jhu.edu/software/stringtie/gffcompare.shtml#transfrag-class-codes
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74
0
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75 ]]></help>
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76 <citations>
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77 <citation type="doi">10.1038/nbt.1621</citation>
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78 </citations>
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79 </tool>