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annotate tsebra.xml @ 0:174c63ee0150 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
author iuc
date Mon, 30 Oct 2023 15:35:25 +0000
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children 681fd806acc4
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174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
iuc
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1 <?xml version="1.0"?>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
iuc
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2 <tool id="tsebra" name="TSEBRA" version="@TOOL_VERSION@+galaxy0" profile="21.05">
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
iuc
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3 <description>tanscript selector for BRAKER</description>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
iuc
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4 <macros>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
iuc
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5 <import>macros.xml</import>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
iuc
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6 </macros>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
iuc
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7 <requirements>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
iuc
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8 <requirement type="package" version="@TOOL_VERSION@">tsebra</requirement>
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iuc
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9 </requirements>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
iuc
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10 <command detect_errors="exit_code"><![CDATA[
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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11 tsebra.py
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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12
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
iuc
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13 #if str( $gtf_file_param ) == "GTF":
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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14 -g '$gtf_input'
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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15 #elif str( $gtf_file_param ) == "KEEP_GTF":
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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16 -k '$gtf_input'
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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17 #end if
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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18
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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19 #if $hint_file
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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20 -e '$hint_file'
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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21 #end if
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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22 #if $cfg_file
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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23 -c '$cfg_file'
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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24 #end if
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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25
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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26 $ignore_tx_phase
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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27 #if $filter_exon
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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28 --filter_single_exon_genes
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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29 #end if
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
iuc
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30 #if $score_tab
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
iuc
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31 --score_tab '$output_tab'
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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32 #end if
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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33
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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34 -o '$output'
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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35 ]]></command>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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36 <inputs>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
iuc
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37 <param name="gtf_input" type="data" format="gtf" label="GTF input"/>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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38 <param name="gtf_file_param" type="select" label="Choose the analysis parameter for the gtf file">
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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39 <option value="GTF" selected="true">List of gene prediciton files</option>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
iuc
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40 <option value="KEEP_GTF">All transcripts from these gene sets will be included in the output</option>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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41 </param>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
iuc
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42 <param name="hint_file" argument="-e" type="data" format="gff" optional="true" label="List of files containing extrinsic evidence"/>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
iuc
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43 <param name="cfg_file" argument="-c" type="data" format="txt" optional="true" label="Configuration file" help="Find the recommanded parameter at config/default.cfg"/>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
iuc
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44 <param name="score_tab" argument="-s" type="boolean" checked="false" label="Print the transcript scores as a table to the specified file"/>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
iuc
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45 <param name="ignore_transcrpts" type="boolean" label="Ignore the phase transcripts while detecting clusters of overlapping transcripts"/>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
iuc
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46 <param name="filter_exon" type="boolean" label="Filter out all single-exon genes"/>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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47 <param argument="--ignore_tx_phase" type="boolean" truevalue="--ignore_tx_phase" falsevalue="" label="Ignore the phase transcripts while detecting clusters of overlapping transcripts"/>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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48 </inputs>
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49
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50 <outputs>
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51 <data name="output" format="gtf" label="TSEBRA on ${on_string}"/>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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52 <data name="output_tab" format="txt" label="TSEBRA on ${on_string} : tab">
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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53 <actions>
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54 <action name="column_names" type="metadata" default="TX_ID,intron_support,stasto_support,s1,s2,s3,s4" />
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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55 </actions>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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56 <filter>score_tab</filter>
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57 </data>
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58 </outputs>
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59
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60 <tests>
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61 <test expect_num_outputs="1">
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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62 <param name="gtf_input" value="braker.gtf" ftype="gtf"/>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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63 <param name="hint_file" value="hintsfile.gff" ftype="gff"/>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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64 <param name="score_tab" value="false"/>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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65 <param name="gtf_file_param" value="GTF"/>
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66 <output name="output" ftype="gtf" file="output.gtf" lines_diff="2"/>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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67 </test>
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68
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69 <test expect_num_outputs="2">
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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70 <param name="gtf_input" value="braker.gtf" ftype="gtf"/>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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71 <param name="hint_file" value="hintsfile.gff" ftype="gff"/>
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72 <param name="score_tab" value="true"/>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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73 <param name="gtf_file_param" value="GTF"/>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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74 <output name="output" ftype="gtf" file="output.gtf" lines_diff="2"/>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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75 <output name="output_tab" ftype="txt">
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76 <assert_contents>
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77 <has_size value="32000" delta="300"/>
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78 <has_text text="anno1;g1.t1"/>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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79 <has_text text="anno1;g59.t1"/>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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80 <has_text text="anno1;g169.t1"/>
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81 </assert_contents>
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82 </output>
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83 </test>
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84 </tests>
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85
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86 <help><![CDATA[
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87 tsebra_ TSEBRA is a combinatorial tool that selects transcripts from genetic predictions based on support by extrinsic evidence
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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88 in the form of introns and start/stop codpns. This tool has been developed to combine BRAKER predictions.
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
iuc
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89
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
iuc
parents:
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90
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
iuc
parents:
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91 .. _tsebra: https://github.com/Gaius-Augustus/TSEBRA
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
iuc
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92 ]]></help>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
iuc
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93 <expand macro="citation"></expand>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
iuc
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94 </tool>