Mercurial > repos > iuc > tsebra

annotate tsebra.xml @ 4:69dcd75c0f5f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 490c0509fbaaacd763091baf3e1ebdf0b69a829e
author iuc
date Thu, 26 Sep 2024 15:27:15 +0000
parents 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
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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
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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
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4 <macros>
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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
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6 </macros>
3
681fd806acc4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit c009a4d4c26febdb75f46c5d3cb71352698d61f8
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7 <xrefs>
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8 <xref type="bio.tools">tsebra</xref>
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9 </xrefs>
0
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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10 <requirements>
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11 <requirement type="package" version="@TOOL_VERSION@">tsebra</requirement>
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12 </requirements>
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13 <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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14 tsebra.py
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174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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16 #if str( $gtf_file_param ) == "GTF":
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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17 -g '$gtf_input'
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18 #elif str( $gtf_file_param ) == "KEEP_GTF":
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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19 -k '$gtf_input'
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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20 #end if
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22 #if $hint_file
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23 -e '$hint_file'
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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 #if $cfg_file
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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26 -c '$cfg_file'
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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27 #end if
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29 $ignore_tx_phase
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30 #if $filter_exon
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31 --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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32 #end if
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33 #if $score_tab
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34 --score_tab '$output_tab'
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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35 #end if
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36
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37 -o '$output'
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38 ]]></command>
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39 <inputs>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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40 <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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41 <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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42 <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
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43 <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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44 </param>
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45 <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
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46 <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
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47 <param name="score_tab" argument="-s" type="boolean" checked="false" label="Print the transcript scores as a table to the specified file"/>
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48 <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
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49 <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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50 <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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51 </inputs>
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52
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53 <outputs>
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54 <data name="output" format="gtf" label="TSEBRA on ${on_string}"/>
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55 <data name="output_tab" format="txt" label="TSEBRA on ${on_string} : tab">
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56 <actions>
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57 <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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58 </actions>
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59 <filter>score_tab</filter>
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60 </data>
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61 </outputs>
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62
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63 <tests>
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64 <test expect_num_outputs="1">
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65 <param name="gtf_input" value="braker.gtf" ftype="gtf"/>
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66 <param name="hint_file" value="hintsfile.gff" ftype="gff"/>
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67 <param name="score_tab" value="false"/>
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68 <param name="gtf_file_param" value="GTF"/>
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69 <output name="output" ftype="gtf" file="output.gtf" lines_diff="2"/>
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70 </test>
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71
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72 <test expect_num_outputs="2">
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73 <param name="gtf_input" value="braker.gtf" ftype="gtf"/>
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74 <param name="hint_file" value="hintsfile.gff" ftype="gff"/>
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75 <param name="score_tab" value="true"/>
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76 <param name="gtf_file_param" value="GTF"/>
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77 <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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78 <output name="output_tab" ftype="txt">
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79 <assert_contents>
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80 <has_size value="32000" delta="300"/>
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81 <has_text text="anno1;g1.t1"/>
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82 <has_text text="anno1;g59.t1"/>
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83 <has_text text="anno1;g169.t1"/>
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84 </assert_contents>
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85 </output>
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86 </test>
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87 </tests>
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88
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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89 <help><![CDATA[
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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90 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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91 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
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92
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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93
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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94 .. _tsebra: https://github.com/Gaius-Augustus/TSEBRA
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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95 ]]></help>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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96 <expand macro="citation"></expand>
174c63ee0150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f
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97 </tool>