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comparison 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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-1:000000000000 0:174c63ee0150
1 <?xml version="1.0"?>
2 <tool id="tsebra" name="TSEBRA" version="@TOOL_VERSION@+galaxy0" profile="21.05">
3 <description>tanscript selector for BRAKER</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">tsebra</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 tsebra.py
12
13 #if str( $gtf_file_param ) == "GTF":
14 -g '$gtf_input'
15 #elif str( $gtf_file_param ) == "KEEP_GTF":
16 -k '$gtf_input'
17 #end if
18
19 #if $hint_file
20 -e '$hint_file'
21 #end if
22 #if $cfg_file
23 -c '$cfg_file'
24 #end if
25
26 $ignore_tx_phase
27 #if $filter_exon
28 --filter_single_exon_genes
29 #end if
30 #if $score_tab
31 --score_tab '$output_tab'
32 #end if
33
34 -o '$output'
35 ]]></command>
36 <inputs>
37 <param name="gtf_input" type="data" format="gtf" label="GTF input"/>
38 <param name="gtf_file_param" type="select" label="Choose the analysis parameter for the gtf file">
39 <option value="GTF" selected="true">List of gene prediciton files</option>
40 <option value="KEEP_GTF">All transcripts from these gene sets will be included in the output</option>
41 </param>
42 <param name="hint_file" argument="-e" type="data" format="gff" optional="true" label="List of files containing extrinsic evidence"/>
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"/>
44 <param name="score_tab" argument="-s" type="boolean" checked="false" label="Print the transcript scores as a table to the specified file"/>
45 <param name="ignore_transcrpts" type="boolean" label="Ignore the phase transcripts while detecting clusters of overlapping transcripts"/>
46 <param name="filter_exon" type="boolean" label="Filter out all single-exon genes"/>
47 <param argument="--ignore_tx_phase" type="boolean" truevalue="--ignore_tx_phase" falsevalue="" label="Ignore the phase transcripts while detecting clusters of overlapping transcripts"/>
48 </inputs>
49
50 <outputs>
51 <data name="output" format="gtf" label="TSEBRA on ${on_string}"/>
52 <data name="output_tab" format="txt" label="TSEBRA on ${on_string} : tab">
53 <actions>
54 <action name="column_names" type="metadata" default="TX_ID,intron_support,stasto_support,s1,s2,s3,s4" />
55 </actions>
56 <filter>score_tab</filter>
57 </data>
58 </outputs>
59
60 <tests>
61 <test expect_num_outputs="1">
62 <param name="gtf_input" value="braker.gtf" ftype="gtf"/>
63 <param name="hint_file" value="hintsfile.gff" ftype="gff"/>
64 <param name="score_tab" value="false"/>
65 <param name="gtf_file_param" value="GTF"/>
66 <output name="output" ftype="gtf" file="output.gtf" lines_diff="2"/>
67 </test>
68
69 <test expect_num_outputs="2">
70 <param name="gtf_input" value="braker.gtf" ftype="gtf"/>
71 <param name="hint_file" value="hintsfile.gff" ftype="gff"/>
72 <param name="score_tab" value="true"/>
73 <param name="gtf_file_param" value="GTF"/>
74 <output name="output" ftype="gtf" file="output.gtf" lines_diff="2"/>
75 <output name="output_tab" ftype="txt">
76 <assert_contents>
77 <has_size value="32000" delta="300"/>
78 <has_text text="anno1;g1.t1"/>
79 <has_text text="anno1;g59.t1"/>
80 <has_text text="anno1;g169.t1"/>
81 </assert_contents>
82 </output>
83 </test>
84 </tests>
85
86 <help><![CDATA[
87 tsebra_ TSEBRA is a combinatorial tool that selects transcripts from genetic predictions based on support by extrinsic evidence
88 in the form of introns and start/stop codpns. This tool has been developed to combine BRAKER predictions.
89
90
91 .. _tsebra: https://github.com/Gaius-Augustus/TSEBRA
92 ]]></help>
93 <expand macro="citation"></expand>
94 </tool>