Add tsebra

tools/tsebra/.shed.yml

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+categories:
+  - Genome annotation
+description: This tool has been developed to combine BRAKER predictions.
+long_description: |
+  TSEBRA is a combinatorial tool that selects transcripts from genetic predictions based on support by extrinsic evidence 
+  in the form of introns and start/stop codpns.
+homepage_url: https://github.com/Gaius-Augustus/TSEBRA
+owner: iuc
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra
+type: unrestricted

tools/tsebra/macros.xml

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+<macros>
+    <token name="@TOOL_VERSION@">1.1.1</token>
+    <xml name="citation">
+        <citations>
+            <citation type="doi">/10.1186/s12859-021-04482-0</citation> 
+        </citations>
+    </xml>
+</macros>

tools/tsebra/tsebra.xml

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+<?xml version="1.0"?>
+<tool id="tsebra" name="TSEBRA" version="@TOOL_VERSION@+galaxy0" profile="21.05">
+    <description>tanscript selector for BRAKER</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">tsebra</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    tsebra.py
+
+    #if $gtf_file
+        -g '$gtf_file'
+    #end if        
+    #if $keep_gtf
+        -k '$keep_gtf'
+    #end if
+    #if $hint_file
+        -e '$hint_file'
+    #end if
+    #if $cfg_file
+        -c '$cfg_file'
+    #end if
+
+    $ignore_tx_phase
+    $filter_single_exon_genes
+    #if $score_tab
+        --score_tab '$output_tab'
+    #end if 
+
+    -o '$output' 
+
+    ]]></command>
+    <inputs>
+        <param name="gtf_file" argument="-g" type="data" format="gtf" optional="true" label="List of gene prediciton files"/>
+        <param name="keep_gtf" argument="-k" type="data" format="gtf" optional="true" label="Gene prediction list" help="All transcripts from these gene sets will be included in the output"/>
+        <param name="hint_file" argument="-e" type="data" format="gff" optional="true" label="List of files containing extrinsic evidence"/>
+        <param name="cfg_file" argument="-c" type="data" format="txt" optional="true" label="Configuration file" help="Find the recommanded parameter at config/default.cfg"/>
+        <param name="score_tab" argument="-s" type="boolean" checked="false" label="Print the transcript scores as a table to the specified file"/>
+        <param argument="--ignore_tx_phase" type="boolean" truevalue="--ignore_tx_phase" falsevalue="" label="Ignore the phase transcripts while detecting clusters of overlapping transcripts"/>
+        <param argument="--filter_single_exon_genes" type="boolean" truevalue="--filter_single_exon_genes" falsevalue="" label="Filter out all single-exon genes"/>
+    </inputs>
+
+    <outputs>
+        <data name="output" format="gtf" label="TSEBRA on ${on_string}"/>
+        <data name="output_tab" format="txt" label="TSEBRA on ${on_string} : tab">
+            <actions>
+                <action name="column_names" type="metadata" default="TX_ID,intron_support,stasto_support,s1,s2,s3,s4" />
+            </actions>
+            <filter>score_tab</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="gtf_file" value="braker.gtf" ftype="gtf"/>
+            <param name="hint_file" value="hintsfile.gff" ftype="gff"/>
+            <output name="output" ftype="gtf" file="output.gtf" lines_diff="2"/>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="gtf_file" value="braker.gtf" ftype="gtf"/>
+            <param name="hint_file" value="hintsfile.gff" ftype="gff"/>
+            <param name="score_tab" value="true"/>
+            <param name="ignore_transcrpts" value="false"/>
+            <param name="filter_exon" value="false"/>
+            <output name="output" ftype="gtf" file="output.gtf" lines_diff="2"/>
+            <output name="output_tab" ftype="txt" file="output_tab.txt">
+                <assert_contents>
+                    <has_n_lines n="668"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        tsebra_  TSEBRA is a combinatorial tool that selects transcripts from genetic predictions based on support by extrinsic evidence 
+        in the form of introns and start/stop codpns. This tool has been developed to combine BRAKER predictions.
+
+
+        .. _tsebra: https://github.com/Gaius-Augustus/TSEBRA
+    ]]></help> 
+    <expand macro="citation"></expand>
+</tool>