Add tsebra (#5483)

* Add tsebra * error typo * add .shed.yml * Update .shed.yml * add column names and number-test * size test inputs + modify test section * modify test 2 * new output.gtf * test * Add tsebra * modify test 2 * Modify test 2 * test 2 * test 2 * test 2 * small changes * modify tsebra.xml * change tsebra.xml * News modifications --------- Co-authored-by: Björn Grüning <[email protected]>
galaxyproject · Oct 19, 2023 · 7dadb01 · 7dadb01
1 parent 07802a6
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diff --git a/tools/tsebra/.shed.yml b/tools/tsebra/.shed.yml
@@ -0,0 +1,10 @@
+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
diff --git a/tools/tsebra/macros.xml b/tools/tsebra/macros.xml
@@ -0,0 +1,8 @@
+<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>
diff --git a/tools/tsebra/test-data/braker.gtf b/tools/tsebra/test-data/braker.gtf
diff --git a/tools/tsebra/test-data/hintsfile.gff b/tools/tsebra/test-data/hintsfile.gff
diff --git a/tools/tsebra/test-data/output.txt b/tools/tsebra/test-data/output.txt
diff --git a/tools/tsebra/test-data/output_tab.txt b/tools/tsebra/test-data/output_tab.txt
diff --git a/tools/tsebra/tsebra.xml b/tools/tsebra/tsebra.xml
@@ -0,0 +1,94 @@
+<?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 str( $gtf_file_param ) == "GTF":
+        -g '$gtf_input'
+    #elif str( $gtf_file_param ) == "KEEP_GTF":
+        -k '$gtf_input'
+    #end if
+    
+
+    #if $hint_file
+        -e '$hint_file'
+    #end if
+    #if $cfg_file
+        -c '$cfg_file'
+    #end if
+    
+    $ignore_tx_phase
+    #if $filter_exon
+        --filter_single_exon_genes
+    #end if
+    #if $score_tab
+        --score_tab '$output_tab'
+    #end if 
+    
+    -o '$output' 
+
+    ]]></command>
+    <inputs>
+        <param name="gtf_input" type="data" format="gtf" label="GTF input"/>
+        <param name="gtf_file_param" type="select" label="Choose the analysis parameter for the gtf file">
+            <option value="GTF" selected="true">List of gene prediciton files</option>
+            <option value="KEEP_GTF">All transcripts from these gene sets will be included in the output</option>
+        </param>
+        <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 name="ignore_transcrpts" type="boolean" label="Ignore the phase transcripts while detecting clusters of overlapping transcripts"/>
+        <param name="filter_exon" type="boolean" label="Filter out all single-exon genes"/>
+        <param argument="--ignore_tx_phase" type="boolean" truevalue="--ignore_tx_phase" falsevalue="" label="Ignore the phase transcripts while detecting clusters of overlapping transcripts"/>    
+    </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_input" value="braker.gtf" ftype="gtf"/>
+            <param name="hint_file" value="hintsfile.gff" ftype="gff"/>
+            <param name="score_tab" value="false"/>
+            <param name="gtf_file_param" value="GTF"/>
+            <output name="output" ftype="gtf" file="output.gtf" lines_diff="2"/>
+        </test>
+
+        <test expect_num_outputs="2">
+            <param name="gtf_input" value="braker.gtf" ftype="gtf"/>
+            <param name="hint_file" value="hintsfile.gff" ftype="gff"/>
+            <param name="score_tab" value="true"/>
+            <param name="gtf_file_param" value="GTF"/>
+            <output name="output" ftype="gtf" file="output.gtf" lines_diff="2"/>
+            <output name="output_tab" ftype="txt" file="output_tab.txt">
+                <assert_contents>
+                    <has_text text="anno1;g1.t1"/>
+                    <has_text text="anno1;g84.t1"/>
+                </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>