--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEfinder.xml	Mon Aug 08 19:41:18 2022 +0000
@@ -0,0 +1,114 @@
+<tool id="te_finder" name="TEfinder" version="1.0.1" profile="21.05">
+    <description>Transposable element insertions finder</description>
+
+    <requirements>
+        <requirement type="package" version="1.15.1">samtools</requirement>
+        <requirement type="package" version="2.30.0">bedtools</requirement>
+        <requirement type="package" version="2.27.4">picard</requirement>
+        <requirement type="package" version="3.4">grep</requirement>
+        <requirement type="package" version="1.07.1">bc</requirement>
+    </requirements>
+
+    <command>
+        <![CDATA[
+            '$__tool_directory__/TEfinder' -fa '$required_inputs.FastaFile' 
+            -alignment '$required_inputs.alignmentFile' 
+            -gtf '$required_inputs.TransposonsInGenome' 
+            -te '$required_inputs.TransposonsToSearch' 
+            -bamo '$discordantreads' 
+            -bedo '$bteinsertion' 
+            -threads '\${GALAXY_SLOTS:-1}' 
+            -fis $($advanced_options.FragmentInsertSize) 
+            -md $($advanced_options.MaxDistanceForMerge) 
+            -k $($advanced_options.MaxTSDLength)
+            #if str( $advanced_options.OutFormat) == "gtf":
+            -gtfo '$gteinsertion'
+            -out $($advanced_options.OutFormat)
+            #end if
+        ]]>
+    </command>
+
+    <inputs>
+        <!-- <param format="fasta" name="input" type="data" label="Source file"/> -->
+        <section name="required_inputs" title="Required Inputs" expanded="True">
+            <param name="FastaFile" type="data" format="fasta" label="Select reference genome FASTA index (FA/FASTA file)" />
+            <param name="alignmentFile" type="data" format="bam" label="Select sample reads aligned to reference genome (BAM/SAM file)" />
+            <param name="TransposonsInGenome" type="data" format="gtf" label="Select reference genome TE annotation (GFF/GTF file)" />
+            <param name="TransposonsToSearch" type="data" format="text" label="Select TE names" help="Single column text file" />
+        </section>
+        <!-- Advanced Options  -->
+        <section name="advanced_options" title="Advanced Options" expanded="False">
+            <param name="FragmentInsertSize" argument="-fis" type="integer" min="0" value="400" label="Short-read sequencing fragment insert size" />
+            <param name="MaxDistanceForMerge" argument="-md" type="integer" min="0" value="150" label="Maximum distance between reads for bedtools merge" />
+            <param name="MaxTSDLength" argument="-k" type="integer" min="0" value="20" label="Maximum TE target site duplication (TSD) length" />
+            <param name="OutFormat" argument="-out" type="select" display="radio" label="Select output format as BED [GTF]" help="See help below for more details">
+                <option value="bed" selected="True">Default format is BED</option>
+                <option value="gtf">Other available format is GTF (-out gtf)</option>
+            </param>
+        </section>
+    </inputs>
+
+    <outputs>
+        <data format="bed" name="bteinsertion" label="${tool.name} on ${on_string}: BED" />
+        <data format="gtf" name="gteinsertion" label="${tool.name} on ${on_string}: GTF">
+            <filter>advanced_options['OutFormat'] and 'gtf' in advanced_options['OutFormat']</filter>
+        </data>
+        <data format="bam" name="discordantreads" />
+    </outputs>
+
+    <tests>
+        <!-- Test for the most simple case for BED output : Running TEfinder with a .bam file and a .fasta file -->
+        <test expect_num_outputs="2">
+            <!-- TEfinder commands: TEfinder -alignment sample.bam -fa reference.fa -gtf TEs.gtf -te List_of_TEs.txt -->
+            <param name="FastaFile" ftype="fasta" value="reference.fa"/>
+            <param name="alignmentFile" ftype="bam" value="sample.bam"/>
+            <param name="TransposonsInGenome" ftype="gtf" value="TEs.gtf"/>
+            <param name="TransposonsToSearch" ftype="txt" value="List_of_TEs.txt"/>
+            <param name="OutFormat" value="bed" />
+            <output name="bteinsertion" file="TEinsertions.bed" ftype="bed"/>
+            <output name="discordantreads" file="DiscordantReads.bam" ftype="bam"/>  
+        </test>
+
+        <!-- Test for the GTF output -->
+        <test expect_num_outputs="3">
+            <!-- TEfinder commands: TEfinder -alignment sample.bam -fa reference.fa -gtf TEs.gtf -te List_of_TEs.txt -out gtf -->
+            <param name="FastaFile" ftype="fasta" value="reference.fa"/>
+            <param name="alignmentFile" ftype="bam" value="sample.bam"/>
+            <param name="TransposonsInGenome" ftype="gtf" value="TEs.gtf"/>
+            <param name="TransposonsToSearch" ftype="txt" value="List_of_TEs.txt"/>
+            <param name="OutFormat" value="gtf" />
+            <output name="bteinsertion" file="TEinsertions.bed" ftype="bed"/>
+            <output name="gteinsertion" file="TEinsertions.gtf" ftype="gtf"/>
+            <output name="discordantreads" file="DiscordantReads.bam" ftype="bam"/>
+        </test>
+    </tests>
+
+    <help>
+        <![CDATA[
+        A bioinformatics tool for detecting novel transposable element insertions
+
+        Authors: Vista Sohrab & Dilay Hazal Ayhan
+
+        TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data.
+
+        **Output files**::
+
+            TE_insertions.bed contains identified TE insertion events in sample (in the final column, FILTER attribute with "PASS" refers to high confidence insertion events while instances labeled as "in_repeat", "weak_evidence", "strand bias" or a combination of these three labels indicate less confident insertion events)
+            
+            TE_insertions.gtf is provided with the same information as the BED file if using -out GTF
+            
+            DiscordantReads.bam contains all discordant reads that have been identified based on the TEs of interest that have been submitted to TEfinder
+
+        **Note**::
+
+            Modifying the maximum TSD length (-k) could be useful if there is an unexpected number of insertion events identified with the default parameter. The optimal maximum TSD length can vary across datasets.
+            Modifying the fragment insert size (-fis) based on the sequencing library preparation can be useful.
+
+        ]]>
+    </help>
+
+    <citations>
+        <citation type="doi">10.5281/zenodo.4479946</citation>
+    </citations>
+
+</tool>