changeset 0:c701eddc9fec draft

planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 181f00441ba635991889a85b90fa9741a8c8e978-dirty

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+++ b/do_not_track_info.md	Tue Aug 08 11:26:39 2023 +0000
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+### Version system:
+@TOOL_VERSION@ correspond to Tidecluster version + .X for version of xml tool definition

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Aug 08 11:26:39 2023 +0000
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+<macros>
+    <token name="@TOOL_VERSION@">0.8.1</token>
+    <token name="@REQUIREMENT_VERSION@">0.0.8</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@REQUIREMENT_VERSION@">tidecluster</requirement>
+        </requirements>
+    </xml>
+</macros>
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tidecluster.xml	Tue Aug 08 11:26:39 2023 +0000
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+<tool id="tidecluster" name="TideCluster" version="@TOOL_VERSION@">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <description>Identify tandem repeats in genome assemblies</description>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir -p output && cd output &&
+        TideCluster.py run_all
+        -f '$fasta'
+        -pr 'tidecluster'
+        #if $library:
+        -l '$library'
+        #end if
+        -m $min_length
+        -T ' -p $min_period -P $max_period -e $max_diverg'
+        -nd $no_dust
+        -c \${GALAXY_SLOTS:-1}
+        -M $min_total_length
+        &&
+        cp tidecluster_tidehunter.gff3 '$gff3_tidehunter'
+        &&
+        cp tidecluster_clustering.gff3 '$gff3_clustering'
+        &&
+        cp tidecluster_tarean_report.html '$tarean_report'
+        &&
+        mkdir -p ${tarean_report.extra_files_path}
+        &&
+        cp -r tidecluster_tarean ${tarean_report.extra_files_path}/
+        &&
+        zip -r output.zip *
+
+
+        #if $library:
+        &&
+        cp tidecluster_annotation.gff3 '$gff3_annotation'
+        &&
+        cp tidecluster_annotation.tsv '$csv_annotation'
+        #end if
+        &&
+        mv output.zip '$output_archive'
+
+    ]]></command>
+    <inputs>
+        <param type="data" name="fasta" format="fasta" label="Reference fasta"
+               help="Path to reference sequence in fasta format"/>
+        <param type="data" name="library" format="fasta" label="Library"
+               help="Path to library of tandem repeats" optional="true"/>
+        <param type="integer" name="min_length" value="5000"
+               label="Minimum length of tandem repeat"/>
+        <param type="integer" name="min_period" value="40"
+               label="Minimum period size of tandem repeat" min="2"/>
+        <param type="integer" name="max_period" value="3000"
+               label="Maximum period size of tandem repeat" max="20000"/>
+        <param type="float" name="max_diverg" value="0.25"
+               label="Maximum allowed divergence rate between two consecutive repeats"
+               min="0" max="1"/>
+        <param type="boolean" name="no_dust" truevalue="--no_dust" falsevalue=""
+               checked="false" label="Do not use dust filter in blastn when clustering"/>
+        <param type="integer" name="min_total_length" value="50000"
+               label="Minimum combined length of tandem repeat arrays within a single cluster"/>
+    </inputs>
+    <outputs>
+        <data name="output_archive" format="zip"
+              label="${tool.name} on ${on_string}: Archive with complete results"/>
+        <data name="gff3_tidehunter" format="gff3"
+              label="${tool.name} on ${on_string}: GFF3 TideHunter Output" hidden="true"/>
+        <data name="gff3_clustering" format="gff3"
+              label="${tool.name} on ${on_string}: GFF3 TideCluster Output"/>
+        <data name="gff3_annotation" format="gff3"
+              label="${tool.name} on ${on_string}: GFF3 TideCluster Annotated Output">
+            <filter>library is not None</filter>
+        </data>
+        <data name="csv_annotation" format="tsv"
+              label="${tool.name} on ${on_string}: TSV TideCluster Annotated Output">
+            <filter>library is not None</filter>
+        </data>
+        <data name="tarean_report" format="html"
+              label="${tool.name} on ${on_string}: TAREAN Report"/>
+
+
+
+    </outputs>
+    <help><![CDATA[
+    **TideCluster** is a software tool designed to identify tandem repeats in genome assemblies by utilizing Tidehunter to detect tandem repeats clustering these repeats based on similarity using mmseqs2 and NCBI BLAST. The software runs in four steps as outlined below:
+
+- **Tidehunter step**: In this initial step, Tidehunter is utilized to identify tandem repeats. As TideHunter's performance diminishes with larger sequences, the input fasta file is divided into smaller overlapping segments, with each segment analyzed individually. Results from individual segments are parsed and merged into a single GFF3 file. Tandem repeats detected in this step are often fragmented into multiple overlapping pieces.
+
+- **Clustering step**: Prior to clustering, all arrays that do not meet the minimum length requirement are removed from the analysis and saved in a separate GFF3 file. Arrays exceeding the minimum length requirement are clustered based on similarity. Clustering occurs in two stages. First, mmseqs2 is employed in the initial round of clustering. The second round involves an all-to-all comparison using NCBI-BLAST, followed by graph-based clustering. The GFF3 file from the Tidehunter step is updated to include cluster assignment information. Simple sequence repeats are excluded from the clustering step and are analyzed separately.
+
+- **Annotation step**: Consensus sequences from TideHunter for each cluster are examined by RepeatMasker against a library of tandem repeats. The resulting annotation for each tandem repeat is used to update the information in the GFF3 file. This step is optional.
+
+- **TAREAN step**: In this final step, the Tandem Repeat Analyzer (TAREAN) estimates consensus sequences using a k-mer-based approach on the original sequences from the reference. Consensus sequences of simple sequence repeats are evaluated separately, as TAREAN performs poorly on tandem repeats with short monomers. The results of the analysis are saved in an HTML summary.
+
+**Credits**
+
+TideCluster utilizes Tidehunter [https://github.com/Xinglab/TideHunter] for tandem repeat detection and TAREAN for reconstruction of consensus sequences of tandem repeats. If you use TideCluster please cite:
+
+- https://github.com/kavonrtep/TideCluster
+- TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads (https://doi.org/10.1093/nar/gkx257)
+- TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain (https://doi.org/10.1093/bioinformatics/btz376)
+    ]]></help>
+    <citations>
+
+    </citations>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tidecluster_annotation.xml	Tue Aug 08 11:26:39 2023 +0000
@@ -0,0 +1,47 @@
+<tool id="tidecluster_annotation" name="TideCluster Annotation" version="@TOOL_VERSION@">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <description>Annotate tandem repeats identified by TideCluster using custom library of tandem repeats</description>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        #set $prefix = 'tidecluster'
+        mkdir extracted &&
+        unzip '$input_archive' -d extracted && cd extracted &&
+        TideCluster.py annotation
+        -pr '$prefix'
+        -l '$library'
+        -c \${GALAXY_SLOTS:-1}
+        &&
+        cp '${prefix}_annotation.gff3' '$gff3_annotation'
+        &&
+        cp '${prefix}_annotation.tsv' '$tsv_annotation'
+    ]]></command>
+    <inputs>
+        <param type="data" name="input_archive" format="zip" label="Output archive from previous TideCluster run" help="The zip archive containing the output from a previous TideCluster run."/>
+        <param type="data" name="library" format="fasta" label="Library of tandem repeats" help="Path to library of tandem repeats."/>
+    </inputs>
+    <outputs>
+        <data name="gff3_annotation" format="gff3" label="${tool.name} on ${on_string}: GFF3 TideCluster Annotated Output"/>
+        <data name="tsv_annotation" format="tsv" label="${tool.name} on ${on_string}: TSV TideCluster Annotated Output"/>
+    </outputs>
+    <help><![CDATA[
+    **TideCluster Annotation Step**
+
+    This step of TideCluster is responsible for annotating the tandem repeats using a library of tandem repeats. The consensus sequences from TideHunter for each cluster are examined by RepeatMasker against a library of tandem repeats. The resulting annotation for each tandem repeat is used to update the information in the GFF3 file.
+
+    **Inputs:**
+
+
+    - Output archive from previous TideCluster run: The zip archive containing the output from a previous TideCluster run.
+    - Library of tandem repeats: FASTA library with tandem repeats, Library must be in RepeatMasker format
+
+    **Outputs:**
+
+    - GFF3 TideCluster Annotated Output: GFF3 file with tandem repeats annotated by RepeatMasker. Attribute Annotation is added to GFF3 file.
+    - TSV TideCluster Annotated Output: Summarized annotation for each TRC cluster in a tab-delimited format.
+    ]]></help>
+    <citations>
+        <!-- Add citations here -->
+    </citations>
+</tool>