changeset 2:299f14a6050a draft

planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd

--- a/macros.xml	Tue Aug 08 11:30:17 2023 +0000
+++ b/macros.xml	Thu Aug 17 14:23:02 2023 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.8.1</token>
-    <token name="@REQUIREMENT_VERSION@">0.0.8</token>
+    <token name="@TOOL_VERSION@">1.1</token>
+    <token name="@REQUIREMENT_VERSION@">1.0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@REQUIREMENT_VERSION@">tidecluster</requirement>

--- a/tidecluster.xml	Tue Aug 08 11:30:17 2023 +0000
+++ b/tidecluster.xml	Thu Aug 17 14:23:02 2023 +0000
@@ -28,9 +28,9 @@
         &&
         cp -r tidecluster_tarean ${tarean_report.extra_files_path}/
         &&
+        cp tidecluster_consensus_dimer_library.fasta ${trc_library}
+        &&
         zip -r output.zip *
-
-
         #if $library:
         &&
         cp tidecluster_annotation.gff3 '$gff3_annotation'
@@ -71,10 +71,14 @@
               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 ${on_string}: TSV TideCluster Annotated Output">
             <filter>library is not None</filter>
         </data>
+
+        <data name="trc_library" format="fasta"
+              label="${tool.name} on ${on_string}: Library of tandem repeats"/>
         <data name="tarean_report" format="html"
               label="${tool.name} on ${on_string}: TAREAN Report"/>
 

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tidecluster_reannotate.xml	Thu Aug 17 14:23:02 2023 +0000
@@ -0,0 +1,30 @@
+<tool id="tc_reannotate" name="TideCluster Reannotate" version="@TOOL_VERSION">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <description>Reannotate tandem repeats using similarity-based approach</description>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        tc_reannotate.py
+        -s '$ref_seq'
+        -f '$fasta_file'
+        -c \${GALAXY_SLOTS:-1}
+        -o '$output'
+    ]]></command>
+    <inputs>
+        <param type="data" name="ref_seq" format="fasta" label="Reference sequence" help="FASTA file to be annotated by TRC library"/>
+        <param type="data" name="fasta_file" format="fasta" label="Tandem repeat library" help="FASTA file with tandem repeat library from TideCluster"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="gff3" label="${tool.name} on ${on_string}: GFF3 Output"/>
+    </outputs>
+    <help><![CDATA[
+        This is a tool for reannotating tandem repeats using a similarity-based approach. This tool runs RepeatMasker using the tandem repeat
+        library generated by TAREAN in TideCluster. Resulting RepeatMasker output is processed to retain only high-quality tandem repeat hits.
+        Overlapping tandem repeat annotation are merged, and regions shorter than twice the monomer length are excluded from the output.
+        Reannotate tandem repeats using similarity-based approach can fill in gaps in annotation provided by TideCluster/TideHunter.
+    ]]></help>
+    <citations>
+        <!-- Add citations here -->
+    </citations>
+</tool>
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