annotate tidecluster_annotation.xml @ 10:971dbc97e607 draft default tip

planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 5269b4297ea690bce0802c3c1cb217f24290f1ec-dirty
author petr-novak
date Fri, 08 Mar 2024 13:16:45 +0000
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1 <tool id="tidecluster_annotation" name="TideCluster- Annotate Clusters" version="@TOOL_VERSION@">
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2 <macros>
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3 <import>macros.xml</import>
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4 </macros>
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5 <description>Annotate tandem repeats clusters identified by TideCluster using custom library of tandem repeats</description>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 #set $prefix = 'tidecluster'
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9 mkdir extracted &&
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10 unzip '$input_archive' -d extracted && cd extracted &&
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11 TideCluster.py annotation
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12 -pr '$prefix'
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13 -l '$library'
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14 -c \${GALAXY_SLOTS:-1}
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15 &&
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16 cp '${prefix}_annotation.gff3' '$gff3_annotation'
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17 &&
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18 cp '${prefix}_annotation.tsv' '$tsv_annotation'
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19 ]]></command>
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20 <inputs>
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21 <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."/>
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22 <param type="data" name="library" format="fasta" label="Library of tandem repeats" help="Path to library of tandem repeats."/>
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23 </inputs>
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24 <outputs>
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25 <data name="gff3_annotation" format="gff3" label="${tool.name} on ${on_string}: GFF3 TideCluster Annotated Output"/>
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26 <data name="tsv_annotation" format="tsv" label="${tool.name} on ${on_string}: TSV TideCluster Annotated Output"/>
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27 </outputs>
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28 <help><![CDATA[
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29 **TideCluster Annotation Step**
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31 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.
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33 **Inputs:**
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36 - Output archive from previous TideCluster run: The zip archive containing the output from a previous TideCluster run.
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37 - Library of tandem repeats: FASTA library with tandem repeats, Library must be in RepeatMasker format
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39 **Outputs:**
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41 - GFF3 TideCluster Annotated Output: GFF3 file with tandem repeats annotated by RepeatMasker. Attribute Annotation is added to GFF3 file.
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42 - TSV TideCluster Annotated Output: Summarized annotation for each TRC cluster in a tab-delimited format.
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43 ]]></help>
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44 <citations>
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45 <!-- Add citations here -->
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46 </citations>
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47 </tool>