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annotate repeatmodeler.xml @ 6:fbe22cb3c869 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler commit 4e56d2284d79d5f0d5d103e5a165835b73d580ab
author iuc
date Mon, 06 Nov 2023 20:29:35 +0000
parents 8661b2607b7e
children 4a172d211285
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dda44fd49bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler commit a4bb321c4a8bd6e8d331df6ed840e00d1c4599f2"
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1 <tool id="repeatmodeler" name="RepeatModeler" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>Model repetitive DNA</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <expand macro="requirements" />
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 BuildDatabase -name 'rmdb' '$input_file'
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dda44fd49bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler commit a4bb321c4a8bd6e8d331df6ed840e00d1c4599f2"
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12 &&
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8661b2607b7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler commit 652ae30a67649b070efd62ba90159e079c5e7bd5
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14 RepeatModeler -database 'rmdb' -threads \${GALAXY_SLOTS:-1}
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15 ]]></command>
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16 <inputs>
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17 <param type="data" name="input_file" format="fasta" label="Input genome fasta"/>
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18 </inputs>
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19 <outputs>
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20 <data format="fasta" name="sequences" from_work_dir="rmdb-families.fa" label="${tool.name} on ${on_string}: consensus sequences" />
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21 <data format="stockholm" name="seeds" from_work_dir="rmdb-families.stk" label="${tool.name} on ${on_string}: seed alignments" />
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="input_file" value="eco.fasta.gz" ftype="fasta.gz"/>
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26 <output name="sequences" ftype="fasta">
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27 <assert_contents>
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28 <has_text text="( RepeatScout Family Size ="/>
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29 <has_text text="rnd-1_family-0"/>
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30 </assert_contents>
dda44fd49bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler commit a4bb321c4a8bd6e8d331df6ed840e00d1c4599f2"
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31 </output>
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32 <output name="seeds" ftype="stockholm">
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33 <assert_contents>
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34 <has_text text="#=GF DE RepeatModeler Generated"/>
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35 </assert_contents>
dda44fd49bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler commit a4bb321c4a8bd6e8d331df6ed840e00d1c4599f2"
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36 </output>
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37 </test>
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38 </tests>
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39 <help><![CDATA[
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40 RepeatModeler is a de novo transposable element (TE) family identification and modeling package. At the heart of RepeatModeler are three de-novo repeat finding programs ( RECON, RepeatScout and LtrHarvest/Ltr_retriever ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data.
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41
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42 RepeatModeler assists in automating the runs of the various algorithms given a genomic database, clustering redundant results, refining and classifying the families and producing a high quality library of TE families suitable for use with RepeatMasker and ultimately for submission to the Dfam database (http://dfam.org).
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43 ]]></help>
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44 <expand macro="citations" />
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45 </tool>