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annotate repeatmodeler.xml @ 2:41bfbaf3c959 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler commit e9a018e8e2c7ff57925f7cbaaab7bb00fd302f23"
author iuc
date Sat, 27 Nov 2021 10:07:06 +0000
parents dda44fd49bcd
children a9fb165808c8
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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">
dda44fd49bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler commit a4bb321c4a8bd6e8d331df6ed840e00d1c4599f2"
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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>
dda44fd49bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler commit a4bb321c4a8bd6e8d331df6ed840e00d1c4599f2"
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5 </macros>
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6 <requirements>
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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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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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dda44fd49bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler commit a4bb321c4a8bd6e8d331df6ed840e00d1c4599f2"
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14 ## "RMBlast jobs will use 4 cores each"
dda44fd49bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler commit a4bb321c4a8bd6e8d331df6ed840e00d1c4599f2"
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15 pa=\$(( (\${GALAXY_SLOTS:-1}+3)/4 ))
dda44fd49bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler commit a4bb321c4a8bd6e8d331df6ed840e00d1c4599f2"
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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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17 &&
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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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19 RepeatModeler -database 'rmdb' -pa \$pa
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20 ]]></command>
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21 <inputs>
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22 <param type="data" name="input_file" format="fasta" label="Input genome fasta"/>
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23 </inputs>
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24 <outputs>
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25 <data format="fasta" name="sequences" from_work_dir="rmdb-families.fa" label="${tool.name} on ${on_string}: consensus sequences" />
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26 <data format="stockholm" name="seeds" from_work_dir="rmdb-families.stk" label="${tool.name} on ${on_string}: seed alignments" />
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="input_file" value="eco.fasta.gz" ftype="fasta.gz"/>
dda44fd49bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler commit a4bb321c4a8bd6e8d331df6ed840e00d1c4599f2"
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31 <output name="sequences" ftype="fasta">
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32 <assert_contents>
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33 <has_text text="( RepeatScout Family Size ="/>
dda44fd49bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler commit a4bb321c4a8bd6e8d331df6ed840e00d1c4599f2"
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34 <has_text text="rnd-1_family-0"/>
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35 </assert_contents>
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36 </output>
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37 <output name="seeds" ftype="stockholm">
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38 <assert_contents>
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39 <has_text text="#=GF DE RepeatModeler Generated"/>
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40 </assert_contents>
dda44fd49bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler commit a4bb321c4a8bd6e8d331df6ed840e00d1c4599f2"
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41 </output>
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42 </test>
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43 </tests>
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44 <help><![CDATA[
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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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45 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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46
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47 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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48 ]]></help>
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49 <expand macro="citations" />
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50 </tool>