Mercurial > repos > bgruening > rnaz_annotate

annotate rnazAnnotate.xml @ 0:8c250234fe1d draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
author bgruening
date Wed, 30 Jan 2019 03:57:11 -0500
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8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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1 <tool id="rnaz_annotate" name="Annotate RNAz" version="2.1">
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2 <requirements>
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3 <requirement type="package" version="2.1">rnaz</requirement>
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4 <requirement type="package" version="3.6.7">python</requirement>
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5 <requirement type="package" version="0.8.0">pybedtools</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code"><![CDATA[
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8 python3 '$__tool_directory__/AnnotateRNAz.py'
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9 --bed '$bed'
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10 --input '$input'
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11 --bedout '$output1'
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12 --rnazout '$output2'
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13 ]]></command>
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14 <inputs>
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15 <param format="txt" name="input" type="data" label="RNAz output to annotate" />
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16 <param type="data" name="bed" format="bed" label="Bed file with annotation" />
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17 </inputs>
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18 <outputs>
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19 <data name="output1" format="bed" />
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20 <data name="output2" format="txt" />
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="input" value="unknown.rnaz.clustered"/>
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25 <param name="bed" value="Annotation.bed"/>
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26 <output name="output1" file="unknown.rnaz.clustered.annotated.bed"/>
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27 <output name="output2" file="unknown.rnaz.clustered.annotated.rnaz"/>
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28 </test>
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29 <test>
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30 <param name="input" value="tRNA.rnaz.clustered"/>
8c250234fe1d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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31 <param name="bed" value="Annotation.bed"/>
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32 <output name="output1" file="tRNA.rnaz.clustered.annotated.bed"/>
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33 <output name="output2" file="tRNA.rnaz.clustered.annotated.rnaz"/>
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34 </test>
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35 </tests>
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36 <help><![CDATA[
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37
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38 Annotated rnaz hits with an annotation BED file,
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39 replaces rnazAnnotate.pl and rnazIndex.pl.
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40 Best used after clustering of RNAz hits.
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41
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42 usage: AnnotateRNAz.py [-h] [-b BED] [-i INPUT] [-o BEDOUT] [-r RNAZOUT]
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43
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44 Intersect RNAz output with Annotation from BED
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45
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46 optional arguments:
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47 -h, --help show this help message and exit
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48 -b BED, --bed BED Annotation BED file
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49 -i INPUT, --input INPUT (RNAz output)
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50 -o BEDOUT, --bedout BEDOUT (Annotated BED output)
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51 -r RNAZOUT, --rnazout RNAZOUT (Annotated rnaz-format output)
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52 ]]>
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53 </help>
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54
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55 <citations>
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56 <citation type="doi">10.1142/9789814295291_0009</citation>
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57 </citations>
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58
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59 </tool>