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annotate dapars.xml @ 0:bb84ee2f2137 draft

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planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
author mvdbeek
date Tue, 27 Oct 2015 10:14:33 -0400
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children 47b0044bc7f8
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bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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1 <tool id="dapars" name="dapars" version="0.1.4">
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2 <description>infer de-novo alternative polyadenylation from rna-seq</description>
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3 <requirements>
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4 <requirement type="package" version="1.9">numpy</requirement>
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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5 <requirement type="package" version="2.22">bedtools</requirement>
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" />
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9 </stdio>
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10 <command interpreter="python"><![CDATA[
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11 dapars.py -c
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12 #for $c in $controls:
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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13 "$c"
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14 #end for
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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15 -t
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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16 #for $t in $treatments:
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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17 "$t"
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18 #end for
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19 -u "$utr"
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20 -o "$apa_sites"
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21 -cpu \${GALAXY_SLOTS:-4}
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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22 --coverage_threshold "$coverage_threshold"
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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23 --search_start "$search_start"
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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24 #if $make_breakpoint:
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25 -b "$breakpoint_bed"
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26 #end if
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27 ]]></command>
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28 <inputs>
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29 <param type="data" name="utr" format="gtf" label="GFF file containing 3prime UTRs" help="featureType of the UTRs
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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30 must be UTR, and the attribute group must have geneid in first position."/>
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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31 <param type="data" name="controls" format="bam,sam" multiple="True" label="Control alignment files" help="Select control alignment files" />
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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32 <param type="data" name="treatments" format="bam,sam" multiple="True" label="Treatment alignment files" help="Select treatment alignment files" />
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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33 <param type="integer" name="search_start" value="100" optional="False" min="1" label="Search start" help="Search start in nucleotides downstream of the start of the UTR. Necessary to correct for proximal drops in coverage. Select 200 for humans. Genomes with short UTRs may require more prpximal search start points."/>
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34 <param type="float" name="coverage_threshold" value="20" optional="False" label="Coverage threshold" help="Skip the analysis of UTRs whose mean coverage is below the Coverage Threshold in any of the alignment files."/>
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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35 <param name="make_breakpoint" type="boolean" checked="False" label="Output bedfile with breakpoint positions?"/>
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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36 </inputs>
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37 <outputs>
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38 <data name="apa_sites" format="tabular" />
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39 <data name="breakpoint_bed" format="bed6">
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40 <filter>(make_breakpoint == True)</filter>
bb84ee2f2137 planemo upload for repository https://github.com/mvdbeek/dapars commit 868f8f2f7ac5d70c39b7d725ff087833b0f24f52-dirty
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41 </data>
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42 </outputs>
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43 <help><![CDATA[
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44 TODO: Fill in help.
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45 ]]></help>
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46 <citations>
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47 <citation type="doi">10.1038/ncomms6274</citation>
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48 </citations>
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49 </tool>