Mercurial > repos > iuc > funannotate_sort

annotate funannotate_sort.xml @ 0:998b719a94cb draft

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"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
author iuc
date Thu, 26 Aug 2021 06:56:18 +0000
parents
children 520e30695ec3
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1 <tool id="funannotate_sort" name="Sort assembly" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description></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 <version_command>funannotate check --show-versions</version_command>
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10 <command><![CDATA[
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11 funannotate sort
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12 --input '${input}'
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13 --out '${output}'
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14 --base '${base}'
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15 --minlen ${minlen}
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16 ]]></command>
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17 <inputs>
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18 <param argument="--input" type="data" format="fasta" label="Assembly to sort" />
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19
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20 <param argument="--base" type="text" value="scaffold" label="Base name to relabel contigs">
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21 <validator type="regex" message="No special characters allowed">^(?:\w+)?$</validator>
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22 </param>
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23 <param argument="--minlen" type="integer" value="0" label="Shorter contigs are discarded" />
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24 </inputs>
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25 <outputs>
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26 <data name='output' format='fasta' label="${tool.name} on ${on_string}: sorted assembly" />
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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" value="genome.fa" />
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31 <output name="output">
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32 <assert_contents>
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33 <has_text text=">scaffold_1" />
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34 <has_text text=">scaffold_4" />
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35 </assert_contents>
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36 </output>
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37 </test>
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38 <test>
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39 <param name="input" value="genome.fa" />
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40 <param name="base" value="something" />
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41 <param name="minlen" value="2100" />
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42 <output name="output">
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43 <assert_contents>
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44 <has_text text=">something_1" />
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45 <not_has_text text=">something_4" />
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46 </assert_contents>
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47 </output>
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48 </test>
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49 </tests>
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50 <help><![CDATA[
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51 Funannotate_ sort
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52 -----------------
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53
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54 Funannotate_ is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).
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55
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56 This script sorts the input contigs by size (longest->shortest) and then relabels
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57 the contigs with a simple name (e.g. scaffold_1). Augustus can have problems with
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58 some complicated contig names.
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59
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60 .. _Funannotate: http://funannotate.readthedocs.io
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61 ]]></help>
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62 <expand macro="citations" />
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63 </tool>