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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit a80e3e4aa3a40970af507bf9119cf7f1c2ffb336
author iuc
date Mon, 16 Dec 2024 14:40:31 +0000
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cf3ac75c232c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit a80e3e4aa3a40970af507bf9119cf7f1c2ffb336
iuc
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1 <tool id="glimmer_acgt_content" name="ACGT Content" version="@WRAPPER_VERSION@" profile="@PROFILE_VERSION@">
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2 <description>of windows in each sequence</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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cf3ac75c232c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit a80e3e4aa3a40970af507bf9119cf7f1c2ffb336
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <command><![CDATA[
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9 window-acgt
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10 $percentage
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11 $input_win_len
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12 $input_win_skip
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13 < '$infile' > '$output'
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14
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15 ##TODO prettify the output
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16 ]]></command>
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17 <inputs>
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18 <param name="infile" type="data" format="fasta" label="Genome Sequence"/>
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19 <param name="input_win_len" type="integer" value="10" label="The width of the sliding window"/>
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20 <param name="input_win_skip" type="integer" value="10" label="The number of positions between windows to report"/>
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21 <param name="percentage" type="boolean" truevalue="-p" falsevalue="" checked="true" label="Report percentages instead of counts"/>
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22 </inputs>
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23 <outputs>
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24 <data name="output" format="tabular"/>
0d866616c437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="infile" value="streptomyces_Tu6071_genomic.fasta" />
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29 <output name="output" file="streptomyces_Tu6071_genomic.acgt" />
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30 </test>
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31 </tests>
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32 <help>
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33 <![CDATA[
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35 **What it does**
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37 This tool calculates the ACGT-Content from a given Sequence, given a sliding window.
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39 -------
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41 **Output**
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0d866616c437 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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43 Output is in the format:
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45 window-start window-len A's C's G's T's #other %GC
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47 Note the last window in the sequence can be shorter than *window-len* if the sequence ends prematurely
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48 ]]>
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49 </help>
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50 <expand macro="citation" />
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51 </tool>