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annotate gc_skew.xml @ 5:a64dc31ab7f2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 39a0176dab234a07118a79ac44ca7d79469d3b91"
author iuc
date Thu, 23 Jan 2020 07:27:22 -0500
parents 014a21767ac4
children df7356989ac1
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014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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1 <?xml version="1.0"?>
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2 <tool id="circos_gc_skew" name="GC Skew" version="@WRAPPER_VERSION@">
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3 <description>calculates skew over genomic sequences</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements">
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8 </expand>
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9 <command detect_errors="exit_code"><![CDATA[
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10 ln -s -f
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11 #if $reference_genome.reference_genome_source == "history"
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12 '$reference_genome.history_item'
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13 #else
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14 '$reference_genome.builtin.fields.path'
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15 #end if
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16 reference.fa &&
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17
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18 python '$__tool_directory__/gc_skew.py' reference.fa '$window' '$output'
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19 ]]></command>
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20 <inputs>
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21 <conditional name="reference_genome">
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22 <param label="Source for reference genome" name="reference_genome_source" type="select">
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23 <option selected="True" value="history">Use a genome from history</option>
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24 <option value="builtin">Use a built-in genome"</option>
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25 </param>
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26 <when value="history">
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27 <param format="fasta" type="data" name="history_item" label="Select a reference genome"/>
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28 </when>
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29 <when value="builtin">
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30 <param label="Select a reference genome" name="builtin" type="select">
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31 <options from_data_table="all_fasta">
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32 <filter column="2" type="sort_by" />
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33 <validator message="No genomes are available for the selected input dataset" type="no_options" />
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34 </options>
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35 </param>
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36 </when>
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37 </conditional>
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38 <param argument="window" type="integer" min="1" value="100000" label="Window size" />
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39 </inputs>
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40 <outputs>
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41 <data name="output" format="bigwig" />
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42 </outputs>
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43 <tests>
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44 <test>
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45 <conditional name="reference_genome">
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46 <param name="reference_genome_source" value="history" />
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47 <param name="history_item" value="gc_skew/1.fa" ftype="fasta"/>
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48 </conditional>
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49 <param name="window" value="2" />
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50 <output name="output" file="gc_skew/1.bw" ftype="bigwig" />
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51 </test>
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52 </tests>
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53 <help><![CDATA[
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54 Calculate GC skew (G-C)/(G+C) for multiple windows along the sequence.
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55
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56 Returns a list of ratios (floats), controlled by the length of the sequence and the size of the window.
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57
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58 Returns 0 for windows without any G/C by handling zero division errors.
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59
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60 Does NOT look at any ambiguous nucleotides.
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61 ]]></help>
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62 <expand macro="citations" />
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63 </tool>