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annotate emboss_isochore.xml @ 20:21a9fb508031 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:05:39 +0000
parents 27c43fb015f0
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1 <tool id="EMBOSS: isochore47" name="isochore" version="@VERSION@.1">
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2 <description>Plots isochores in large DNA sequences</description>
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3 <expand macro="bio_tools" />
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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 <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' isochore -sequence '$input1' -outfile '$ofile2' -goutfile '$ofile1' -graph png -window $window -shift $shift -auto</command>
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9 <inputs>
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10 <param name="input1" type="data" format="fasta" label="Sequences" />
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11 <param name="window" type="integer" value="1000" label="Window size" />
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12 <param name="shift" type="integer" value="100" label="Shift increment" />
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13 </inputs>
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14 <outputs>
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15 <data name="ofile1" format="png" />
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16 <data name="ofile2" format="isochore" />
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17 </outputs>
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18 <!-- <tests>
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19 <test>
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20 <param name="input1" value="2.fasta"/>
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21 <param name="window" value="1000"/>
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22 <param name="shift" value="100"/>
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23 <output name="ofile1" file="emboss_isochore_out.isochore"/>
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24 <output name="ofile2" file="emboss_isochore_out.isochore"/>
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25 </test>
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26 <test>
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27 <param name="input1" value="2.fasta"/>
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28 <param name="window" value="1000"/>
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29 <param name="shift" value="100"/>
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30 <output name="ofile2" file="emboss_isochore_out.isochore"/>
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31 </test>
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32 </tests>-->
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33 <help>
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34 .. class:: warningmark
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36 The input dataset needs to be sequences.
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38 -----
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40 **Syntax**
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41
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42 This application plots GC content over a sequence. It is intended for large sequences such as complete chromosomes or large genomic contigs, although interesting results can also be obtained from shorter sequences. You can view the original documentation here_.
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43
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44 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/isochore.html
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46 - Both **Window size** and **Shift increment** are intergers.
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48 -----
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50 **Example**
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52 - Input sequences::
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54 >hg18_dna range=chrX:151073054-151073376 5'pad=0 3'pad=0 revComp=FALSE strand=? repeatMasking=none
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55 TTTATGTCTATAATCCTTACCAAAAGTTACCTTGGAATAAGAAGAAGTCA
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56 GTAAAAAGAAGGCTGTTGTTCCGTGAAATACTGTCTTTATGCCTCAGATT
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57 TGGAGTGCTCAGAGCCTCTGCAGCAAAGATTTGGCATGTGTCCTAGGCCT
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58 GCTCAGAGCAGCAAATCCCACCCTCTTGGAGAATGAGACTCATAGAGGGA
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59 CAGCTCCCTCCTCAGAGGCTTCTCTAATGGGACTCCAAAGAGCAAACACT
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60 CAGCCCCATGAGGACTGGCCAGGCCAAGTGGTGTGTGGGAACAGGGAGCA
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61 GCGGTTTCCAAGAGGATACAGTA
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62
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63 - Output data file::
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64
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65 Position Percent G+C 1 .. 323
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66 80 0.422
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67 112 0.460
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68 144 0.509
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69 176 0.534
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70 208 0.553
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71 240 0.553
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73 - Output graphics file:
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75 .. image:: ./static/emboss_icons/isochore.png
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76 </help>
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77 <expand macro="citations" />
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78 </tool>