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annotate emboss_isochore.xml @ 10:9b98d3d903c6 draft

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author devteam
date Fri, 12 Aug 2016 19:17:10 -0400
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1 <tool id="EMBOSS: isochore47" name="isochore" version="5.0.0">
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2 <description>Plots isochores in large DNA sequences</description>
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3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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4 <command interpreter="perl">emboss_single_outputfile_wrapper.pl isochore -sequence $input1 -outfile $ofile2 -goutfile $ofile1 -graph png -window $window -shift $shift -auto</command>
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5 <!-- <command interpreter="perl">emboss_single_outputfile_wrapper.pl isochore -sequence $input1 -goutfile $ofile1 -graph png -window $window -shift $shift -auto</command>-->
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6 <inputs>
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7 <param format="fasta" name="input1" type="data">
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8 <label>Sequences</label>
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9 </param>
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10 <param name="window" type="text" value="1000">
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11 <label>Window size</label>
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12 </param>
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13 <param name="shift" type="text" value="100">
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14 <label>Shift increment</label>
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15 </param>
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16 </inputs>
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17 <outputs>
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18 <data format="png" name="ofile1" />
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19 <data format="isochore" name="ofile2" />
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20 </outputs>
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21 <!-- <tests>
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22 <test>
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23 <param name="input1" value="2.fasta"/>
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24 <param name="window" value="1000"/>
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25 <param name="shift" value="100"/>
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26 <output name="ofile1" file="emboss_isochore_out.isochore"/>
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27 <output name="ofile2" file="emboss_isochore_out.isochore"/>
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28 </test>
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29 <test>
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30 <param name="input1" value="2.fasta"/>
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31 <param name="window" value="1000"/>
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32 <param name="shift" value="100"/>
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33 <output name="ofile2" file="emboss_isochore_out.isochore"/>
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34 </test>
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35 </tests>-->
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36 <help>
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37
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38 .. class:: warningmark
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39
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40 The input dataset needs to be sequences.
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41
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42 -----
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43
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44 **Syntax**
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45
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46 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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47
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48 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/isochore.html
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49
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50 - Both **Window size** and **Shift increment** are intergers.
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51
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52 -----
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53
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54 **Example**
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55
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56 - Input sequences::
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57
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58 >hg18_dna range=chrX:151073054-151073376 5'pad=0 3'pad=0 revComp=FALSE strand=? repeatMasking=none
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59 TTTATGTCTATAATCCTTACCAAAAGTTACCTTGGAATAAGAAGAAGTCA
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60 GTAAAAAGAAGGCTGTTGTTCCGTGAAATACTGTCTTTATGCCTCAGATT
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61 TGGAGTGCTCAGAGCCTCTGCAGCAAAGATTTGGCATGTGTCCTAGGCCT
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62 GCTCAGAGCAGCAAATCCCACCCTCTTGGAGAATGAGACTCATAGAGGGA
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63 CAGCTCCCTCCTCAGAGGCTTCTCTAATGGGACTCCAAAGAGCAAACACT
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64 CAGCCCCATGAGGACTGGCCAGGCCAAGTGGTGTGTGGGAACAGGGAGCA
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65 GCGGTTTCCAAGAGGATACAGTA
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66
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67 - Output data file::
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68
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69 Position Percent G+C 1 .. 323
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70 80 0.422
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71 112 0.460
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72 144 0.509
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73 176 0.534
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74 208 0.553
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75 240 0.553
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77 - Output graphics file:
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79 .. image:: ./static/emboss_icons/isochore.png
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81 ------
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83 **Citation**
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85 For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
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87 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
parents:
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88
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
parents:
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89 </help>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
devteam
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90 </tool>