[2] | 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" size="4" 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" size="4" 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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| 76 | |
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| 77 | - Output graphics file: |
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| 78 | |
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| 79 | .. image:: ../static/emboss_icons/isochore.png |
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| 80 | |
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| 81 | </help> |
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| 82 | </tool> |
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