/tools/emboss_5/emboss_isochore.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 88 lines · 53 code · 19 blank · 16 comment · 0 complexity · 13687829c173d9b2bd8f81875d0753a1 MD5 · raw file
- <tool id="EMBOSS: isochore47" name="isochore" version="5.0.0">
- <description>Plots isochores in large DNA sequences</description>
- <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
- <command interpreter="perl">emboss_single_outputfile_wrapper.pl isochore -sequence $input1 -outfile $ofile2 -goutfile $ofile1 -graph png -window $window -shift $shift -auto</command>
- <!-- <command interpreter="perl">emboss_single_outputfile_wrapper.pl isochore -sequence $input1 -goutfile $ofile1 -graph png -window $window -shift $shift -auto</command>-->
- <inputs>
- <param format="fasta" name="input1" type="data">
- <label>Sequences</label>
- </param>
- <param name="window" size="4" type="text" value="1000">
- <label>Window size</label>
- </param>
- <param name="shift" size="4" type="text" value="100">
- <label>Shift increment</label>
- </param>
- </inputs>
- <outputs>
- <data format="png" name="ofile1" />
- <data format="isochore" name="ofile2" />
- </outputs>
- <!-- <tests>
- <test>
- <param name="input1" value="2.fasta"/>
- <param name="window" value="1000"/>
- <param name="shift" value="100"/>
- <output name="ofile1" file="emboss_isochore_out.isochore"/>
- <output name="ofile2" file="emboss_isochore_out.isochore"/>
- </test>
- <test>
- <param name="input1" value="2.fasta"/>
- <param name="window" value="1000"/>
- <param name="shift" value="100"/>
- <output name="ofile2" file="emboss_isochore_out.isochore"/>
- </test>
- </tests>-->
- <help>
- .. class:: warningmark
- The input dataset needs to be sequences.
- -----
- **Syntax**
- 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_.
- .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/isochore.html
- - Both **Window size** and **Shift increment** are intergers.
- -----
- **Example**
- - Input sequences::
- >hg18_dna range=chrX:151073054-151073376 5'pad=0 3'pad=0 revComp=FALSE strand=? repeatMasking=none
- TTTATGTCTATAATCCTTACCAAAAGTTACCTTGGAATAAGAAGAAGTCA
- GTAAAAAGAAGGCTGTTGTTCCGTGAAATACTGTCTTTATGCCTCAGATT
- TGGAGTGCTCAGAGCCTCTGCAGCAAAGATTTGGCATGTGTCCTAGGCCT
- GCTCAGAGCAGCAAATCCCACCCTCTTGGAGAATGAGACTCATAGAGGGA
- CAGCTCCCTCCTCAGAGGCTTCTCTAATGGGACTCCAAAGAGCAAACACT
- CAGCCCCATGAGGACTGGCCAGGCCAAGTGGTGTGTGGGAACAGGGAGCA
- GCGGTTTCCAAGAGGATACAGTA
- - Output data file::
- Position Percent G+C 1 .. 323
- 80 0.422
- 112 0.460
- 144 0.509
- 176 0.534
- 208 0.553
- 240 0.553
- - Output graphics file:
- .. image:: ./static/emboss_icons/isochore.png
- ------
- **Citation**
- 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. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_
- </help>
- </tool>