Mercurial > repos > devteam > emboss_5
view emboss_isochore.xml @ 16:33381b9c268c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 431486be049407b094d495ae4a68bf76d27fa522
author | iuc |
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date | Mon, 28 Jan 2019 14:49:47 -0500 |
parents | 27c43fb015f0 |
children | 21a9fb508031 |
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<tool id="EMBOSS: isochore47" name="isochore" version="@VERSION@.1"> <description>Plots isochores in large DNA sequences</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' isochore -sequence '$input1' -outfile '$ofile2' -goutfile '$ofile1' -graph png -window $window -shift $shift -auto</command> <inputs> <param name="input1" type="data" format="fasta" label="Sequences" /> <param name="window" type="integer" value="1000" label="Window size" /> <param name="shift" type="integer" value="100" label="Shift increment" /> </inputs> <outputs> <data name="ofile1" format="png" /> <data name="ofile2" format="isochore" /> </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://galaxy-iuc.github.io/emboss-5.0-docs/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 </help> <expand macro="citations" /> </tool>