Mercurial > repos > devteam > emboss_5
diff emboss_isochore.xml @ 11:0e2484b6829b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
| author | iuc |
|---|---|
| date | Mon, 30 Jan 2017 13:27:40 -0500 |
| parents | 9b98d3d903c6 |
| children | 27c43fb015f0 |
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--- a/emboss_isochore.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_isochore.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,29 +1,25 @@ -<tool id="EMBOSS: isochore47" name="isochore" version="5.0.0"> +<tool id="EMBOSS: isochore47" name="isochore" version="5.0.0.1"> <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 $shift -auto</command>--> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' isochore -sequence '$input1' -outfile '$ofile2' -goutfile '$ofile1' -graph png -window $window -shift $shift -auto</command> <inputs> - <param format="fasta" name="input1" type="data"> - <label>Sequences</label> - </param> - <param name="window" type="text" value="1000"> - <label>Window size</label> - </param> - <param name="shift" type="text" value="100"> - <label>Shift increment</label> - </param> + <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 format="png" name="ofile1" /> - <data format="isochore" name="ofile2" /> + <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="ofile1" file="emboss_isochore_out.isochore"/> <output name="ofile2" file="emboss_isochore_out.isochore"/> </test> <test> @@ -31,10 +27,9 @@ <param name="window" value="1000"/> <param name="shift" value="100"/> <output name="ofile2" file="emboss_isochore_out.isochore"/> - </test> + </test> </tests>--> <help> - .. class:: warningmark The input dataset needs to be sequences. @@ -43,9 +38,9 @@ **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_. +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 + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/isochore.html - Both **Window size** and **Shift increment** are intergers. @@ -77,14 +72,6 @@ - Output graphics file: .. image:: ./static/emboss_icons/isochore.png - ------- - -**Citation** - -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. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -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> + <expand macro="citations" /> </tool>