Mercurial > repos > devteam > emboss_5
diff emboss_newcpgreport.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 (2017-01-30) |
parents | 9b98d3d903c6 |
children | 27c43fb015f0 |
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--- a/emboss_newcpgreport.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_newcpgreport.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,29 +1,20 @@ -<tool id="EMBOSS: newcpgreport57" name="newcpgreport" version="5.0.0"> - <description>Report CpG rich areas</description> - <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>newcpgreport -sequence $input1 -window $window -shift $shift -minlen $minlen -minpc $minpc -outfile $out_file1 -minoe $minoe -auto</command> - <inputs> - <param format="data" name="input1" type="data"> - <label>Sequence</label> - </param> - <param name="window" type="text" value="100"> - <label>Window Size</label> - </param> - <param name="shift" type="text" value="1"> - <label>Step size (shift)</label> - </param> - <param name="minlen" type="text" value="200"> - <label>Minimum length</label> - </param> - <param name="minoe" type="text" value="0.6"> - <label>Minimum average observed to expected ratio</label> - </param> - <param name="minpc" type="text" value="50.0"> - <label>Minimum average percentage of G plus C</label> - </param> - </inputs> - <outputs> - <data format="newcpgreport" name="out_file1" /> +<tool id="EMBOSS: newcpgreport57" name="newcpgreport" version="5.0.0.1"> + <description>Report CpG rich areas</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command>newcpgreport -sequence '$input1' -window $window -shift $shift -minlen $minlen -minpc $minpc -outfile '$out_file1' -minoe $minoe -auto</command> + <inputs> + <param name="input1" type="data" format="data" label="Sequence" /> + <param name="window" type="integer" value="100" label="Window size" /> + <param name="shift" type="integer" value="1" label="Step size (shift)" /> + <param name="minlen" type="integer" value="200" label="Minimum length" /> + <param name="minoe" type="float" value="0.6" label="Minimum average observed to expected ratio" /> + <param name="minpc" type="float" value="50.0" label="Minimum average percentage of G plus C" /> + </inputs> + <outputs> + <data name="out_file1" format="newcpgreport" /> </outputs> <tests> <test> @@ -35,18 +26,11 @@ <param name="minpc" value="50.0"/> <output name="out_file1" file="emboss_newcpgreport_out.newcpgreport"/> </test> - </tests> + </tests> <help> You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newcpgreport.html - ------- - -**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>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/newcpgreport.html </help> -</tool> \ No newline at end of file + <expand macro="citations" /> +</tool>