Mercurial > repos > devteam > emboss_5
diff emboss_showfeat.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 |
line wrap: on
line diff
--- a/emboss_showfeat.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_showfeat.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,131 +1,97 @@ -<tool id="EMBOSS: showfeat85" name="showfeat" version="5.0.0"> +<tool id="EMBOSS: showfeat85" name="showfeat" version="5.0.0.1"> <!-- tool gives memory errors --> - <description>Show features of a sequence</description> - <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>showfeat -sequence $input1 -outfile $out_file1 -matchsource "$matchsource" -matchtype "$matchtype" -matchtag "$matchtag" -matchvalue "$matchvalue" -sort $sort -annotation "$annotation" -id - $id -description "$description" -scale "$scale" -width "$width" -collapse $collapse -forward $forward -reverse $reverse -unknown $unknown -strand $strand -source $source -position $position -type - $type -tags $tags -values $values -stricttags $stricttags -html $html_out1 -auto</command> - <inputs> - <param format="data" name="input1" type="data"> - <label>Sequences</label> - </param> - <param name="html_out1" type="select"> - <label>Format output as an HTML table</label> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <param name="matchsource" type="text" value="*"> - <label>Feature source to match</label> - </param> - <param name="matchtype" type="text" value="*"> - <label>Feature type to match</label> - </param> - <param name="matchtag" type="text" value="*"> - <label>Feature tags to match</label> - </param> - <param name="matchvalue" type="text" value="*"> - <label>Tag values to match</label> - </param> - <param name="sort" type="select"> - <label>Sort by</label> - <option value="start">Start position</option> - <option value="source">Source</option> - <option value="type">Type</option> - <option value="nosort">No sorting done</option> - <option value="join">Join coding regions together</option> - </param> - <param name="annotation" type="text" value=""> - <label>Regions to annotate by marking</label> - </param> - <param name="id" type="select"> - <label>Display the ID name of the sequence</label> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> - <param name="description" type="select"> - <label>Display the description of the sequence</label> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> - <param name="scale" type="select"> - <label>Display the scale line</label> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> - <param name="width" type="text" value="60"> - <label>Screen width</label> - </param> - <param name="collapse" type="select"> - <label>Collapse features</label> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <param name="forward" type="select"> - <label>Display forward sense features</label> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> - <param name="reverse" type="select"> - <label>Display reverse sense features</label> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> - <param name="unknown" type="select"> - <label>Display unknown sense features</label> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> - <param name="strand" type="select"> - <label>Display the strand of the features</label> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <param name="source" type="select"> - <label>Display the source of the features</label> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <param name="position" type="select"> - <label>SDisplay the start and end position of the features</label> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <param name="type" type="select"> - <label>Display the type of the features</label> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> - <param name="tags" type="select"> - <label>Display the tags and values of the features</label> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <param name="values" type="select"> - <label>Display the tag values of the features</label> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> - <param name="stricttags" type="select"> - <label>Display only those tag/value pairs in a feature that match the specified tag and value</label> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - </inputs> - <outputs> - <data format="showfeat" name="out_file1" /> - </outputs> - <code file="emboss_format_corrector.py" /> + <description>Show features of a sequence</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <code file="emboss_format_corrector.py" /> + <command>showfeat -sequence '$input1' -outfile '$out_file1' -matchsource '$matchsource' -matchtype '$matchtype' -matchtag '$matchtag' -matchvalue '$matchvalue' -sort $sort -annotation '$annotation' -id + $id -description $description -scale $scale -width $width -collapse $collapse -forward $forward -reverse $reverse -unknown $unknown -strand $strand -source $source -position $position -type + $type -tags $tags -values $values -stricttags $stricttags -html $html_out1 -auto</command> + <inputs> + <param name="input1" type="data" format="data" label="Sequences" /> + <param name="html_out1" type="select" label="Format output as an HTML table"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="matchsource" type="text" value="*" label="Feature source to match" /> + <param name="matchtype" type="text" value="*" label="Feature type to match" /> + <param name="matchtag" type="text" value="*" label="Feature tags to match" /> + <param name="matchvalue" type="text" value="*" label="Tag values to match" /> + <param name="sort" type="select" label="Sort by"> + <option value="start">Start position</option> + <option value="source">Source</option> + <option value="type">Type</option> + <option value="nosort">No sorting done</option> + <option value="join">Join coding regions together</option> + </param> + <param name="annotation" type="text" value="" label="Regions to annotate by marking" /> + <param name="id" type="select" label="Display the ID name of the sequence"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="description" type="select" label="Display the description of the sequence"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="scale" type="select" label="Display the scale line"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="width" type="integer" value="60" label="Screen width" /> + <param name="collapse" type="select" label="Collapse features"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="forward" type="select" label="Display forward sense features"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="reverse" type="select" label="Display reverse sense features"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="unknown" type="select" label="Display unknown sense features"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="strand" type="select" label="Display the strand of the features"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="source" type="select" label="Display the source of the features"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="position" type="select" label="Display the start and end position of the features"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="type" type="select" label="Display the type of the features"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="tags" type="select" label="Display the tags and values of the features"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="values" type="select" label="Display the tag values of the features"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="stricttags" type="select" label="Display only those tag/value pairs in a feature that match the specified tag and value"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + </inputs> + <outputs> + <data name="out_file1" format="showfeat" /> + </outputs> <help> You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/showfeat.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/showfeat.html </help> -</tool> \ No newline at end of file + <expand macro="citations" /> +</tool>