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view 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 |
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date | Mon, 30 Jan 2017 13:27:40 -0500 |
parents | 9b98d3d903c6 |
children | 27c43fb015f0 |
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<tool id="EMBOSS: showfeat85" name="showfeat" version="5.0.0.1"> <!-- tool gives memory errors --> <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://galaxy-iuc.github.io/emboss-5.0-docs/showfeat.html </help> <expand macro="citations" /> </tool>