Mercurial > repos > devteam > emboss_5
diff emboss_sixpack.xml @ 14:27c43fb015f0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753
author | iuc |
---|---|
date | Fri, 22 Jun 2018 03:24:29 -0400 |
parents | 0e2484b6829b |
children | 21a9fb508031 |
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--- a/emboss_sixpack.xml Mon Apr 23 13:04:47 2018 -0400 +++ b/emboss_sixpack.xml Fri Jun 22 03:24:29 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="EMBOSS: sixpack90" name="sixpack" version="5.0.0.1"> +<tool id="EMBOSS: sixpack90" name="sixpack" version="@VERSION@+galaxy2"> <!-- tool adds file description and timestamp to output data --> <description>Display a DNA sequence with 6-frame translation and ORFs</description> <macros> @@ -6,8 +6,12 @@ </macros> <expand macro="requirements" /> <code file="emboss_format_corrector.py" /> - <command>sixpack -sequence '$input1' -outfile '$ofile1' -outseq '$ofile2' -table $table -firstorf $firstorf -lastorf $lastorf -mstart $mstart -reverse $reverse -orfminsize $orfminsize -uppercase - '$uppercase' -number $number -width $width -length $length -margin $margin -name $disp_name -description $description -offset $offset -html $html_out1 -osformat $out_format2 -auto</command> + <command><![CDATA[ + sixpack -sequence '$input1' -outfile '$ofile1' -outseq '$ofile2' -table $table -firstorf $firstorf -lastorf $lastorf -mstart $mstart -reverse $reverse -orfminsize $orfminsize + #if str($uppercase): + -uppercase '$uppercase' + #end if + -number $number -width $width -length $length -margin $margin -name $disp_name -description $description -offset $offset -html $html_out1 -osformat $out_format2 -auto]]></command> <inputs> <param name="input1" type="data" format="fasta" label="Sequences" /> <param name="table" type="select" label="Code to use"> @@ -47,7 +51,7 @@ <option value="no">No</option> </param> <param name="orfminsize" type="integer" value="1" label="Minimum size of Open Reading Frames (ORFs) to display in the translations" /> - <param name="uppercase" type="text" value="" label="Regions to put in uppercase" /> + <param name="uppercase" type="text" value="" label="Regions to put in uppercase" help="If this is left blank, then the sequence case is left alone. A set of regions is specified by a set of pairs of positions. The positions are integers. They are separated by any non-alpha-numeric character. Three examples of region specifications are: 1) 24-45, 56-78 2) 1:45, 67=99;765..888 3) 1,5,8,10,23,45,57,99"/> <param name="number" type="select" label="Number the sequence at the beginning and the end of each line"> <option value="yes">Yes</option> <option value="no">No</option> @@ -104,7 +108,7 @@ <data name="ofile1" format="sixpack" /> <data name="ofile2" format="fasta" /> </outputs> -<!-- <tests> + <tests> <test> <param name="input1" value="2.fasta"/> <param name="table" value="0"/> @@ -123,9 +127,10 @@ <param name="offset" value="1"/> <param name="html_out1" value="no"/> <param name="out_format2" value="fasta"/> + <output name="ofile1" file="emboss_sixpack_out2.sixpack" /> <output name="ofile2" file="emboss_sixpack_out.fasta"/> </test> - </tests> --> + </tests> <help> .. class:: warningmark