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comparison Codonlogo.xml @ 9:f3462128e87c

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Minor alterations to the galaxy interface with some better examples and error messages added.
author davidmurphy
date Mon, 30 Jan 2012 08:17:57 -0500
parents 5149eb3a89c2
children 20716450be87
comparison
equal deleted inserted replaced
8:5149eb3a89c2 9:f3462128e87c
1 <tool id="codonlogo" name="Codon Logo" version="3"> 1 <tool id="codonlogo" name="Codon Logo" version="3">
2 <description>generator for fasta (eg Clustal alignments)</description> 2 <description>generator for fasta (eg Clustal alignments)</description>
3 <command interpreter="/usr/tmp/bin/python2.7 -W ignore::DeprecationWarning"> 3 <command interpreter="python -W ignore::DeprecationWarning">
4 codonlogo -F $outformat -s $size -f $input -o $output -t "$logoname" -m $frame -n $stacks -X $showxaxis --show-yaxis $showyaxis --errorbars $errorbars -G $strict --fineprint "$fineprint" --stack-width $stackwidth --stack-height $stackheight --box $box --resolution $resolution --scale-width $scalewidth 4 codonlogo -F $outformat -s $size -f $input -o $output -t "$logoname" -m $frame -n $stacks -X $showxaxis --show-yaxis $showyaxis --errorbars $errorbars -G $strict --fineprint "$fineprint" --stack-width $stackwidth --stack-height $stackheight --box $box --resolution $resolution --scale-width $scalewidth
5 5
6 #if str($ylabel) != '' 6 #if str($ylabel) != ''
7 -x "$xlabel" 7 -x "$xlabel"
8 #end if 8 #end if
22 #end if 22 #end if
23 #if str($comp.mode) == 'file' 23 #if str($comp.mode) == 'file'
24 -R $compfile 24 -R $compfile
25 #end if 25 #end if
26 #if str($comp.mode) == 'Escherichiacoli' 26 #if str($comp.mode) == 'Escherichiacoli'
27 -R Escherichiacoli.txt 27 --comp escherichiacoli
28 #end if 28 #end if
29 #if str($comp.mode) == 'Saccharomycescerevisiae' 29 #if str($comp.mode) == 'Saccharomycescerevisiae'
30 -R Saccharomycescerevisiae.txt 30 --comp saccharomycescerevisiae
31 #end if 31 #end if
32 #if str($comp.mode) == 'Homosapiens' 32 #if str($comp.mode) == 'Homosapiens'
33 -R Homosapiens.txt 33 --comp homosapiens
34 #end if 34 #end if
35 35
36 #if $colours.colour == 'part' 36 #if $colours.colour == 'part'
37 37
38 #if str( $colours.colorAAA) != '' 38 #if str( $colours.colorAAA) != ''
402 </param> 402 </param>
403 </when> 403 </when>
404 </conditional> 404 </conditional>
405 <conditional name="comp"> 405 <conditional name="comp">
406 <param name="mode" type="select" label="Select expected composition: 'equiprobable', 'none' (no small sample correction), or supply a file"> 406 <param name="mode" type="select" label="Select expected composition: 'equiprobable', 'none' (no small sample correction), or supply a file">
407 407 <option value="none" >No small sample correction</option>
408 <option value="equiprobable" >equiprobable</option> 408 <option value="equiprobable" >Equiprobable</option>
409 <option value="none" >none</option> 409 <option value="Homosapiens" >Human</option>
410 <!-- <option value="Escherichiacoli" >Escherichiacoli</option> 410 <option value="Yeast" >Saccharomycescerevisiae</option>
411 <option value="Homosapiens" >Homosapiens</option> 411 <option value="E.Coli" >Escherichiacoli</option>
412 <option value="Saccharomycescerevisiae" >Saccharomycescerevisiae</option>--> 412 <option value="From File">from file</option>
413 <option value="file">from file</option>
414 413
415 </param> 414 </param>
416 <when value="auto"> 415 <when value="auto">
417 </when> 416 </when>
418 <when value="equiprobable"> 417 <when value="equiprobable">