Mercurial > repos > cpt > cpt_fasta_charges
changeset 3:a39d312f95c7 draft default tip
planemo upload commit 83c1184008f5967a8265194a4b3496042827cda1
| author | cpt |
|---|---|
| date | Fri, 20 Sep 2024 05:36:05 +0000 |
| parents | defd34aad2dd |
| children | |
| files | fasta_charges.xml |
| diffstat | 1 files changed, 38 insertions(+), 38 deletions(-) [+] |
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--- a/fasta_charges.xml Fri Jan 05 05:50:48 2024 +0000 +++ b/fasta_charges.xml Fri Sep 20 05:36:05 2024 +0000 @@ -4,58 +4,58 @@ <import>macros.xml</import> </macros> - <expand macro="requirements"/> + <expand macro="requirements"> </expand> <command detect_errors="aggressive"><![CDATA[ -'$__tool_directory__/fasta_charges.py' +python '$__tool_directory__/fasta_charges.py' '$svg' -@SEQUENCE@ +@SEQUENCE@ --width '$width' #if $scheme.cs == "default": ---aa HSQTNCY AVILMPFWG ERDK ---fgColor "#000000" "#000000" "#ffffff" ---bgColor "#ffffff" "#999999" "#000000" + --aa HSQTNCY AVILMPFWG ERDK + --fgColor "#000000" "#000000" "#ffffff" + --bgColor "#ffffff" "#999999" "#000000" #elif $scheme.cs == "rb": ---aa KR ED HSQTNCYAVILMPFWG ---fgColor "#ffffff" "#ffffff" "#000000" ---bgColor "#00b0f0" "#fc0000" "#ffffff" + --aa KR ED HSQTNCYAVILMPFWG + --fgColor "#ffffff" "#ffffff" "#000000" + --bgColor "#00b0f0" "#fc0000" "#ffffff" #elif $scheme.cs == "rbgb": ---aa KR ED P C HSQTNYAVILMFWG ---fgColor "#ffffff" "#ffffff" "#ffffff" "#ffffff" "#000000" ---bgColor "#00b0f0" "#fc0000" "#1cb026" "#805839" "#ffffff" + --aa KR ED P C HSQTNYAVILMFWG + --fgColor "#ffffff" "#ffffff" "#ffffff" "#ffffff" "#000000" + --bgColor "#00b0f0" "#fc0000" "#1cb026" "#805839" "#ffffff" #else: - --aa - #for group in '$scheme.groups': - "$group.aminoAcids" - #end for - --fgColor - #for group in '$scheme.groups': - "$group.fgColour" - #end for - --bgColor - #for group in '$scheme.groups': - "$group.bgColour" - #end for + --aa + #for group in $scheme.groups: + "$group.aminoAcids" + #end for + --fgColor + #for group in $scheme.groups: + "$group.fgColour" + #end for + --bgColor + #for group in $scheme.groups: + "$group.bgColour" + #end for #end if - -> $html ]]> -</command> +]]></command> <inputs> - <expand macro="input/fasta/protein"/> - <param label="Output format" name="svg" type="select"> + <expand macro="input/fasta/protein"></expand> + <label for="output-format">Output format</label> + <select id="output-format" name="svg"> <option value="">HTML</option> <option value="--svg">SVG</option> - </param> + </select> <conditional name="scheme"> - <param label="Colour scheme" name="cs" type="select"> + <label for="Colour scheme">Colour scheme</label> + <select id="Colour scheme" name="cs"> <option value="default">Default hyrophobic/polar/charged</option> <option value="rb">Positives Blue, Negatives Red</option> <option value="rbgb">Positives Blue, Negatives Red, Prolines Green, Cysteines Brown</option> <option value="custom">Custom Colour Scheme</option> - </param> - <when value="default"/> - <when value="rb"/> + </select> + <when value="default"></when> + <when value="rb"></when> <when value="custom"> <repeat name="groups" title="Colour Group"> <param name="aminoAcids" type="text" label="Amino Acids" help="Amino acids to colour a specific colour"/> @@ -69,7 +69,7 @@ <outputs> <data format="html" name="html"> <change_format> - <when input="svg" value="--svg" format="svg"/> + <when input="svg" value="--svg" format="svg"></when> </change_format> </data> </outputs> @@ -78,7 +78,7 @@ <param name="sequences" value="prot.fa"/> <param name="cs" value="default"/> <param name="width" value="120"/> - <output name="html" file="charges.html"/> + <output name="html" file="charges.html"></output> </test> </tests> <help> @@ -86,5 +86,5 @@ Colors fasta (protein) sequences based on rules, and displays outputs as HTML. </help> - <expand macro="citations"/> -</tool> + <expand macro="citations"></expand> +</tool> \ No newline at end of file