Mercurial > repos > dfornika > snippy_clean_full_aln
changeset 5:201302fa7651 draft default tip
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/snippy_clean commit 66a9f18802686a105b392e73e82c0078d0cdf2a4"
| author | dfornika |
|---|---|
| date | Thu, 30 Jan 2020 01:20:57 +0000 |
| parents | 0bd30a111a55 |
| children | |
| files | snippy_clean_full_aln.xml test-data/core.full.nonclean.aln |
| diffstat | 2 files changed, 23 insertions(+), 14 deletions(-) [+] |
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--- a/snippy_clean_full_aln.xml Thu Jan 30 00:02:46 2020 +0000 +++ b/snippy_clean_full_aln.xml Thu Jan 30 01:20:57 2020 +0000 @@ -10,22 +10,30 @@ <command detect_errors="exit_code"><![CDATA[ snippy-clean_full_aln '${full_aln}' - --to '${to_char}' + #if $custom_char.custom_char_selector: + --to '${custom_char.to_char}' + #end if > '${clean_full_aln}' ]]></command> <inputs> <param name="full_aln" type="data" format="fasta" label="Snippy core.full.aln file" help="" /> - <param name="to_char" type="text" default="N" label="Replacement character" help="Replace non-[AGTCN-] chars with this character" > - <sanitizer> - <valid initial="string.printable"> - <remove value="'" /> - </valid> - <mapping initial="none"> - <add source="'" target="'"'"'" /> - </mapping> - </sanitizer> - </param> + <conditional name="custom_char"> + <param name="custom_char_selector" type="boolean" display="radio" label="Use custom replacement character" /> + <when value="false" /> + <when value="true"> + <param name="to_char" type="text" label="Replacement character" help="Replace non-[AGTCN-] chars with this character, defaults to 'N' if none entered" > + <sanitizer> + <valid initial="string.printable"> + <remove value="'" /> + </valid> + <mapping initial="none"> + <add source="'" target="'"'"'" /> + </mapping> + </sanitizer> + </param> + </when> + </conditional> </inputs> <outputs> <data name="clean_full_aln" format="fasta" label="${tool.name} on ${on_string} cleaned core alignment" /> @@ -35,16 +43,17 @@ <param name="full_aln" value="core.full.nonclean.aln" /> <output name="clean_full_aln"> <assert_contents> - <has_line line="GCNNGC" /> + <has_line line="GCNNCG" /> </assert_contents> </output> </test> <test> <param name="full_aln" value="core.full.nonclean.aln" /> + <param name="custom_char_selector" value="true" /> <param name="to_char" value="X" /> <output name="clean_full_aln"> <assert_contents> - <has_line line="GCXXGC" /> + <has_line line="GCXXCG" /> </assert_contents> </output> </test>