Mercurial > repos > oinizan > frogs
diff preprocess.xml @ 21:74a9b83110a7 draft
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f481f7af0d70c862c493d55f386b375e7f968c5c-dirty
| author | oinizan |
|---|---|
| date | Thu, 30 Mar 2023 06:09:01 +0000 |
| parents | d73e09b3bc26 |
| children | 57824202c333 |
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--- a/preprocess.xml Fri Mar 10 14:03:08 2023 +0000 +++ b/preprocess.xml Thu Mar 30 06:09:01 2023 +0000 @@ -15,7 +15,7 @@ --min-amplicon-size $sequencer_type.min_amplicon_size --max-amplicon-size $sequencer_type.max_amplicon_size #if $sequencer_type.sequencer_selected in ('illumina', 'longreads') - #if $sequencer_type.is_primer_in_seq.primer_choice + #if $sequencer_type.is_primer_in_seq.primer_choice == "true" --five-prim-primer '$sequencer_type.is_primer_in_seq.five_prim_primer' --three-prim-primer '$sequencer_type.is_primer_in_seq.three_prim_primer' #else @@ -38,7 +38,7 @@ #if $sequencer_type.input_type.archive_type.merge_software_type.merge_software == "flash" --expected-amplicon-size $sequencer_type.input_type.archive_type.merge_software_type.expected_amplicon_size #end if - #if $sequencer_type.input_type.archive_type.keep_unmerged + #if $sequencer_type.input_type.archive_type.keep_unmerged == "Yes" --keep-unmerged #end if #end if @@ -67,7 +67,7 @@ #if $sequencer_type.input_type.files_by_samples_type.merge_software_type.merge_software == "flash" --expected-amplicon-size $sequencer_type.input_type.files_by_samples_type.merge_software_type.expected_amplicon_size #end if - #if $sequencer_type.input_type.files_by_samples_type.keep_unmerged + #if $sequencer_type.input_type.files_by_samples_type.keep_unmerged == "Yes" --keep-unmerged #end if #end if @@ -119,7 +119,10 @@ </when> <when value="vsearch"></when> </conditional> - <param argument="--keep-unmerged" type="boolean" label="Would you like to keep unmerged reads?" help="No = Unmerged reads will be excluded; Yes = unmerged reads will be artificially combined with 100 N. (default No)" /> + <param argument="--keep-unmerged" type="select" label="Would you like to keep unmerged reads?" help="No = Unmerged reads will be excluded; Yes = unmerged reads will be artificially combined with 100 N. (default No)" display="radio"> + <option value="No" selected="true">No, unmerged reads will be excluded.</option> + <option value="Yes">Yes, unmerged reads will be artificially combined.</option> + </param> </when> <when value="already_merged"></when> </conditional> @@ -153,7 +156,10 @@ </when> <when value="vsearch"></when> </conditional> - <param argument="--keep-unmerged" type="boolean" label="Would you like to keep unmerged reads?" help="No = Unmerged reads will be excluded; Yes = unmerged reads will be artificially combined with 100 N. (default No)" /> + <param argument="--keep-unmerged" type="select" label="Would you like to keep unmerged reads?" help="No = Unmerged reads will be excluded; Yes = unmerged reads will be artificially combined with 100 N. (default No)" display="radio"> + <option value="No" selected="true">No, unmerged reads will be excluded</option> + <option value="Yes">Yes, unmerged reads will be artificially combined.</option> + </param> </when> <when value="already_merged"> <repeat name="samples" title="Samples" min="1"> @@ -171,7 +177,10 @@ <param argument="--max-amplicon-size" type="integer" value="" label="Maximum amplicon size" help="The maximum size of the amplicons (with primers)"/> <!-- Primers --> <conditional name="is_primer_in_seq"> - <param name="primer_choice" type="boolean" checked="true" label="Do the sequences have PCR primers?" help=""/> + <param name="primer_choice" type="select" label="Do the sequences have PCR primers?" help="" display="radio"> + <option value="true" selected="true">Yes</option> + <option value="false">No</option> + </param> <when value="true"> <param argument="--five-prim-primer" type="text" label="5' primer" help="The 5' primer sequence (wildcards are accepted). This primer must be written in 5' to 3' orientation (see details in 'Primers parameters' help section)"> <sanitizer invalid_char=""> @@ -216,7 +225,10 @@ <!-- Primers --> <conditional name="is_primer_in_seq"> - <param name="primer_choice" type="boolean" checked="true" label="Do the sequences have PCR primers?" help=""/> + <param name="primer_choice" type="select" label="Do the sequences have PCR primers?" help="" display="radio"> + <option value="true" selected="true">Yes</option> + <option value="false">No</option> + </param> <when value="true"> <param argument="--five-prim-primer" type="text" label="5' primer" help="The 5' primer sequence (wildcards are accepted). This primer must be written in 5' to 3' orientation (see details in 'Primers parameters' help section)"> <sanitizer invalid_char="">