Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_taxa_barplot.xml @ 6:de4c22a52df4 draft
Fixes
author | florianbegusch |
---|---|
date | Tue, 13 Aug 2019 07:46:48 -0400 |
parents | 914fa4daf16a |
children | f190567fe3f6 |
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--- a/qiime2/qiime_taxa_barplot.xml Mon Aug 05 01:29:30 2019 -0400 +++ b/qiime2/qiime_taxa_barplot.xml Tue Aug 13 07:46:48 2019 -0400 @@ -7,8 +7,17 @@ <command><![CDATA[ qiime taxa barplot + +#if str( $id_to_taxonomy_fp.selector ) == 'history' + #set $tax = $id_to_taxonomy_fp.taxonomy_fp + --i-taxonomy '$tax' +#else: + #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path + --i-taxonomy '$tax' +#end if + + --i-table=$itable ---i-taxonomy=$itaxonomy #if $input_files_mmetadatafile: #def list_dict_to_string(list_dict): @@ -28,11 +37,27 @@ && mv '$ovisualization.files_path/index.html' '$ovisualization'; ]]></command> <inputs> - <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels. [required]" name="itable" optional="False" type="data"/> - <param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required]" name="itaxonomy" optional="False" type="data"/> - <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]"> - <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> + <conditional name="id_to_taxonomy_fp" optional="True"> + <param name="selector" type="select" label="Reference taxonomy to query"> + <option value="cached">Public databases</option> + <option value="history">Databases from your history</option> + </param> + <when value="cached"> + <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True"> + <options from_data_table="qiime_taxonomy" /> + </param> + </when> + <when value="history"> + <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" /> + </when> + </conditional> + + + <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels. [required]" name="itable" optional="False" type="data"/> + + <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file [required]"> + <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" optional="False" /> </repeat> </inputs>