Mercurial > repos > iuc > ncbi_datasets
diff datasets_gene.xml @ 21:0f3b3813b6ae draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit c1c3f90e4aa7dc258aa61d98ec4eac0b97eef426
| author | iuc |
|---|---|
| date | Mon, 21 Jul 2025 19:28:16 +0000 |
| parents | da8260eba74b |
| children |
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--- a/datasets_gene.xml Mon Mar 17 11:05:45 2025 +0000 +++ b/datasets_gene.xml Mon Jul 21 19:28:16 2025 +0000 @@ -4,7 +4,7 @@ <import>macros.xml</import> </macros> <expand macro="bio_tools"/> - <expand macro="requirements"></expand> + <expand macro="requirements"/> <expand macro="version_command"/> <command><![CDATA[ #import re @@ -41,7 +41,7 @@ #if $filters.fasta_filter_cond.fasta_filter_select #if $filters.fasta_filter_cond.fasta_filter_select == 'text' - --fasta-filter #echo ",".join(f"'{x}'" for x in $filters.fasta_filter_cond.fasta_filter.split(',') if x) + --fasta-filter #echo ",".join(f"'{x}'" for x in str($filters.fasta_filter_cond.fasta_filter).split(',') if x) #else --fasta-filter-file '$filters.fasta_filter_cond.fasta_filter_file' #end if @@ -97,8 +97,8 @@ <param argument="--taxon" type="text" value="human" label="Species for gene symbol" help="NCBI taxid, common or scientific name"> <sanitizer invalid_char=""> <valid initial="string.letters"> - <add value=" " /> - <add value="-" /> + <add value=" "/> + <add value="-"/> </valid> </sanitizer> </param> @@ -109,8 +109,8 @@ <param argument="--taxon-filter" type="text" value="" label="Limit gene sequences and annotation report file to specified taxon" help="any rank, only available for WP accessions"> <sanitizer invalid_char=""> <valid initial="string.letters"> - <add value=" " /> - <add value="-" /> + <add value=" "/> + <add value="-"/> </valid> </sanitizer> </param> @@ -133,7 +133,7 @@ <param argument="--fasta-filter" type="text" label="RefSeq nucleotide and protein accessions" help="Comma separated"> <sanitizer invalid_char=""> <valid initial="string.letters,string.digits"> - <add value="," /> + <add value=","/> </valid> </sanitizer> </param> @@ -235,12 +235,12 @@ </output> <output name="rna_fasta"> <assert_contents> - <has_text text=">"/> + <has_text text=">"/> </assert_contents> </output> <output name="protein_fasta"> <assert_contents> - <has_text text=">"/> + <has_text text=">"/> </assert_contents> </output> </test> @@ -263,12 +263,12 @@ </output> <output name="rna_fasta"> <assert_contents> - <has_text text=">"/> + <has_text text=">"/> </assert_contents> </output> <output name="protein_fasta"> <assert_contents> - <has_text text=">"/> + <has_text text=">"/> </assert_contents> </output> </test> @@ -284,6 +284,7 @@ </conditional> <section name="file_choices"> <conditional name="kingdom_cond"> + <param name="kingdom_sel" value="gene"/> <param name="include" value="gene,cds"/> </conditional> </section> @@ -297,17 +298,17 @@ </output> <output name="gene_fasta"> <assert_contents> - <has_text text=">"/> + <has_text text=">"/> </assert_contents> </output> <output name="cds_fasta"> <assert_contents> - <has_text text=">"/> + <has_text text=">"/> </assert_contents> </output> </test> <!-- 4: datasets download gene symbol tp53 --> - <test expect_num_outputs="1"> + <test expect_num_outputs="3"> <conditional name="query|subcommand"> <param name="download_by" value="symbol"/> <conditional name="text_or_file"> @@ -315,11 +316,6 @@ <param name="accession" value="tp53"/> </conditional> </conditional> - <section name="file_choices"> - <conditional name="kingdom_cond"> - <param name="include" value=""/> - </conditional> - </section> <output name="gene_data_report"> <assert_contents> <has_text text="human"/> @@ -361,17 +357,17 @@ </output> <output name="threep_utr_fasta"> <assert_contents> - <has_text text=">"/> + <has_text text=">"/> </assert_contents> </output> <output name="fivep_utr_fasta"> <assert_contents> - <has_text text=">"/> + <has_text text=">"/> </assert_contents> </output> </test> <!-- 6: datasets download gene symbol brca1 \-\-ortholog --> - <test expect_num_outputs="1"> + <test expect_num_outputs="3"> <conditional name="query|subcommand"> <param name="download_by" value="symbol"/> <conditional name="text_or_file"> @@ -380,11 +376,6 @@ </conditional> <param name="ortholog" value="rodentia"/> </conditional> - <section name="file_choices"> - <conditional name="kingdom_cond"> - <param name="include" value=""/> - </conditional> - </section> <output name="gene_data_report"> <assert_contents> <has_text text="rat"/> @@ -395,7 +386,7 @@ </output> </test> <!-- 7: datasets download gene accession NP_000483.3 --> - <test expect_num_outputs="1"> + <test expect_num_outputs="3"> <conditional name="query|subcommand"> <param name="download_by" value="accession"/> <conditional name="text_or_file"> @@ -403,11 +394,6 @@ <param name="accession" value="NP_000483.3"/> </conditional> </conditional> - <section name="file_choices"> - <conditional name="kingdom_cond"> - <param name="include" value=""/> - </conditional> - </section> <output name="gene_data_report"> <assert_contents> <has_text text="human"/> @@ -417,7 +403,7 @@ </output> </test> <!-- 8: datasets download gene accession NM_000546.6 NM_000492.4 + ortholog--> - <test expect_num_outputs="1"> + <test expect_num_outputs="3"> <conditional name="query|subcommand"> <param name="download_by" value="accession"/> <conditional name="text_or_file"> @@ -426,11 +412,6 @@ </conditional> <param name="ortholog" value="all"/> </conditional> - <section name="file_choices"> - <conditional name="kingdom_cond"> - <param name="include" value=""/> - </conditional> - </section> <output name="gene_data_report"> <assert_contents> <has_text text="human"/> @@ -439,7 +420,6 @@ </assert_contents> </output> </test> - <!-- 9: datasets download gene accession WP_003249567.1 + include_flanks_bp --> <test expect_num_outputs="4"> <conditional name="query|subcommand"> @@ -466,24 +446,23 @@ </output> <output name="gene_fasta"> <assert_contents> - <has_text text=">"/> + <has_text text=">"/> </assert_contents> </output> <output name="gene_flanks"> <assert_contents> - <has_text text=">"/> + <has_text text=">"/> </assert_contents> </output> <output name="protein_fasta"> <assert_contents> - <has_text text=">"/> + <has_text text=">"/> </assert_contents> </output> <assert_command> <has_text text="include-flanks-bp 100"/> </assert_command> - </test> - + </test> <!-- 10: datasets download gene taxon human --> <!-- <test expect_num_outputs="1"> <conditional name="query|subcommand">