Mercurial > repos > galaxyp > uniprotxml_downloader
diff uniprotxml_downloader.xml @ 6:a371252a2cf6 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
| author | galaxyp |
|---|---|
| date | Thu, 06 Jul 2023 21:15:39 +0000 |
| parents | 265c35540faa |
| children |
line wrap: on
line diff
--- a/uniprotxml_downloader.xml Fri Nov 04 15:08:37 2022 +0000 +++ b/uniprotxml_downloader.xml Thu Jul 06 21:15:39 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="uniprotxml_downloader" name="UniProt" version="2.3.0" profile="21.01"> +<tool id="uniprotxml_downloader" name="UniProt" version="2.4.0" profile="21.01"> <description>download proteome as XML or fasta</description> <macros> <import>macros.xml</import> @@ -12,32 +12,32 @@ <command> <![CDATA[ python '$__tool_directory__/uniprotxml_downloader.py' -#if $taxid.input_choice == 'common': - --taxon $taxid.organism +#if $input_method.input_choice == 'common': + --search-id $input_method.organism --field taxonomy_id - #if $taxid.reviewed: - --reviewed=$taxid.reviewed + #if $input_method.reviewed: + --reviewed=$input_method.reviewed #end if -#elif $taxid.input_choice == 'taxids': - --field $taxid.field - #for $id in $taxid.taxons.split(','): - -t '$id' +#elif $input_method.input_choice == 'enter_ids': + --field $input_method.field + #for $id in $input_method.ids.split(','): + --search-id '$id' #end for -#elif $taxid.input_choice == 'history': - --field $taxid.field - --input='${taxid.taxon_file}' - --column=#echo int(str($taxid.column)) - 1# +#elif $input_method.input_choice == 'history': + --field $input_method.field + --input='${input_method.id_file}' + --column=#echo int(str($input_method.column)) - 1# #end if --format $format --output '${proteome}' ]]> </command> <inputs> - <conditional name="taxid"> + <conditional name="input_method"> <param name="input_choice" type="select" label="Select"> <option value="common">A Common Organism</option> - <option value="taxids">A manually entered list of Taxon IDs or names</option> - <option value="history">A history dataset with a column containing Taxon IDs or names</option> + <option value="enter_ids">A manually entered list of Uniprot IDs</option> + <option value="history">A history dataset with a column containing Uniprot IDs</option> </param> <when value="common"> <param name="organism" type="select" label="Common Organisms" @@ -59,16 +59,16 @@ <option value="no">UniProtKB/TrEMBL (unreviewed only)</option> </param> </when> - <when value="taxids"> - <param name="taxons" type="text" label="NCBI Taxon IDs or names" - help="Enter one or more Organsim IDs (separated by commas) from http://www.uniprot.org/proteomes/"> + <when value="enter_ids"> + <param name="ids" type="text" label="Search ID values" + help="Enter one or more IDs (separated by commas) from http://www.uniprot.org/proteomes/"> <validator type="regex" message="OrganismID[,OrganismID]">^\w+( \w+)*(,\w+( \w+)*)*$</validator> </param> <expand macro="query_field"/> </when> <when value="history"> - <param name="taxon_file" type="data" format="tabular,txt" label="Dataset (tab separated) with Taxon ID/Name column"/> - <param name="column" type="data_column" data_ref="taxon_file" label="Column with Taxon ID/name"/> + <param name="id_file" type="data" format="tabular,txt" label="Dataset (tab separated) with ID column"/> + <param name="column" type="data_column" data_ref="id_file" label="Column with ID"/> <expand macro="query_field"/> </when> </conditional> @@ -86,8 +86,8 @@ </outputs> <tests> <test> - <param name="input_choice" value="taxids"/> - <param name="taxons" value="1566990"/> + <param name="input_choice" value="enter_ids"/> + <param name="ids" value="1566990"/> <param name="format" value="xml"/> <output name="proteome"> <assert_contents> @@ -96,8 +96,8 @@ </output> </test> <test> - <param name="input_choice" value="taxids"/> - <param name="taxons" value="765963,512562"/> + <param name="input_choice" value="enter_ids"/> + <param name="ids" value="765963,512562"/> <param name="field" value="taxonomy_id"/> <param name="format" value="fasta"/> <output name="proteome"> @@ -108,8 +108,8 @@ </output> </test> <test> - <param name="input_choice" value="taxids"/> - <param name="taxons" value="Shi470,PeCan4"/> + <param name="input_choice" value="enter_ids"/> + <param name="ids" value="Shi470,PeCan4"/> <param name="field" value="taxonomy_name"/> <param name="format" value="fasta"/> <output name="proteome"> @@ -120,8 +120,20 @@ </output> </test> <test> + <param name="input_choice" value="enter_ids"/> + <param name="ids" value="E1Q2I0,E1Q3C4"/> + <param name="field" value="accession"/> + <param name="format" value="fasta"/> + <output name="proteome"> + <assert_contents> + <has_text text="E1Q2I0" /> + <has_text text="E1Q3C4" /> + </assert_contents> + </output> + </test> + <test> <param name="input_choice" value="history"/> - <param name="taxon_file" value="Helicobacter_strains.tsv" ftype="tabular"/> + <param name="id_file" value="Helicobacter_strains.tsv" ftype="tabular"/> <param name="column" value="1"/> <param name="field" value="taxonomy_name"/> <param name="format" value="fasta"/> @@ -134,7 +146,7 @@ </test> <test> <param name="input_choice" value="history"/> - <param name="taxon_file" value="Helicobacter_strains_ids.tsv" ftype="tabular"/> + <param name="id_file" value="Helicobacter_strains_ids.tsv" ftype="tabular"/> <param name="column" value="2"/> <param name="field" value="taxonomy_id"/> <param name="format" value="fasta"/> @@ -145,6 +157,19 @@ </assert_contents> </output> </test> + <test> + <param name="input_choice" value="history"/> + <param name="id_file" value="Helicobacter_protein_accessions.tsv" ftype="tabular"/> + <param name="column" value="1"/> + <param name="field" value="accession"/> + <param name="format" value="fasta"/> + <output name="proteome"> + <assert_contents> + <has_text text="E1Q2I0" /> + <has_text text="E1Q3C4" /> + </assert_contents> + </output> + </test> </tests> <help> <![CDATA[ @@ -160,7 +185,11 @@ Example taxon: http://www.uniprot.org/taxonomy/512562 -Taxon IDs or names can be entered as text or read from a column in a tabular dataset from your history. +Example protein: https://www.uniprot.org/uniprotkb/E1Q2I0/entry + +Description of query fields: https://www.uniprot.org/help/query-fields + +IDs can be entered as text or read from a column in a tabular dataset from your history. Example IDs and names releated to the Bacteria Helicobacter pylori (strain Shi470) :: @@ -171,6 +200,11 @@ - Helicobacter - Helicobacteraceae + Example protein accession numbers from Helicobacter pylori: + + - E1Q2I0 + - E1Q3C4 + UniProtKB help: http://www.uniprot.org/help/uniprotkb