Mercurial > repos > q2d2 > qiime2__rescript__get_ncbi_genomes

changeset 2:f8ac470cc306 draft default tip

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
author q2d2
date Wed, 30 Oct 2024 19:55:35 +0000
parents 660b904210ca
children
files qiime2__rescript__get_ncbi_genomes.xml
diffstat 1 files changed, 47 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/qiime2__rescript__get_ncbi_genomes.xml	Mon Jun 03 23:30:45 2024 +0000
+++ b/qiime2__rescript__get_ncbi_genomes.xml	Wed Oct 30 19:55:35 2024 +0000
@@ -6,14 +6,17 @@
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.5.0)
+    q2galaxy (version: 2024.10.0)
 for:
-    qiime2 (version: 2024.5.0)
+    qiime2 (version: 2024.10.1)
 -->
-<tool name="qiime2 rescript get-ncbi-genomes" id="qiime2__rescript__get_ncbi_genomes" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 rescript get-ncbi-genomes" id="qiime2__rescript__get_ncbi_genomes" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
     <description>Fetch entire genomes and associated taxonomies and metadata using NCBI Datasets.</description>
+    <xrefs>
+        <xref type="bio.tools">qiime2</xref>
+    </xrefs>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
     </requirements>
     <version_command>q2galaxy version rescript</version_command>
     <command detect_errors="exit_code">q2galaxy run rescript get_ncbi_genomes '$inputs'</command>
@@ -28,9 +31,10 @@
             <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
         </param>
         <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
-            <param name="assembly_source" type="select" label="assembly_source: Str % Choices('refseq', 'genbank')" display="radio">
+            <param name="assembly_source" type="select" label="assembly_source: Str % Choices('refseq', 'genbank', 'all')" display="radio">
                 <option value="refseq" selected="true">refseq</option>
                 <option value="genbank">genbank</option>
+                <option value="all">all</option>
             </param>
             <repeat name="assembly_levels" help="[default: ['complete_genome']]  Fetch only genome assemblies that are one of the specified assembly levels." title="assembly_levels: List[Str % Choices('complete_genome', 'chromosome', 'scaffold', 'contig')]">
                 <param name="element" type="select" label="element: Str % Choices('complete_genome', 'chromosome', 'scaffold', 'contig')" display="radio">
@@ -43,8 +47,46 @@
                 </param>
             </repeat>
             <param name="only_reference" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="only_reference: Bool" help="[default: Yes]  Fetch only reference and representative genome assemblies."/>
+            <param name="only_genomic" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="only_genomic: Bool" help="[default: No]  Exclude plasmid, mitochondrial and chloroplast molecules from the final results (i.e., keep only genomic DNA)."/>
             <param name="tax_exact_match" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="tax_exact_match: Bool" help="[default: No]  If true, only return assemblies with the given NCBI Taxonomy ID, or name. Otherwise, assemblies from taxonomy subtree are included, too."/>
             <param name="page_size" type="integer" min="20" max="1000" value="20" label="page_size: Int % Range(20, 1000, inclusive_end=True)" help="[default: 20]  The maximum number of genome assemblies to return per request. If number of genomes to fetch is higher than this number, requests will be repeated until all assemblies are fetched."/>
+            <repeat name="ranks" help="[default: ['kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species']]  List of taxonomic ranks for building a taxonomy from the NCBI Taxonomy database." title="ranks: List[Str % Choices('domain', 'superkingdom', 'kingdom', 'subkingdom', 'superphylum', 'phylum', 'subphylum', 'infraphylum', 'superclass', 'class', 'subclass', 'infraclass', 'cohort', 'superorder', 'order', 'suborder', 'infraorder', 'parvorder', 'superfamily', 'family', 'subfamily', 'tribe', 'subtribe', 'genus', 'subgenus', 'species group', 'species subgroup', 'species', 'subspecies', 'forma')]">
+                <param name="element" type="select" label="element: Str % Choices('domain', 'superkingdom', 'kingdom', 'subkingdom', 'superphylum', 'phylum', 'subphylum', 'infraphylum', 'superclass', 'class', 'subclass', 'infraclass', 'cohort', 'superorder', 'order', 'suborder', 'infraorder', 'parvorder', 'superfamily', 'family', 'subfamily', 'tribe', 'subtribe', 'genus', 'subgenus', 'species group', 'species subgroup', 'species', 'subspecies', 'forma')">
+                    <option value="__q2galaxy__::literal::None">Selection required</option>
+                    <option value="domain">domain</option>
+                    <option value="superkingdom">superkingdom</option>
+                    <option value="kingdom">kingdom</option>
+                    <option value="subkingdom">subkingdom</option>
+                    <option value="superphylum">superphylum</option>
+                    <option value="phylum">phylum</option>
+                    <option value="subphylum">subphylum</option>
+                    <option value="infraphylum">infraphylum</option>
+                    <option value="superclass">superclass</option>
+                    <option value="class">class</option>
+                    <option value="subclass">subclass</option>
+                    <option value="infraclass">infraclass</option>
+                    <option value="cohort">cohort</option>
+                    <option value="superorder">superorder</option>
+                    <option value="order">order</option>
+                    <option value="suborder">suborder</option>
+                    <option value="infraorder">infraorder</option>
+                    <option value="parvorder">parvorder</option>
+                    <option value="superfamily">superfamily</option>
+                    <option value="family">family</option>
+                    <option value="subfamily">subfamily</option>
+                    <option value="tribe">tribe</option>
+                    <option value="subtribe">subtribe</option>
+                    <option value="genus">genus</option>
+                    <option value="subgenus">subgenus</option>
+                    <option value="species group">species group</option>
+                    <option value="species subgroup">species subgroup</option>
+                    <option value="species">species</option>
+                    <option value="subspecies">subspecies</option>
+                    <option value="forma">forma</option>
+                    <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
+                </param>
+            </repeat>
+            <param name="rank_propagation" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="rank_propagation: Bool" help="[default: Yes]  If a rank has no taxonomy associated with it, the taxonomy from the upper-level rank of that lineage, will be propagated downward. For example, if we are missing the genus label for 'f__Pasteurellaceae; g__'then the 'f__' rank will be propagated to become: 'f__Pasteurellaceae; g__Pasteurellaceae'."/>
         </section>
     </inputs>
     <outputs>