diff macros.xml @ 10:a3395b1d871b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30

--- a/macros.xml	Wed Aug 24 13:00:58 2022 +0000
+++ b/macros.xml	Mon Nov 21 11:40:05 2022 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">13.35.0</token>
+    <token name="@TOOL_VERSION@">14.3</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.01</token>
     <token name="@LICENSE@">MIT</token>
@@ -11,28 +11,25 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">ncbi-datasets-cli</requirement>
-            <requirement type="package" version="2022.6.15">ca-certificates</requirement>
+            <requirement type="package" version="2022.9.24">ca-certificates</requirement>
             <requirement type="package" version="16.02">p7zip</requirement>
         </requirements>
     </xml>
     <xml name="annotation">
         <param argument="--annotated" type="boolean" truevalue="--annotated" falsevalue="" label="Only include genomes with annotation ?"/>
     </xml>
-    <xml name="dehydrated">
-        <param argument="--dehydrated" type="boolean" truevalue="--dehydrated" falsevalue="" label="Download a dehydrated zip archive including the data report and locations of data files ?" help="Use the rehydrate tools to retrieve data files"/>
-    </xml>
     <xml name="assembly_level">
         <param argument="--assembly-level" type="select" label="Restrict assemblies to a comma-separated list of one or more of these" multiple="true" optional="true">
             <option value="chromosome">Chromosome</option>
-            <option value="complete_genome">Complete Genome</option>
+            <option value="complete">Complete Genome</option>
             <option value="contig">Contig</option>
             <option value="scaffold">Scaffold</option>
         </param>
     </xml>
     <xml name="assembly_source">
-        <param argument="--assembly-source" type="select" optional="true">
+        <param argument="--assembly-source" type="select" optional="true" label="Assembly source" help="Default (nothing selected) is both " >
             <option value="refseq">RefSeq</option>
-            <option value="genabnk">GenBank</option>
+            <option value="genbank">GenBank</option>
         </param>
     </xml>
     <xml name="text_or_file" token_what="accession" token_what_extended="NCBI Assembly accession" token_help="Can be NCBI Assembly or BioProject accession">
@@ -62,58 +59,47 @@
             </sanitizer>
         </param>
     </xml>
-    <xml name="include" token_include_what="gbff" token_include_label="Include GenBank flat file sequence and annotation, if available">
-        <param argument="--include-@INCLUDE_WHAT@" type="boolean" truevalue="--include-@INCLUDE_WHAT@" falsevalue="" label="@INCLUDE_LABEL@" />
-    </xml>
-    <xml name="includes_genome">
-        <expand macro="include" include_what="gbff" include_label="Include GenBank flat file sequence and annotation, if available"/>
-        <expand macro="include" include_what="gtf" include_label="Include gtf annotation file, if available"/>
-    </xml>
-    <xml name="exclude" token_exclude_what="gff3" token_exclude_label="Exclude gff3 annotation file" token_checked="false">
-        <param argument="--exclude-@EXCLUDE_WHAT@" type="boolean" truevalue="--exclude-@EXCLUDE_WHAT@" falsevalue="" label="@EXCLUDE_LABEL@" checked="@CHECKED@"/>
-    </xml>
-    <xml name="excludes_genome">
-        <expand macro="exclude" exclude_what="seq" exclude_label="Exclude genomic sequence file"/>
-        <expand macro="exclude" exclude_what="gff3" exclude_label="Exclude gff3 annotation file"/>
-        <expand macro="exclude" exclude_what="genomic-cds" exclude_label="Exclude cds from genomic sequence file"/>
-        <expand macro="exclude" exclude_what="protein" exclude_label="Exclude protein sequence file"/>
-        <expand macro="exclude" exclude_what="rna" exclude_label="Exclude transcript sequence file"/>
-    </xml>
-    <xml name="excludes_gene">
-        <expand macro="exclude" exclude_what="gene" exclude_label="Exclude gene sequence file"/>
-        <expand macro="exclude" exclude_what="protein" exclude_label="Exclude protein sequence file"/>
-        <expand macro="exclude" exclude_what="rna" exclude_label="Exclude transcript sequence file"/>
+    <xml name="include">
+        <param argument="--include" type="select" multiple="true" optional="true">
+            <option value="genome" selected="true">genomic sequence (genome)</option>
+            <option value="rna">transcript (rna)</option>
+            <option value="protein">amnio acid sequences (protein)</option>
+            <option value="cds">nucleotide coding sequences (cds)</option>
+            <option value="gff3">general feature file (gff3)</option>
+            <option value="gtf">gene transfer format (gtf)</option>
+            <option value="gbff">GenBank flat file (gbff)</option>
+            <option value="seq-report">sequence report file (seq-report)</option>
+        </param>
     </xml>
-    <xml name="excludes_virus_protein">
-        <yield/>
-        <expand macro="exclude" exclude_what="protein" exclude_label="Exclude protein sequence file"/>
-        <expand macro="exclude" exclude_what="pdb" exclude_label="Exclude protein structure files (pdb)"/>
-        <expand macro="exclude" exclude_what="gpff" exclude_label="Exclude protein sequence and annotation in GenPept flat file"/>
-        <expand macro="exclude" exclude_what="cds" exclude_label="Exclude CDS sequence file"/>
-    </xml>
-    <xml name="excludes_virus_genome">
-        <expand macro="excludes_virus_protein">
-            <expand macro="exclude" exclude_what="seq" exclude_label="Exclude genomic sequence file"/>
-        </expand>
-    </xml>
-    <token name="@EXCLUDES_GENOME@">$file_choices.exclude_gff3 $file_choices.exclude_genomic_cds $file_choices.exclude_protein $file_choices.exclude_rna $file_choices.exclude_seq</token>
-    <token name="@EXCLUDES_GENE@">$exclude_gene $exclude_protein $exclude_rna</token>
-    <token name="@EXCLUDES_VIRUS_PROTEIN@">$exclude_protein $exclude_pdb $exclude_gpff $exclude_cds</token>
-    <token name="@EXCLUDES_VIRUS_GENOME@">$exclude_seq @EXCLUDES_VIRUS_PROTEIN@</token>
-    <xml name="includes_virus_genome">
-        <expand macro="include" include_what="gbff" include_label="Include GenBank flat file sequence and annotation"/>
-    </xml>
-    <token name="@INCLUDES_GENOME@">$file_choices.include_gbff $file_choices.include_gtf</token>
-    <token name="@INCLUDES_VIRUS_GENOME@">$include_gbff</token>
+    <token name="@INCLUDE@"><![CDATA[
+        --include
+        #if $file_choices.include
+            #echo ",".join($file_choices.include)
+        #else
+            none
+        #end if
+    ]]></token>
     <xml name="released_options" token_released_what="genomes" token_before_or_after="before">
-        <param argument="--released-@BEFORE_OR_AFTER@" type="text" optional="true" label="Only include @RELEASED_WHAT@ that have been released @BEFORE_OR_AFTER@ a specified date (MM/DD/YYYY)"></param>
+        <param argument="--released-@BEFORE_OR_AFTER@" type="text" optional="true" label="Only include @RELEASED_WHAT@ that have been released @BEFORE_OR_AFTER@ a specified date (MM/DD/YYYY)">
+            <validator type="regex" message="enter a date in the form MM/DD/YYYY">[0-9]{2}/[0-9]{2}/[0-9]{4}</validator>
+        </param>
     </xml>
     <token name="@RELEASED_BEFORE@">#if $filters.released_before:
 --released-before '$filters.released_before'
 #end if
     </token>
-    <token name="@RELEASED_SINCE@">#if $filters.released_since:
---released-since '$filters.released_since'
+    <token name="@RELEASED_AFTER@">#if $filters.released_after:
+--released-after '$filters.released_after'
 #end if
     </token>
+
+    <xml name="genome_fasta_assert" tokens="el1,el2,expression" token_expression_n="1">
+        <element name="@EL1@">
+            <element name="@EL2@">
+                <assert_contents>
+                    <has_text_matching expression="@EXPRESSION@" n="@EXPRESSION_N@"/>
+                </assert_contents>
+            </element>
+        </element>
+    </xml>
 </macros>