diff uniprotxml_downloader.xml @ 4:12692567c7f9 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"

--- a/uniprotxml_downloader.xml	Tue Jul 02 21:46:14 2019 -0400
+++ b/uniprotxml_downloader.xml	Tue Jun 01 11:54:47 2021 +0000
@@ -1,37 +1,37 @@
-<tool id="uniprotxml_downloader" name="UniProt" version="2.1.0">
+<tool id="uniprotxml_downloader" name="UniProt" version="2.2.0" profile="21.01">
     <description>download proteome as XML or fasta</description>
     <requirements>
-        <requirement type="package" version="2.7">python</requirement>
+        <requirement type="package" version="2.25.1">requests</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:"  level="fatal" description="Error downloading proteome." />
     </stdio>
     <command>
 <![CDATA[
-python $__tool_directory__/uniprotxml_downloader.py -v 
+python '$__tool_directory__/uniprotxml_downloader.py'
 #if $taxid.input_choice == 'common':
---taxon $taxid.organism
-#if $taxid.reviewed:
---reviewed=$taxid.reviewed
-#end if
+    --taxon $taxid.organism
+    #if $taxid.reviewed:
+        --reviewed=$taxid.reviewed
+    #end if
 #elif $taxid.input_choice == 'taxids':
-#for $id in $taxid.taxons.split(','):
--t "$id"
-#end for
+    #for $id in $taxid.taxons.split(','):
+        -t '$id'
+    #end for
 #elif $taxid.input_choice == 'history':
---input="${taxid.taxon_file}"
---column=#echo int(str($taxid.column)) - 1#
+    --input='${taxid.taxon_file}'
+    --column=#echo int(str($taxid.column)) - 1#
 #end if
---format=$format
---output="${proteome}"
+--format $format
+--output '${proteome}'
 ]]>
     </command>
     <inputs>
         <conditional name="taxid">
             <param name="input_choice" type="select" label="Select">
                 <option value="common">A Common Organism</option>
-                <option value="taxids">By Organism IDs</option>
-                <option value="history">A history dataset with an Organism Taxonomy Name column</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>
             </param>
             <when value="common">
                 <param name="organism" type="select" label="Common Organisms"
@@ -60,8 +60,8 @@
                 </param>
             </when>
             <when value="history">
-                <param name="taxon_file" type="data" format="tabular" label="Dataset with Taxon Name column"/>
-                <param name="column" type="data_column" data_ref="taxon_file" label="Column with Taxon name"/>
+                <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"/>
             </when>
         </conditional>
         <param name="format" type="select" label="uniprot output format">
@@ -110,6 +110,18 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <param name="input_choice" value="history"/>
+            <param name="taxon_file" value="Helicobacter_strains_ids.tsv" ftype="tabular"/>
+            <param name="column" value="2"/>
+            <param name="format" value="fasta"/>
+            <output name="proteome">
+                <assert_contents>
+                    <has_text text="Shi470" />
+                    <has_text text="PeCan4" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 <![CDATA[