Mercurial > repos > dfornika > ncbi_acc_download

changeset 9:27d1dd60d7b5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 1b5c34749ec9a60e5fb5daeaae1584f19bed7df9-dirty"
author dfornika
date Mon, 25 Nov 2019 21:18:12 +0000
parents 6d055dfcfcf5
children 1abc6c72287e
files ncbi_acc_download.xml
diffstat 1 files changed, 57 insertions(+), 22 deletions(-) [+]
line wrap: on
line diff
--- a/ncbi_acc_download.xml	Sat Nov 23 00:39:58 2019 +0000
+++ b/ncbi_acc_download.xml	Mon Nov 25 21:18:12 2019 +0000
@@ -16,35 +16,44 @@
         cd outdir &&
         while read accession; do
         ncbi-acc-download
-            --molecule '${molecule}'
+            --molecule '${molecule.select}'
             --format '${format}'
             --extended-validation all
             \${accession} && sleep 5;
         done < ../accessions
     ]]></command>
     <inputs>
-      <conditional name="query_source">
-          <param name="select" type="select" label="Select source for IDs">
-            <option value="accession_file">File containing Accessions (one per line)</option>
-            <option value="accession_list">Direct Entry</option>
-          </param>
-          <when value="accession_file">
-              <param label="Accession File" name="accession_file" type="data" format="text,tabular"/>
-          </when>
-          <when value="accession_list">
+        <conditional name="query_source">
+            <param name="select" type="select" label="Select source for IDs">
+                <option value="accession_file">File containing Accessions (one per line)</option>
+                <option value="accession_list">Direct Entry</option>
+            </param>
+            <when value="accession_file">
+                <param label="Accession File" name="accession_file" type="data" format="text,tabular"/>
+            </when>
+            <when value="accession_list">
               <param label="ID List" name="accession_list" type="text" area="true" help="Newline/Comma separated list of IDs"/>
-          </when>
+            </when>
         </conditional>
-        <param name="molecule" type="select" label="Molecule Type">
-            <option value="nucleotide" selected="true">Nucleotide</option>
-            <option value="protein">Protein</option>
-        </param>
-        <param name="format" type="select" label="File Format">
-            <option value="fasta" selected="true">FASTA</option>
-            <option value="genbank">GenBank</option>
-            <option value="featuretable">Feature Table</option>
-            <option value="gff3">GFF3</option>
-        </param>
+        <conditional name="molecule">
+            <param name="select" type="select" label="Molecule Type">
+                <option value="nucleotide" selected="true">Nucleotide</option>
+                <option value="protein">Protein</option>
+            </param>
+            <when value="nucleotide">
+                <param name="format" type="select" label="File Format">
+                    <option value="fasta" selected="true">FASTA</option>
+                    <option value="genbank">GenBank</option>
+                    <option value="featuretable">Feature Table</option>
+                    <option value="gff3">GFF3</option>
+                </param>
+            </when>
+            <when value="protein">
+                <param name="format" type="select" label="File Format">
+                    <option value="fasta" selected="true">FASTA</option>
+                </param>
+            </when>
+        </conditional>
     </inputs>
     <outputs>
         <collection name="output" type="list" label="Output">
@@ -90,7 +99,7 @@
         <test>
             <param name="molecule" value="nucleotide"/>
             <param name="format" value="fasta"/>
-            <param name="query_source.select" value="accession_list"/>
+            <param name="select" value="accession_list"/>
             <param name="accession_list" value="CP011064,CP021680"/>
             <output_collection name="output" type="list">
                 <element name="CP011064">
@@ -105,6 +114,32 @@
                 </element>
             </output_collection>
         </test>
+        <test>
+            <param name="molecule" value="protein"/>
+            <param name="format" value="fasta"/>
+            <param name="select" value="accession_list"/>
+            <param name="accession_list" value="NP_003192"/>
+            <output_collection name="output" type="list">
+                <element name="NP_003192">
+                    <assert_contents>
+                        <has_line line=">NP_003192.1 transcription factor A, mitochondrial isoform 1 precursor [Homo sapiens]" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+        <test>
+            <param name="molecule" value="protein"/>
+            <param name="format" value="genbank"/>
+            <param name="select" value="accession_list"/>
+            <param name="accession_list" value="NP_003192"/>
+            <output_collection name="output" type="list">
+                <element name="NP_003192">
+                    <assert_contents>
+                        <has_line line="DEFINITION  transcription factor A, mitochondrial isoform 1 precursor [Homo" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
     </tests>
     <help><![CDATA[
     ]]></help>