Mercurial > repos > iuc > pysradb_search

diff pysradb.xml @ 1:f63cf0adfd87 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb commit ce41250f1a9525090296ce9351b8a38a521af6b1
author iuc
date Wed, 30 Nov 2022 13:19:36 +0000
parents 1005ffbccd86
children b91e1e70f3a1
line wrap: on
line diff
--- a/pysradb.xml	Fri Nov 11 07:35:39 2022 +0000
+++ b/pysradb.xml	Wed Nov 30 13:19:36 2022 +0000
@@ -78,8 +78,8 @@
                 <option value="sra">SRA: Sequence Read Archive</option>
                 <option value="ena">ENA: European Nucleotide Archive</option>
             </param>
-            <param argument="--query" type="text" value=""
-                label="Query keywords" help="Multiple keywords should be separated by spaces. Example: colorectal cancer">
+            <param argument="--query" type="text" value="" optional="true"
+                label="Query keywords/BioProject ID" help="Multiple keywords should be separated by spaces. Example: colorectal cancer">
                 <sanitizer invalid_char="">
                     <valid initial="string.letters,string.digits">
                         <add value="_" />
@@ -90,7 +90,7 @@
                 <validator type="regex">[0-9a-zA-Z_ -]+</validator>
             </param>
             <conditional name="conditional_mode">
-                <param name="selector" type="select" label="Genetic material recovered directly from environmental or clinical samples" help="Enable this option if you are interested in metagenomic data. Default: disabled">
+                <param name="selector" type="select" label="Metagenomic data" help="Enable this option if you are interested in genetic material recovered directly from environmental or clinical samples. Default: disabled">
                     <option value="false" selected="true">Disabled</option>
                     <option value="true">Enabled</option>
                 </param>
@@ -299,7 +299,6 @@
             <!-- Test 02: Specific search options-->
             <test expect_num_outputs="2">
                 <param name="database" value="sra"/>
-                <param name="query" value="colorectal cancer"/>
                 <conditional name="conditional_platform">
                     <param name="platform" value="illumina"/>
                     <param name="instrument" value="NovaSeq 6000"/>
@@ -332,7 +331,7 @@
                 <conditional name="conditional_mode">
                     <param name="selector" value="false"/>
                     <param name="source" value="genomic"/>
-                    <param name="organism" value="homo sapiens"/>
+                    <param name="organism" value="Homo sapiens"/>
                 </conditional>
                 <output name="metadata_file" file="test_03.tabular" ftype="tsv"/>
                 <output name="stats" file="test_03.txt" ftype="txt"/>