Mercurial > repos > iuc > obi_convert

diff obiconvert.xml @ 5:c5a81ce6414c draft default tip

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/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
author iuc
date Thu, 30 Oct 2025 16:02:11 +0000
parents c62e77c0a83c
children
line wrap: on
line diff
--- a/obiconvert.xml	Wed Sep 01 07:50:15 2021 +0000
+++ b/obiconvert.xml	Thu Oct 30 16:02:11 2025 +0000
@@ -1,9 +1,9 @@
 <tool id="obi_convert" name="obiconvert" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>converts sequence files to different output formats</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <command><![CDATA[
@@ -29,13 +29,13 @@
         @GENERATE_GALAXY_JSON@
     ]]></command>
     <inputs>
-        <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file" help="database used for the in silico PCR. The database must be in the ecoPCR format (for example output of obiconvert)" />
-        <param name="db" type="data" optional="true" format="txt,tabular" label="ecoPCR taxonomy database" />
+        <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file" help="database used for the in silico PCR. The database must be in the ecoPCR format (for example output of obiconvert)"/>
+        <param name="db" type="data" optional="true" format="txt,tabular" label="ecoPCR taxonomy database"/>
         <param name="tax" type="data" optional="true" format="txt,tabular" label="NCBI taxonomy dump repository"/>
         <expand macro="input_format_options_macro"/>
         <expand macro="out_format_macro"/>
-        <param name="ecopcrdb" type="boolean" truevalue="--ecopcrdb" falsevalue="" label="Do you want to create an ecoPCR database from sequence records results?"  help="Use this option if you want to generate an ecoPCR database output file" />
-        <param name="uppercase" type="boolean" truevalue="--uppercase" falsevalue=""  label="Do you want to print sequences in upper case?" />
+        <param name="ecopcrdb" type="boolean" truevalue="--ecopcrdb" falsevalue="" label="Do you want to create an ecoPCR database from sequence records results?"  help="Use this option if you want to generate an ecoPCR database output file"/>
+        <param name="uppercase" type="boolean" truevalue="--uppercase" falsevalue=""  label="Do you want to print sequences in upper case?"/>
     </inputs>
     <outputs>
         <data format="txt" name="ecopcrdb_output" label="${tool.name} on ${on_string}: ecopcrdb">
@@ -44,7 +44,7 @@
         <data format="auto" name="output"/>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input" value="output_obisort.fasta" />
             <param name="options_inputtype" value="--fasta"/>
             <param name="options_seqtype" value="--nuc"/>