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changeset 5:8b08ea650060 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 2d87b0b9c2491ed6fc611b6820b5ebea1d6def23
author iuc
date Fri, 19 Jan 2024 21:29:40 +0000
parents c7553ba39670
children ca1142e5df8b
files macros.xml mitos.xml test-data/NC_012920_trnA.svg
diffstat 3 files changed, 13 insertions(+), 194 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Wed Mar 01 22:40:00 2023 +0000
+++ b/macros.xml	Fri Jan 19 21:29:40 2024 +0000
@@ -7,7 +7,7 @@
 
 - A fasta formatted sequence
 
-  - @MITOS_NAME@ processes only FASTA files containing a single sequence. If you have a FASTA file with multiple sequences you may use the tool *Split Fasta files into a collection". The resulting collection can then used as input to @MITOS_NAME@.
+  - @MITOS_NAME@ processes only FASTA files containing a single sequence. If you have a FASTA file with multiple sequences you may use the tool *Split Fasta files into a collection*. The resulting collection can then used as input to @MITOS_NAME@.
   
 - The correct genetic code needs to be selected
 
--- a/mitos.xml	Wed Mar 01 22:40:00 2023 +0000
+++ b/mitos.xml	Fri Jan 19 21:29:40 2024 +0000
@@ -1,14 +1,14 @@
 <tool id="mitos" name="@MITOS_NAME@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>de-novo annotation of metazoan mitochondrial genomes</description>
+  <macros>
+    <import>macros.xml</import>
+    <token name="@MITOS_NAME@">MITOS</token>
+    <token name="@TOOL_VERSION@">1.1.4</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+  </macros>
   <xrefs>
       <xref type='bio.tools'>mitos</xref>
   </xrefs>
-  <macros>
-    <import>macros.xml</import>
-    <token name="@MITOS_NAME@">MITOS</token>
-    <token name="@TOOL_VERSION@">1.1.1</token>
-    <token name="@VERSION_SUFFIX@">0</token>
-  </macros>
   <requirements>
     <requirement type="package" version="@TOOL_VERSION@">mitos</requirement>
   </requirements>
@@ -166,7 +166,12 @@
       <output name="protein_plot_out" file="NC_012920_prot.pdf" ftype="pdf" compare="sim_size"/>
       <output name="ncRNA_plot_out" file="NC_012920_ncrna.pdf" ftype="pdf" compare="sim_size"/>
       <output_collection name="ncRNA_structure_plot_svg_out" type="list" count="24">
-         <element name="trnA-5586-5654" file="NC_012920_trnA.svg" ftype="svg" /> 
+         <element name="trnA-5586-5654" ftype="svg">
+          <assert_contents>
+            <has_text text="&lt;svg"/>
+            <has_size min="100"/>
+          </assert_contents>
+         </element>
       </output_collection>
       <assert_command>
         <has_text text="--code 2"/>
--- a/test-data/NC_012920_trnA.svg	Wed Mar 01 22:40:00 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,186 +0,0 @@
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