diff mitos.xml @ 4:c7553ba39670 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484

--- a/mitos.xml	Tue Jun 14 17:16:57 2022 +0000
+++ b/mitos.xml	Wed Mar 01 22:40:00 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="mitos" name="@MITOS_NAME@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
+<tool id="mitos" name="@MITOS_NAME@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>de-novo annotation of metazoan mitochondrial genomes</description>
   <xrefs>
       <xref type='bio.tools'>mitos</xref>
@@ -6,12 +6,11 @@
   <macros>
     <import>macros.xml</import>
     <token name="@MITOS_NAME@">MITOS</token>
-    <token name="@TOOL_VERSION@">1.0.5</token>
-    <token name="@VERSION_SUFFIX@">1</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>
-    <requirement type="package">zip</requirement>
   </requirements>
   <version_command>python -c "import mitos; print(mitos.__version__)"</version_command>
   <command detect_errors="aggressive"><![CDATA[
@@ -37,16 +36,13 @@
 --fragovl $fragovl
 --fragfac $advanced_prot.fragfac
 --ststrange $advanced_prot.ststrange
-
 #if "raw" in str($addoutputs).split(','):
-  && zip -9 -y -r output.zip outdir/ > /dev/null
+  --zip
 #end if
   ]]></command>
   <inputs>
     <param argument="--input" label="sequence" type="data" format="fasta" help="a single sequence in fasta formated sequence">
-      <options options_filter_attribute="metadata.sequences">
-        <filter type="add_value" value="1"/>
-      </options>
+      <validator type="dataset_metadata_in_range" metadata_name="sequences" min="1" max="1"/>
     </param> 
     <param argument="--code" label="Genetic code" type="select">
       <option value="2">Vertebrate (2)</option>
@@ -122,15 +118,11 @@
     <data name="ncRNA_plot_out" format="pdf" from_work_dir="outdir/plots/rna.pdf" label="${tool.name} on ${on_string}: ncRNA prediction plot">
       <filter>"protein_plot" in str(addoutputs)</filter>
     </data>
-    <!--<collection name="ncRNA_structure_plot_ps_out" type="list" label="${tool.name} on ${on_string}: ncRNA postscript structure plots">
-      <discover_datasets pattern="(?P&lt;name&gt;.+)\.ps" format="ps" directory="outdir/plots" />
-      <filter>"ncRNA_structure_ps_plots" in str(addoutputs)</filter>
-    </collection>-->
     <collection name="ncRNA_structure_plot_svg_out" type="list" label="${tool.name} on ${on_string}: ncRNA svg structure plots">
       <discover_datasets pattern="(?P&lt;name&gt;.+)\.svg" format="svg" directory="outdir/plots" />
       <filter>"ncRNA_structure_svg_plots" in str(addoutputs)</filter>
     </collection>
-    <data name="rawout" format="zip" from_work_dir="output.zip" label="${tool.name} on ${on_string}: raw data">
+    <data name="rawout" format="zip" from_work_dir="outdir.zip" label="${tool.name} on ${on_string}: raw data">
       <filter>"raw" in str(addoutputs)</filter>
     </data>
   </outputs>
@@ -167,7 +159,7 @@
       <output name="faaout" file="NC_012920.faa" ftype="fasta" />
       <output name="rawout" ftype="zip">
           <assert_contents>
-              <has_archive_member path=".*/result.bed"/>
+              <has_archive_member path="result.bed"/>
           </assert_contents>
       </output>
       <output name="geneorderout" file="NC_012920.geneorder" ftype="fasta" />