diff mitos2.xml @ 4:033755194fe9 draft

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

--- a/mitos2.xml	Tue Jun 14 17:16:16 2022 +0000
+++ b/mitos2.xml	Wed Mar 01 22:39:37 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="mitos2" name="@MITOS_NAME@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="mitos2" 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@">MITOS2</token>
-    <token name="@TOOL_VERSION@">2.0.6</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@TOOL_VERSION@">2.1.3</token>
+    <token name="@VERSION_SUFFIX@">0</token>
   </macros>
   <requirements>
     <requirement type="package" version="@TOOL_VERSION@">mitos</requirement>
-    <requirement type="package" version="3.0">zip</requirement>
   </requirements>
   <version_command>python -c "import mitos; print(mitos.__version__)"</version_command>
   <command detect_errors="aggressive"><![CDATA[
@@ -51,20 +50,17 @@
 #if not ("protein_plot" in $addoutputs or "ncRNA_plot" in $addoutputs):
   --noplots
 #end if
+#if "raw" in str($addoutputs).split(','):
+  --zip
+#end if
 
 #if "missing" in $addoutputs:
     > outdir/missing.txt
 #end if
-
-#if "raw" in str($addoutputs).split(','):
-    && zip -9 -y -r output.zip outdir/ > /dev/null
-#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>
@@ -154,15 +150,11 @@
     <data name="ncRNA_plot_out" format="pdf" from_work_dir="outdir/plots/rna.pdf" label="${tool.name} on ${on_string}: ncRNA prediction plot">
       <filter>"ncRNA_plot" in str(addoutputs)</filter>
     </data>
-    <!--<collection name="ncRNA_structure_plot_ps_out" type="list" label="${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 ${on_string}: raw data">
       <filter>"raw" in str(addoutputs)</filter>
     </data>
     <data name="missing_genes" format="txt" from_work_dir="outdir/missing.txt" label="${tool.name} on ${on_string}: missing genes">
@@ -175,7 +167,7 @@
       <param name="input" value="NC_012920.fasta"/>
       <param name="code" value="2"/>
       <param name="refseqver" value="mitos2-refdata" />
-      <output name="bedout" file="mitos2_NC_012920.bed" ftype="bed"/>
+      <output name="bedout" file="mitos2_NC_012920.bed" compare="re_match" ftype="bed"/>
       <assert_command>
         <has_text text="--code 2"/>
         <has_text text="--finovl 50"/>
@@ -202,7 +194,11 @@
       <param name="input" value="NC_012920.fasta"/>
       <param name="code" value="5"/>
       <param name="refseqver" value="mitos2-refdata" />
-      <output name="bedout" file="mitos2_NC_012920.bed" ftype="bed" compare="sim_size"/>
+      <output name="bedout" ftype="bed">
+        <assert_contents>
+          <has_n_lines n="8"/>
+        </assert_contents>
+      </output>
       <section name="advanced">
         <param name="featuretypes" value="prot,trna,rrna,intron,oril,orih"/>
         <param name="finovl" value="49"/>
@@ -252,9 +248,13 @@
         <param name="maxrrnaovl" value="49"/>
       </section>
       <param name="addoutputs" value="bed,mito,gff,seq,fas,faa,geneorder,protein_plot,ncRNA_plot,ncRNA_structure_svg_plots,raw"/>
-      <output name="bedout" file="mitos2_NC_012920.bed" ftype="bed" compare="sim_size"/>
-      <output name="mitoout" file="mitos2_NC_012920.mitos" ftype="tabular"/>
-      <output name="gffout" file="mitos2_NC_012920.gff" ftype="gff"/>
+      <output name="bedout" ftype="bed">
+        <assert_contents>
+          <has_n_lines n="18"/>
+        </assert_contents>
+      </output>
+      <output name="mitoout" file="mitos2_NC_012920.mitos" compare="re_match" ftype="tabular"/>
+      <output name="gffout" file="mitos2_NC_012920.gff" compare="re_match" ftype="gff"/>
       <output name="seqout" file="mitos2_NC_012920.seq" ftype="txt"/>
       <output name="faa" file="mitos2_NC_012920.faa" ftype="fasta"/>
       <output name="fas" file="mitos2_NC_012920.fas" ftype="fasta"/>
@@ -263,7 +263,7 @@
       <output name="ncRNA_plot_out" file="mitos2_NC_012920_ncrna.pdf" ftype="pdf" compare="sim_size"/>
       <output name="rawout" ftype="zip">
         <assert_contents>
-          <has_archive_member path=".*/result.bed"/>
+          <has_archive_member path="result.bed"/>
         </assert_contents>
       </output>
       <output_collection name="ncRNA_structure_plot_svg_out" type="list" count="17"/>
@@ -299,8 +299,12 @@
       <param name="code" value="2"/>
       <param name="refseqver" value="mitos2-refdata" />
       <param name="addoutputs" value="bed,missing"/>
-      <output name="bedout" file="mitos2_NC_012920.bed" ftype="bed"/>
-      <output name="missing_genes" file="missing_genes.txt" ftype="txt"/>
+      <output name="bedout" file="mitos2_NC_012920.bed" compare="re_match" ftype="bed"/>
+      <output name="missing_genes" ftype="txt">
+        <assert_contents>
+          <has_size value="167"/>
+        </assert_contents>
+      </output>
       <assert_command>
         <has_text text="--code 2"/>
         <has_text text="--finovl 50"/>