# HG changeset patch
# User iuc
# Date 1655226976 0
# Node ID 624606f7c99659bc3a5eaa8805175e1aaac2c6e9
# Parent  80323066acd4826f634dfaa65dd598098f3804e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4

diff -r 80323066acd4 -r 624606f7c996 mitos2.xml
--- a/mitos2.xml	Wed Jun 02 18:39:42 2021 +0000
+++ b/mitos2.xml	Tue Jun 14 17:16:16 2022 +0000
@@ -1,14 +1,17 @@
 <tool id="mitos2" name="@MITOS_NAME@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
   <description>de-novo annotation of metazoan mitochondrial genomes</description>
+  <xrefs>
+      <xref type='bio.tools'>mitos</xref>
+  </xrefs>
   <macros>
     <import>macros.xml</import>
     <token name="@MITOS_NAME@">MITOS2</token>
     <token name="@TOOL_VERSION@">2.0.6</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
   </macros>
   <requirements>
     <requirement type="package" version="@TOOL_VERSION@">mitos</requirement>
-    <requirement type="package">zip</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[
@@ -45,16 +48,20 @@
 --maxtrnaovl $advanced_ncrna.maxtrnaovl
 --maxrrnaovl $advanced_ncrna.maxrrnaovl
 
-#if not ("protein_plot" in str($addoutputs).split(',') or "ncRNA_plot" in str($addoutputs).split(',')):
+#if not ("protein_plot" in $addoutputs or "ncRNA_plot" in $addoutputs):
   --noplots
 #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">
+    <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>
@@ -67,7 +74,7 @@
       <option value="13">Ascidian (13)</option>
       <option value="14">Alternative Flatworm (14)</option>
     </param>
-    <param argument="--refseqver" label="Reference data" type="select" help="contact the administrator of this Galaxy instance if you miss reference data">
+    <param argument="--refseqver" label="Reference data" type="select" help="Contact the administrator of this Galaxy instance if you miss reference data">
         <options from_data_table="mitos">
           <filter type="static_value" value="mitos2" column="2"/>
         </options>
@@ -87,6 +94,7 @@
       <!--<option value="ncRNA_structure_ps_plots" selected="false">ncRNA structure plots - postscript</option>-->
       <option value="ncRNA_structure_svg_plots" selected="false">ncRNA structure plots - svg</option>
       <option value="raw" selected="false">zipped raw results</option>
+      <option value="missing" selected="false">Missing genes</option>
     </param>
     <section name="advanced" title="Advanced options">
       <param name="featuretypes" label="Feature types" help="Feature types that should be predicted by MITOS (--noprot,--notrna,--norrna)" type="select" multiple="true">
@@ -106,7 +114,7 @@
       <param argument="--evalue" label="BLAST E-value Exponent" help="Negation of the exponent of the E-value threshold used by BLAST, i.e. a value X gives an E-value of 10^(-X)" type="float" value="2" min="1"/>
       <param argument="--cutoff" label="Quality cutoff" help="Minimum allowed quality in % of the maximum quality value per reading frame" type="integer" value="50" min="0" max="100"/>
       <param argument="--clipfac" label="Clipping factor" help="Clip overlapping proteins with the same name that differ by less than the specified factor" type="float" value="10" min="0"/>
-      <param argument="--ncbicode" checked="false" label="use start/stop codons as in NCBI (default: learned start/stop codons)" type="boolean" truevalue="--ncbicode" falsevalue=""/>
+      <param argument="--ncbicode" checked="false" label="Use start/stop codons as in NCBI (default: learned start/stop codons)" type="boolean" truevalue="--ncbicode" falsevalue=""/>
       <param argument="--alarab" checked="false" label="Use the hmmer based method of Al Arab et al. 2016. This will consider the evalue, ncbicode, fragovl, fragfac" type="boolean" truevalue="--alarab" falsevalue=""/>
       <param argument="--oldstst" checked="false" label="Use the old start/stop prediction method of MITOS1" type="boolean" truevalue="--oldstst" falsevalue=""/>
     </section>
@@ -157,6 +165,9 @@
     <data name="rawout" format="zip" from_work_dir="output.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">
+      <filter>"missing" in str(addoutputs)</filter>
+    </data>
   </outputs>
   <tests>
     <!-- default options -->
@@ -282,6 +293,35 @@
         <not_has_text text="--noplots"/>
       </assert_command>
     </test>
+    <!-- missing genes -->
+    <test expect_num_outputs="2">
+      <param name="input" value="NC_012920.fasta"/>
+      <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"/>
+      <assert_command>
+        <has_text text="--code 2"/>
+        <has_text text="--finovl 50"/>
+        <not_has_text text="--trna"/>
+        <not_has_text text="--rrna"/>
+        <not_has_text text="--prot"/>
+        <has_text text="--intron 0"/>
+        <has_text text="--oril 0"/>
+        <has_text text="--orih 0"/>
+        <has_text text="--evalue 2.0"/>
+        <has_text text="--cutoff 0.5"/>
+        <has_text text="--clipfac 10.0"/>
+        <not_has_text text="--best"/>
+        <has_text text="--fragovl 0.2"/>
+        <has_text text="--fragfac 10.0"/>
+        <has_text text="--ncev 0.01"/>
+        <has_text text="--maxtrnaovl 50"/>
+        <has_text text="--maxrrnaovl 50"/>
+        <has_text text="--noplots"/>
+      </assert_command>
+    </test>
   </tests>
   <help>@COMMON_HELP@
   <![CDATA[
@@ -349,7 +389,7 @@
 
   By default mitfi searches for ncRNAs using cmsearch's default fast mode first. If a ncRNA type is missing it is searched using the sensitive mode. This can be useful if low scoring copies are expected which might be missed when searching in the two stage mode. 
 
-  - Allow tRNA/rRNA overlap of up to X nt for mitfi
+- Allow tRNA/rRNA overlap of up to X nt for mitfi
 
   Allow that a tRNA/rRNA overlaps with another feature by this number of nucleotides.
 
diff -r 80323066acd4 -r 624606f7c996 test-data/missing_genes.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/missing_genes.txt	Tue Jun 14 17:16:16 2022 +0000
@@ -0,0 +1,1 @@
+missing:cox2 cox3 trnS2 cox1 trnL1 nad3 nad2 nad1 nad5 nad4 atp8 atp6 trnS1 rrnL trnP trnK trnM trnN trnA trnC trnD trnE trnF trnG cob nad4l trnQ trnR trnT trnV trnW