# HG changeset patch
# User iuc
# Date 1769780887 0
# Node ID 6193220e8ceef67dbd6884dc8f35c4fdd93091e8
# Parent  ea46115c7f1e489f4cccb8b234d9f5c3bb45411b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim commit f91494b07d2596500a959b98f3823f76dc4f89b1

diff -r ea46115c7f1e -r 6193220e8cee mitobim.xml
--- a/mitobim.xml	Sun Jan 03 18:21:12 2021 +0000
+++ b/mitobim.xml	Fri Jan 30 13:48:07 2026 +0000
@@ -1,7 +1,8 @@
-<tool id="mitobim" name="MITObim" version="@TOOL_VERSION@" profile="20.01">
+<tool id="mitobim" name="MITObim" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.01">
     <description>mitochondrial baiting and iterative mapping</description>
     <macros>
         <token name="@TOOL_VERSION@">1.9.1</token>
+        <token name="@GALAXY_VERSION@">1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">mitobim</requirement>
@@ -57,12 +58,14 @@
     <inputs>
         <param name="reference" type="data" format="fasta,maf" label="Reference" help="If a FASTA sequence is given it will be used  as bait (using the --quick option). If a MAF alignment is given the reference is extracted from the alignment (using the --maf option)"/>
         <param argument="--ref" type="text" value="" label="Reference ID" help="If resuming, use the same as in previous iteration/initial MIRA assembly">
-            <validator type="regex" message="&quot;, &apos;, and / are not allowed in IDs">[^'\"/]*$</validator>
-	</param>
+            <validator type="empty_field" message="This field is required" />
+            <validator type="regex" message="&quot;, ', and / are not allowed in IDs">[^'\"/]*$</validator>
+        </param>
         <param argument="--readpool" type="data" format="fastq,fastq.gz" label="Read pool" help="Read pairs need to be interleaved for full functionality of the '-pair' option below"/>
-	<param argument="--sample" type="text" value="" label="Sample ID" help="If resuming, the sampleID needs to be identical to that of the previous iteration / MIRA assembly">
-            <validator type="regex" message="&quot;, &apos;, and / are not allowed in IDs">[^'\"/]*$</validator>
-	</param>
+        <param argument="--sample" type="text" value="" label="Sample ID" help="If resuming, the sampleID needs to be identical to that of the previous iteration / MIRA assembly">
+            <validator type="empty_field" message="This field is required" />
+            <validator type="regex" message="&quot;, ', and / are not allowed in IDs">[^'\"/]*$</validator>
+        </param>
         <param argument="--start" type="integer" value="" optional="true" label="Iteration to start with" help="Defaults to 0 when using '--quick' reference"/>
         <param argument="--end" type="integer" value="" optional="true" label="Iteration to end with" help="Default=startiteration, i.e. if not specified otherwise stop after 1 iteration"/>
         <param argument="--kbait" type="integer" value="31" min="1" max="256" label="kmer for baiting stringency" help=""/>
@@ -75,7 +78,6 @@
         <param argument="--denovo" type="boolean" checked="false" truevalue="--denovo" falsevalue="" label="Run MIRA in denovo mode" help=""/>
         <param argument="--pair" type="boolean" checked="false" truevalue="--pair" falsevalue="" label="Extend readpool to contain full read pairs, even if only one member was baited" help="Relies on /1 and /2 header convention for read pairs"/>
         <param argument="--split" type="boolean" checked="false" truevalue="--split" falsevalue="" label="Split reference at positions with more than 5N" help=""/>
-
         <param argument="--trimreads" type="boolean" checked="false" truevalue="--trimreads" falsevalue="" label="Trim data" help="It is recommended to trim beforehand and feed MITObim with pre trimmed data"/>
         <param argument="--trimoverhang" type="boolean" checked="false" truevalue="--trimoverhang" falsevalue="" label="Trim overhang" help=" up- and downstream of reference. That is don't extend the bait"/>
         <param argument="--mismatch" type="integer" value="" optional="true" label="Number of allowed mismatches in mapping" help="Only for illumina data (default: 15% of avg. read length)"/>
@@ -89,27 +91,27 @@
         <!--MITObim.pl -start 1 -end 10 -sample testpool -ref Salpinus_mt_genome -readpool reads.fastq -maf initial-mapping-testpool-to-Salpinus-mt_assembly/initial-mapping-testpool-to-Salpinus-mt_d_results/initial-mapping-testpool-to-Salpinus-mt_out.maf &> log-->
         <test>
             <param name="readpool" ftype="fastqsanger" value="Tthymallus-150bp-300sd50-interleaved.fastq"/>
-	    <param name="sample" value="testpool"/>
+            <param name="sample" value="testpool"/>
             <param name="reference" ftype="maf" value="initial-mapping-testpool-to-Salpinus-mt_out.maf"/>
-	    <param name="ref" value="Salpinus_mt_genome"/>
+            <param name="ref" value="Salpinus_mt_genome"/>
             <param name="start" value="1"/>
             <param name="end" value="10"/>
             <output name="assembly" value="ex1.fasta" ftype="fasta" compare="diff"/>
             <assert_command>
-                 <has_text text="--maf"/>
+                <has_text text="--maf"/>
             </assert_command>
         </test>
         <!---start 1 -end 30 -sample testpool -ref Salpinus_mt_genome -readpool ~/PATH/TO/testdata1/Tthymallus-150bp-300sd50-interleaved.fastq \-\-quick ~/PATH/TO/testdata1/Salpinus-mt-genome-NC_000861.fasta &> log-->
         <test>
             <param name="readpool" ftype="fastqsanger" value="Tthymallus-150bp-300sd50-interleaved.fastq"/>
-	    <param name="sample" value="testpool"/>
+            <param name="sample" value="testpool"/>
             <param name="reference" ftype="fasta" value="Salpinus-mt-genome-NC_000861.fasta"/>
             <param name="ref" value="Salpinus_mt_genome"/>
             <param name="start" value="1"/>
             <param name="end" value="30"/>
             <output name="assembly" value="ex2.fasta" ftype="fasta" compare="diff"/>
             <assert_command>
-                 <has_text text="--quick"/>
+                <has_text text="--quick"/>
             </assert_command>
         </test>
         <!--~/PATH/TO/MITObim.pl -sample testpool -ref Tthymallus-COI -readpool ~/PATH/TO/testdata1/Tthymallus-150bp-300sd50-interleaved.fastq \-\-quick ~/PATH/TO/testdata1/Tthymallus-COI-partial-HQ961018.fasta -end 50 \-\-denovo \-\-paired \-\-clean &> log-->
@@ -122,9 +124,17 @@
             <param name="pair" value="true"/>
             <output name="assembly" value="ex3.fasta" ftype="fasta" compare="diff"/>
             <assert_command>
-                 <has_text text="--quick"/>
+                <has_text text="--quick"/>
             </assert_command>
         </test>
+
+        <!-- Test that it fails without sample or ref IDs -->
+        <test expect_failure="true">
+            <param name="readpool" ftype="fastqsanger" value="Tthymallus-150bp-300sd50-interleaved.fastq"/>
+            <param name="reference" ftype="maf" value="initial-mapping-testpool-to-Salpinus-mt_out.maf"/>
+            <param name="start" value="1"/>
+            <param name="end" value="10"/>
+        </test>
     </tests>
     <help><![CDATA[
 The MITObim procedure (mitochondrial baiting and iterative mapping) represents a highly efficient approach to assembling novel mitochondrial genomes of non-model organisms directly from total genomic DNA derived NGS reads. Labor intensive long-range PCR steps prior to sequencing are no longer required. MITObim is capable of reconstructing mitochondrial genomes without the need of a reference genome of the targeted species by relying solely on (a) mitochondrial genome information of more distantly related taxa or (b) short mitochondrial barcoding sequences (seeds), such as the commonly used cytochrome-oxidase subunit 1 (COI), as a starting reference.