# HG changeset patch
# User iuc
# Date 1674563591 0
# Node ID 688a777e1b199b5e654f0352e458f0a98997a231
# Parent  6941d0d453bad97bbe6f4b9423c9518af883f2ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2388df7187533fb66b7729730340d2eb7b93c112

diff -r 6941d0d453ba -r 688a777e1b19 coverm_contig.xml
--- a/coverm_contig.xml	Tue Apr 26 15:27:37 2022 +0000
+++ b/coverm_contig.xml	Tue Jan 24 12:33:11 2023 +0000
@@ -1,8 +1,7 @@
-<tool id="coverm_contig" name="CoverM-CONTIG" version="@TOOL_VERSION@" python_template_version="3.5">
+<tool id="coverm_contig" name="CoverM contig" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Calculate coverage of individual contigs</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@INPUT_FORMATS@">fasta,fastq,fastq.gz,fasta.gz</token>
-        <token name="@TOOL_VERSION@">0.2.1</token>
     </macros>
     <expand macro="requirements"/>
     <command><![CDATA[
@@ -224,7 +223,7 @@
             #if $cov.contig_end_exclusion:
                 --contig-end-exclusion $cov.contig_end_exclusion
             #end if
-            #if $cov.cond_methods.trimmed_mean
+            #if $cov.cond_methods.trimmed_mean == "trimmed_mean"
                 #if $cov.cond_methods.trim_min:
                     --trim-min $cov.cond_methods.trim_min
                 #end if
@@ -238,7 +237,6 @@
             #end if
             --output-file output.tsv
             --threads \${GALAXY_SLOTS:-1}
-            2> stdout.txt
     ]]></command>
     <inputs>
         <expand macro="reads_for_contig" />
diff -r 6941d0d453ba -r 688a777e1b19 macros.xml
--- a/macros.xml	Tue Apr 26 15:27:37 2022 +0000
+++ b/macros.xml	Tue Jan 24 12:33:11 2023 +0000
@@ -1,12 +1,13 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package">coverm</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">coverm</requirement>
         </requirements>
     </xml>
     <token name="@INPUT_FORMATS@">fasta,fastq,fastq.gz,fasta.gz</token>
-    <token name="@TOOL_VERSION@">0.2.1</token>
+    <token name="@TOOL_VERSION@">0.6.1</token>
     <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">22.01</token>
     <xml name="citation">
         <citations>
             <citation type="bibtex">
@@ -96,7 +97,10 @@
                     </when>
                 </conditional>                    
                 <conditional name="add_genome">
-                    <param name="add_genome" type="boolean" label="Add additional Genome Files"/>
+                    <param name="add_genome" type="select" label="Add additional Genome Files">
+                        <option value="true">Yes</option>
+                        <option value="false" selected="true">No</option>
+                    </param>
                     <when value="true">
                         <conditional name="add_genomic">
                             <param type="select" label="Reference genome source" name="source">
@@ -186,7 +190,7 @@
     <xml name="add_reads">
         <section name="add_reads" title="Add an additional read">
             <conditional name="extra_read">
-                <param type="select" label="Read type" optional="true" name="read_type">
+                <param type="select" label="Read type" name="read_type">
                     <option value="none" selected="true">None</option>
                     <option value="paired">Paired end</option>
                     <option value="paired_collection">Paired collection</option>
@@ -251,7 +255,10 @@
             <param name="relative_abundance" type="boolean" falsevalue="" truevalue="relative_abundance" label="Relative abundance (default)"/>
             <param name="mean" type="boolean" falsevalue="" truevalue="mean" label="Mean"/>
             <conditional name="cond_methods">
-                <param name="trimmed_mean" type="boolean" falsevalue="" truevalue="trimmed_mean" label="Trimmed mean"/>
+                <param name="trimmed_mean" type="select" label="Trimmed mean">
+                    <option value="trimmed_mean">Yes</option>
+                    <option value="" selected="true">No</option>
+                </param>
                 <when value="trimmed_mean">
                     <param name="trim_min" type="integer" min="0" value="5" label="Trim min" help="Remove this smallest fraction of positions when calculating trimmed_mean default: 5"/>
                     <param name="trim_max" type="integer" min="0" value="95" label="Trim max" help="Maximum fraction for trimmed_mean calculations default: 95"/>
diff -r 6941d0d453ba -r 688a777e1b19 test-data/test4_cluster.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test4_cluster.tsv	Tue Jan 24 12:33:11 2023 +0000
@@ -0,0 +1,3 @@
+genome1	genome1
+genome2	genome2
+genome3	genome3
diff -r 6941d0d453ba -r 688a777e1b19 test-data/test4_rep.fa
diff -r 6941d0d453ba -r 688a777e1b19 test-data/test4_rep1.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test4_rep1.fa	Tue Jan 24 12:33:11 2023 +0000
@@ -0,0 +1,4 @@
+>random_sequence_length_500_1
+GAACATGGGGGGTTGTACACCGCTGGCAGGATATAAAAGAGCGAATTCTTCGTGGTGGGATGCAGAATGTTCATGCACCGCAAACCTTAGGCCCTACCCAATAACAGTCAGCTCCTCCCCTAGAAATACCGTGTCTACGTGTATGTAATGTCAAAACCGCGCTGGTCCATAACTGACCACGACATACGCTTAAGCGACGCAGGTCCCCGTTTATGGACGCAGTAAGATGATATGACAGTAACAGAACGAACGCCTTGATAGCCACTTGGCCTGGTGCCAACGGGGAACGACCTATAGGGGCCAAATTGATTCCAGCTGGTCGGGTGCGCGTATCATCCAATCCAGCCAGGCAGCAACCTCGTATAAGCATCCACACAGCGAGATTTCCAGGACCTTTGAGACGCATCTAGCAGTTTTCCCCCCTTCCACTGACACGTAGTTGATCAAATATCTCGTGTCCACCGGAATCCTCAGAGATTCTCTTCTGTCAAAAAACACTC
+>random_sequence_length_500_2
+CGCTCATGTGCCAAGCATGGACGCCGGAGACACATTTGCTAGTCGGGATGTACGCGGTCTTGTCCACTCTAAAGGGTAAATACAGGAAGCGGTCTCTAGGGACGGGCACTTAATGTAGTTGCATTTATCGATCGCGGGTCCAGATCTGATAGCCGTGCTATGCACATACGATGCTCATAACGCGCGTGATTCCCTTCATTAAGGTACGGCTACCCTGCACCTCTAGACTTGTTTGTACTATCTAGAGCAGTGAGTCGAGCGTCGACAATAGGGTCAGGGCCGGGTACTATTTTGAGCTTTACGGTAATTGCCTTGGGCTAGTAAAACCGCTTCTATACCGCAGACTCATCGAATAATGATTCCTGCAAAACGAGCACGATACGGGAGTTCCTTATGACCAGTCTAATGGTCTCAAGGGTCTCCCCCGGGGAATTACGGTGCCAAGAATGTCTCTGTAATTGACCTAAGTTGTCTGTCGATCCAGAAAATCTGACCAAGAT
diff -r 6941d0d453ba -r 688a777e1b19 test-data/test4_rep2.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test4_rep2.fa	Tue Jan 24 12:33:11 2023 +0000
@@ -0,0 +1,4 @@
+>random_sequence_length_500_1
+TCATGAACGGTAGTCAGTCAAGTTTCGCCAGCAATAGGCACAGCTTGTATGGAGGGGTTTAGTCGCCGGAGTGTTACGAGTTTGACGATCCAAAGTTGGAGTCGCCGTGATAATTAATGATATTGCGTCTTCGGTGGGCACGATGAGCCAATCTGCGTCGCACTAGTTTACGTGTTAACGTAGTGAACCTAGACATGACGGGACTATGGCAGTAAGCCGTCACAGCATGTCGGTTCCGGACCACGAGGGTCCATAAGACTAACGATCCACGCTAATTGGCGGATTTACCAAGGCGTCTTCTCTGCGTGTAAGACCCACACCGTGCCTCTGTACCTATGGACGTGCGCGACCATCTTATGATATGAGCATCACATGTTTAATAGAGCGTCCGGTGTCCCTGTAATGCCACCACTTCTGTTTCAACGGACGCTGAATCTAAGCCGATATTTTTGCCTTGATCAGAACGGGGCAGTGAAGGAGCTGCACTAAACTGGCCCTTA
+>random_sequence_length_500_2
+GGATCGGATTACTAATGTTTTTCCAGTCGCCTGTTACTCCAGGCGCGGATGCGAGTGGTCTTTGCCAAGTAGCCCCATGCCACCTGTACAAGGCGGACAAACGCGGATGCGTTTGCATAAATTACCACCGTAAGATACGTTGGCGTATTGCCGTACAAAGGCGGACAGTCCAGATATTTCTTCGGATGTAATTATTGTAGGCGTGCACAACCTACTAGGCGAAAGAGCGGCCCGTTAATCGCGGGTCGCGCCGTGCCCAATTGAACACTTTGCCACGCACGTGACTGGCGGACGGCTCACACGCTATCTCCAAAAATCTACACTTCCGGAGCTAGGCTCCATGACAGGGATGTTCTTATTCAACAAGATGGAGTGCTAATATTAACAATCGACGACACAGGTGAAAAACCTCTTGTCATGTAGCTAGCAGTTATGCGGGCGTACACACTAGTGCTAATCTACTAATCATCCACGGGCCCCTGCTAGAGATCCAAAGGGGT
diff -r 6941d0d453ba -r 688a777e1b19 test-data/test4_rep3.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test4_rep3.fa	Tue Jan 24 12:33:11 2023 +0000
@@ -0,0 +1,4 @@
+>random_sequence_length_500_1
+AGAGGGAGCCTTGCGTCGGTGCTCCACGTCGTAAAGCCGTTGAGACCGCGATTACTTTGTTTATTTTCAATTCACTTGTCACAATCAGAAGGACACCGGCGACGGCCAGTTTCCATCGCCCGTCCAGGGTATCGGGGTACCTCTCTACTCGAACGTCTGCGGGGGTTTATCGGGTCTTTACAGGGGGACCAAATGGTTGGACACGGTACCTCAACGCGATAATATATGTCCTGAGTGTGATCATCGGCTGCTTGATTGACTAGTAAGTAAATAACTCCGCCCGCCGAAAGTGACCATTCTAGGAAAATACCCTCTAGCCTCTTGCTTTTGTACGGACTCACTTTCAACGTCCAGGGGTTGCGAACTAATACAGTGAAAGCGATGACCGACAGTAGCAGTTGAGTCTCCCAATGCACCGGTCCCTAACCTCAACCCGGCGTCTAGTCTGACCAGCCTATACAGATAGCAAACAACGTGGACGCGACGGACATGACGAAATA
+>random_sequence_length_500_2
+GCTACTTTACCGTGCGGAAGTAGGTGGGTAGGCCCACATCCTCGTCCTTCAGTGGGCACCCATCTCTCTAAGTACATCTCAAGTGAGGAGGGCTGAGAAAATTGGACGATCTAGTGGAAGCGCGCCGAAATATGGCCTGAGTGAGATCGACCCCGAGGAGCGAGCTCGTTTTCCGAAGTTCGTTATGAGTATGGCGTTCGTTGCTGGCCGAGTACCCCCTGGTGACGTAAAGTGTTTATTTACACAGCTACTTCTCCGAACCAACGACTTATATGTGGGTCCCTGATTGCCTCCCATAGGTCCGGCATAGTTAAGAAAGTTAACGGAACCAAAGTCCAGTACATGGAGTTCTATGATAGACAGCTGTCTCCATTCCCGTATCTGCCAAAGAGATTAGATCCTAGTTGATCCCAGCAGCTACTCGTAATGACAGGATCCGGCGTGTCACTATACGACGCTTGCGGGAGGATGGTCGCCCTGCCCGTACCGTTACTTAGATC
diff -r 6941d0d453ba -r 688a777e1b19 test-data/test5.tsv
--- a/test-data/test5.tsv	Tue Apr 26 15:27:37 2022 +0000
+++ b/test-data/test5.tsv	Tue Jan 24 12:33:11 2023 +0000
@@ -0,0 +1,2 @@
+Genome	2seqs.bad_read.1.with_supplementary Read Count
+genome1	20