Mercurial > repos > iuc > meryl

changeset 7:51c2360aa807 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8"
author iuc
date Mon, 28 Jun 2021 09:32:16 +0000
parents 31fa26c0692b
children 5ae3496f9ca3
files macros.xml meryl.xml test-data/child.fasta.gz
diffstat 3 files changed, 29 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Tue Jun 08 07:20:29 2021 +0000
+++ b/macros.xml	Mon Jun 28 09:32:16 2021 +0000
@@ -1,6 +1,7 @@
 <macros>
     <token name="@TOOL_VERSION@">1.3</token>
-    <token name="@GALAXY_TOOL_VERSION@">galaxy2</token>
+    <token name="@GALAXY_TOOL_VERSION@">galaxy</token>
+    <token name="@SUFFIX_VERSION@">3</token>
     <xml name="edam_ontology">
         <edam_topics>                                                                                  
             <edam_topic>topic_0196</edam_topic>
--- a/meryl.xml	Tue Jun 08 07:20:29 2021 +0000
+++ b/meryl.xml	Mon Jun 28 09:32:16 2021 +0000
@@ -1,4 +1,4 @@
-<tool id='meryl' name='Meryl' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@' profile='20.01'>
+<tool id='meryl' name='Meryl' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@' profile='20.01'>
     <description>a genomic k-mer counter and sequence utility</description>
     <macros>
         <import>macros.xml</import>
@@ -153,7 +153,7 @@
                     <option value="count-forward">Count-forward: count the occurreces of forward k-mers</option>
                     <option value="count-reverse">Count-reverse: count the occurreces of reverse k-mers</option>
                 </param>
-                <param name="input_reads" type="data" format="fastq,fasta" label="Input sequences" help="Select your reads in FASTA/FASTQ format." />
+                <param name="input_reads" type="data" format="fastq,fastq.gz,fasta,fasta.gz" label="Input sequences" help="Select your reads in FASTA/FASTQ format." />
                 <conditional name="options_kmer_size">
                     <param name="kmer_size" type="select" label="K-mer size selector">
                         <option value="provide">Set a k-mer size</option>
@@ -225,9 +225,9 @@
                 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" />
             </when>
             <when value="trio-mode">
-                <param name="child_reads" type="data" format="fastq,fasta" multiple="true" label="F1 reads" help="Select F1 reads used for generating the assembly" />
-                <param name="paternal_reads" type="data" format="fastq,fasta" multiple="true" optional="true" label="Paternal reads" help="Select the paternal reads used for generating the assembly" />
-                <param name="maternal_reads" type="data" format="fastq,fasta" multiple="true" optional="true" label="Maternal reads" help="Select the maternal reads used for generating the assembly" />
+                <param name="child_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" label="F1 reads" help="Select F1 reads used for generating the assembly" />
+                <param name="paternal_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" optional="true" label="Paternal reads" help="Select the paternal reads used for generating the assembly" />
+                <param name="maternal_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" optional="true" label="Maternal reads" help="Select the maternal reads used for generating the assembly" />
                 <conditional name="options_kmer_size">
                     <param name="kmer_size" type="select" label="K-mer size selector">
                         <option value="provide">Set a k-mer size</option>
@@ -427,7 +427,7 @@
                 </assert_contents>
             </output>
         </test>
-        <!-- test 11 -->
+        <!-- test 12 -->
         <test expect_num_outputs="1">
             <conditional name="operation_type">
                 <param name="command_type" value="arithmetic-kmers" />
@@ -437,7 +437,7 @@
             </conditional>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="37172" delta="300" />
+                    <has_size value="37501" delta="300" />
                 </assert_contents>
             </output>
         </test>
@@ -619,6 +619,26 @@
             </conditional>
             <output name="read_db_print" file="output_25.read-db.tabular" sort="True"/>
         </test>
+        <!--Test compressed files-->
+        <test expect_num_outputs="1">
+            <conditional name="operation_type">
+                <param name="command_type" value="count-kmers" />
+                <param name="count_operation" value="count" />
+                <param name="input_reads" value="child.fasta.gz" />
+                <conditional name="options_kmer_size">
+                    <param name="kmer_size" value="provide" />
+                    <param name="input_kmer_size" value="7" />
+                </conditional>
+            </conditional>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="1851" delta="300" />
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_line line="K-mer size: 7" />
+            </assert_stdout>
+        </test>
     </tests>
     <help><![CDATA[
 
Binary file test-data/child.fasta.gz has changed