Mercurial > repos > iuc > mash_sketch

changeset 4:c73c3dfe1af8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 38a8594d05b6a2fc57db891858b789735dc4a8c3
author iuc
date Thu, 11 Sep 2025 10:22:17 +0000
parents 43f9ca23c132
children 3852f36e3154
files macros.xml mash_sketch.xml test-data/ERR024951_seqtk_sample_1000_1.fastq.gz test-data/ERR024951_seqtk_sample_1000_2.fastq.gz test-data/m64326e_231117_100511.hifi_reads.bc2068--bc2068.msh test-data/m64326e_231130_052019.hifi_reads.bc2068--bc2068.msh test-data/test_01_mash_sketch.msh test-data/test_02_mash_sketch.msh test-data/test_03_mash_sketch.msh test-data/test_04_mash_sketch.msh test-data/test_05_mash_sketch.msh test-data/test_06_mash_sketch.msh test-data/test_07_mash_sketch.msh
diffstat 13 files changed, 21 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Sat Apr 24 13:28:53 2021 +0000
+++ b/macros.xml	Thu Sep 11 10:22:17 2025 +0000
@@ -1,13 +1,17 @@
 <macros>
     <token name="@TOOL_VERSION@">2.3</token>
-    <token name="@INTYPES@">
-        fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz
-    </token>
+    <token name="@PROFILE@">23.2</token>
+    <token name="@INTYPES@">fasta,fasta.gz,fastqsanger,fastqsanger.gz</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">mash</requirement>
         </requirements>
     </xml>
+    <xml name="xref">
+        <xrefs>
+            <xref type="bio.tools">mash</xref>
+        </xrefs>
+    </xml>
     <xml name="citations">
         <citations>
             <citation type="doi">10.1186/s13059-016-0997-x</citation>
--- a/mash_sketch.xml	Sat Apr 24 13:28:53 2021 +0000
+++ b/mash_sketch.xml	Thu Sep 11 10:22:17 2025 +0000
@@ -1,10 +1,9 @@
-<tool id="mash_sketch" name="mash sketch" version="@TOOL_VERSION@+galaxy0" profile="19.01">
-    <description>
-        Create a reduced representation of a sequence or set of sequences, based on min-hashes
-    </description>
+<tool id="mash_sketch" name="mash sketch" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+    <description>Create a reduced sequence representation based on min-hashes</description>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="xref"/>
     <expand macro="requirements" />
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
@@ -78,7 +77,7 @@
         <data name="sketch" format="msh" from_work_dir="sketch.msh"/>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="reads_assembly">
                 <param name="reads_assembly_selector" value="reads"/>
                 <conditional name="reads_input">
@@ -88,40 +87,40 @@
             </conditional>
             <output name="sketch" file="test_01_mash_sketch.msh" compare="sim_size" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="reads_assembly">
                 <param name="reads_assembly_selector" value="reads"/>
                 <conditional name="reads_input">
                     <param name="reads_input_selector" value="single"/>
                     <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
-                    <param name="minimum_kmer_copies" value="10"/>
                 </conditional>
+                <param name="minimum_kmer_copies" value="10"/>
             </conditional>
             <output name="sketch" file="test_02_mash_sketch.msh" compare="sim_size" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="reads_assembly">
                 <param name="reads_assembly_selector" value="reads"/>
                 <conditional name="reads_input">
                     <param name="reads_input_selector" value="single"/>
                     <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
-                    <param name="target_coverage" value="1"/>
                 </conditional>
+                <param name="target_coverage" value="1"/>
             </conditional>
             <output name="sketch" file="test_03_mash_sketch.msh" compare="sim_size" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="reads_assembly">
                 <param name="reads_assembly_selector" value="reads"/>
                 <conditional name="reads_input">
                     <param name="reads_input_selector" value="single"/>
                     <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
-                    <param name="genome_size" value="1000"/>
                 </conditional>
+                <param name="genome_size" value="1000"/>
             </conditional>
             <output name="sketch" file="test_04_mash_sketch.msh" compare="sim_size" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="reads_assembly">
                 <param name="reads_assembly_selector" value="reads"/>
                 <conditional name="reads_input">
@@ -132,7 +131,7 @@
             <param name="sketch_size" value="500"/>
             <output name="sketch" file="test_05_mash_sketch.msh" compare="sim_size" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="reads_assembly">
                 <param name="reads_assembly_selector" value="reads"/>
                 <conditional name="reads_input">
@@ -143,7 +142,7 @@
             <param name="kmer_size" value="17"/>
             <output name="sketch" file="test_06_mash_sketch.msh" compare="sim_size" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="reads_assembly">
                 <param name="reads_assembly_selector" value="reads"/>
                 <conditional name="reads_input">
@@ -154,7 +153,7 @@
             <param name="prob_threshold" value="0.1"/>
             <output name="sketch" file="test_06_mash_sketch.msh" compare="sim_size" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="reads_assembly">
                 <param name="reads_assembly_selector" value="assembly"/>
                 <param name="assembly" value="test_assembly.fasta"/>
Binary file test-data/ERR024951_seqtk_sample_1000_1.fastq.gz has changed
Binary file test-data/ERR024951_seqtk_sample_1000_2.fastq.gz has changed
Binary file test-data/m64326e_231117_100511.hifi_reads.bc2068--bc2068.msh has changed
Binary file test-data/m64326e_231130_052019.hifi_reads.bc2068--bc2068.msh has changed
Binary file test-data/test_01_mash_sketch.msh has changed
Binary file test-data/test_02_mash_sketch.msh has changed
Binary file test-data/test_03_mash_sketch.msh has changed
Binary file test-data/test_04_mash_sketch.msh has changed
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Binary file test-data/test_07_mash_sketch.msh has changed