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changeset 5:0f9b62370529 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 10:22:28 +0000
parents 86dec4abcea8
children 23d6489e2604
files macros.xml mash_screen.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, 45 insertions(+), 29 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Sat Apr 24 11:29:35 2021 +0000
+++ b/macros.xml	Thu Sep 11 10:22:28 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_screen.xml	Sat Apr 24 11:29:35 2021 +0000
+++ b/mash_screen.xml	Thu Sep 11 10:22:28 2025 +0000
@@ -1,10 +1,11 @@
-<tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy3" profile="19.01">
-    <description>determines how well query sequences are contained within a pool of sequences</description>
+<tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@">
+    <description>Determine sequence conservation</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
-    <expand macro="version_command" />
+    <expand macro="xref"/>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
         #if str( $queries_input_source.queries_input_source_selector ) == "tool_data_table":
           ln -s '$queries_input_source.queries.fields.path' queries.msh &&
@@ -56,38 +57,49 @@
                 </param>
             </when>
             <when value="history">
-                <param name="queries" type="data" format="msh" />
+                <param name="queries" type="data" format="msh"/>
             </when>
         </conditional>
-        <param name="winner_takes_all" argument="-w" type="boolean" checked="true" truevalue="-w" falsevalue="" label="'Winner takes all' to remove redundancy in the result"
-            help="If this option is not enabled, every matching strain from the same species of the reference database is reported in the result."/>
-        <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." label="Minimum identity to report" />
-        <param type="float" name="maximum_p_value_to_report" argument="-v" value="1." min="0." max="1." label="Maximum p-value to report" />
+        <param name="winner_takes_all" argument="-w" type="boolean" checked="true" truevalue="-w" falsevalue="" label="'Winner takes all' to remove redundancy in the result" help="If this option is not enabled, every matching strain from the same species of the reference database is reported in the result."/>
+        <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." label="Minimum identity to report"/>
+        <param type="float" name="maximum_p_value_to_report" argument="-v" value="1." min="0." max="1." label="Maximum p-value to report"/>
     </inputs>
     <outputs>
-        <data name="output" format="tabular" />
+        <data name="output" format="tabular"/>
     </outputs>
     <tests>
-        <test>
-            <param name="queries_input_source_selector" value="history"/>
-            <param name="queries" value="NZ_MYON01000010.1.msh"/>
-            <param name="pool_input_selector" value="single"/>
-            <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq"/>
+        <test expect_num_outputs="1">
+            <conditional name="pool_input">
+                <param name="pool_input_selector" value="single"/>
+                <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq"/>
+            </conditional>
+            <conditional name="queries_input_source">
+                <param name="queries_input_source_selector" value="history"/>
+                <param name="queries" value="NZ_MYON01000010.1.msh"/>
+            </conditional>
             <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv"/>
         </test>
-        <test>
-            <param name="queries_input_source_selector" value="tool_data_table"/>
-            <param name="queries" value="test_sketch"/>
-            <param name="pool_input_selector" value="single"/>
-            <param name="pool" value="ERR024951_seqtk_sample_1000_2.fastq"/>
+        <test expect_num_outputs="1">
+            <conditional name="pool_input">
+                <param name="pool_input_selector" value="single"/>
+                <param name="pool" value="ERR024951_seqtk_sample_1000_2.fastq"/>
+            </conditional>
+            <conditional name="queries_input_source">
+                <param name="queries_input_source_selector" value="tool_data_table"/>
+                <param name="queries" value="test_sketch"/>
+            </conditional>
             <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv"/>
         </test>
-        <test>
-            <param name="queries_input_source_selector" value="history"/>
-            <param name="queries" value="NZ_MYON01000010.1.msh"/>
-            <param name="pool_input_selector" value="paired"/>
-            <param name="pool_1" value="ERR024951_seqtk_sample_1000_1.fastq"/>
-            <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/>
+        <test expect_num_outputs="1">
+            <conditional name="pool_input">
+                <param name="pool_input_selector" value="paired"/>
+                <param name="pool_1" value="ERR024951_seqtk_sample_1000_1.fastq"/>
+                <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/>
+            </conditional>
+            <conditional name="queries_input_source">
+                <param name="queries_input_source_selector" value="history"/>
+                <param name="queries" value="NZ_MYON01000010.1.msh"/>
+            </conditional>
             <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/>
         </test>
     </tests>
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
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