diff kraken_taxonomy_report.xml @ 5:bfae8da6082c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5

--- a/kraken_taxonomy_report.xml	Sun Mar 20 16:39:48 2022 +0000
+++ b/kraken_taxonomy_report.xml	Tue Mar 12 09:52:55 2024 +0000
@@ -1,8 +1,16 @@
-<tool id="kraken_taxonomy_report" name="Kraken taxonomic report" version="0.0.3" profile="16.04">
+<tool id="kraken_taxonomy_report" name="Kraken taxonomic report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="16.04">
     <description>view report of classification for multiple samples</description>
+    <macros>
+        <token name="@TOOL_VERSION@">0.0.3</token>
+        <token name="@VERSION_SUFFIX@">1</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">Kraken-Taxonomy-Report</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="1.66">biopython</requirement>
     </requirements>
+
     <version_command>python '${__tool_directory__}/kraken_taxonomy_report.py' --version</version_command>
     <command><![CDATA[
 #for $input_classification in $classification:
@@ -13,17 +21,17 @@
 python '${__tool_directory__}/kraken_taxonomy_report.py'
 
 --db '${kraken_database.fields.name}'
-${show_zeros}
-${header_line}
+${show_zeros_param}
+${header_line_param}
 ${otu_name}
-${taxonomy}
-${show_rank}
-${intermediate}
-${sanitize_names}
-#if str( $cluster.cluster ):
-    --cluster ${cluster.cluster}
+${taxo}
+${rank}
+${intermediate_rank}
+${sanitize_names_param}
+#if str( $cluster.cluster_param ):
+    --cluster ${cluster.cluster_param}
 #else:
-    ${cluster.summation}
+    ${cluster.summ}
 #end if
 
 --output '${output_report}'
@@ -38,8 +46,8 @@
     ]]></command>
     <inputs>
         <param format="tabular" label="Kraken output" multiple="True" name="classification" type="data" />
-        <param checked="False" falsevalue="" argument="--show-zeros" label="Display taxa even if they lack a read in any sample" name="show_zeros" truevalue="--show-zeros" type="boolean" />
-        <param checked="True" falsevalue="" argument="--header-line" label="Display a header line indicating sample IDs" name="header_line" truevalue="--header-line" type="boolean" />
+        <param checked="False" falsevalue="" argument="--show-zeros" label="Display taxa even if they lack a read in any sample" name="show_zeros_param" truevalue="--show-zeros" type="boolean" />
+        <param checked="True" falsevalue="" argument="--header-line" label="Display a header line indicating sample IDs" name="header_line_param" truevalue="--header-line" type="boolean" />
         <param label="Select a Kraken database" name="kraken_database" type="select" help="Select the same database used to classify reads">
             <options from_data_table="kraken_databases">
                 <validator message="No Kraken databases are available" type="no_options" />
@@ -50,12 +58,12 @@
             <option value="--name-long">Taxonified Name</option>
             <option value="--name-id">Node ID</option>
         </param>
-        <param checked="True" falsevalue="" argument="--sanitize-names" label="Sanitize Names" name="sanitize_names" truevalue="--sanitize-names" type="boolean" help="Replace special chars (\t| |\||\.;) with underscore (_)" />
-        <param checked="False" falsevalue="" argument="--show-rank" label="Output Rank Name in (second to) last column" name="show_rank" truevalue="--show-rank" type="boolean" />
-        <param checked="False" falsevalue="" argument="--taxonomy" label="Output taxonomy in last column" name="taxonomy" truevalue="--taxonomy" type="boolean" />
-        <param checked="True" falsevalue="" argument="--intermediate" label="Display intermediate ranks" name="intermediate" truevalue="--intermediate" type="boolean" />
+        <param checked="True" falsevalue="" argument="--sanitize-names" label="Sanitize Names" name="sanitize_names_param" truevalue="--sanitize-names" type="boolean" help="Replace special chars (\t| |\||\.;) with underscore (_)" />
+        <param checked="False" falsevalue="" argument="--show-rank" label="Output Rank Name in (second to) last column" name="rank" truevalue="--show-rank" type="boolean" />
+        <param checked="False" falsevalue="" argument="--taxonomy" label="Output taxonomy in last column" name="taxo" truevalue="--taxonomy" type="boolean" />
+        <param checked="True" falsevalue="" argument="--intermediate" label="Display intermediate ranks" name="intermediate_rank" truevalue="--intermediate" type="boolean" />
         <conditional name="cluster">
-            <param argument="--cluster" help="Combines rows under the selected taxon and reports only selected rank." label="Cluster by taxonomic rank" name="cluster" type="select">
+            <param argument="--cluster" help="Combines rows under the selected taxon and reports only selected rank." label="Cluster by taxonomic rank" name="cluster_param" type="select">
                 <option value="Superkingdom">Superkingdom</option>
                 <option value="Kingdom">Kingdom</option>
                 <option value="Subkingdom">Subkingdom</option>
@@ -87,7 +95,7 @@
                 <option value="" selected="True">No Clustering</option>
             </param>
             <when value="">
-                <param checked="False" falsevalue="" argument="--summation" label="Summation of lower ranks into higher ranks" name="summation" truevalue="--summation" type="boolean" />
+                <param checked="False" falsevalue="" argument="--summation" label="Summation of lower ranks into higher ranks" name="summ" truevalue="--summation" type="boolean" />
             </when>
             <when value="Superkingdom"/>
             <when value="Kingdom"/>
@@ -127,71 +135,71 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="classification" value="input_kraken_1.tabular" ftype="tabular"/>
-            <param name="show_zeros" value="True"/>
-            <param name="header_line" value="True"/>
+            <param name="show_zeros_param" value="True"/>
+            <param name="header_line_param" value="True"/>
             <param name="kraken_database" value="test_db"/>
             <param name="otu_name" value=""/>
-            <param name="sanitize_names" value="True"/>
-            <param name="show_rank" value="True"/>
-            <param name="taxonomy" value="True"/>
-            <param name="intermediate" value="True"/>
+            <param name="sanitize_names_param" value="True"/>
+            <param name="rank" value="True"/>
+            <param name="taxo" value="True"/>
+            <param name="intermediate_rank" value="True"/>
             <conditional name="cluster">
-                <param name="cluster" value=""/>
-                <param name="summation" value="True"/>
+                <param name="cluster_param" value=""/>
+                <param name="summ" value="True"/>
             </conditional>
             <param name="tree" value="True"/>
             <output name="output_report" file="output_abundance_1.tabular" ftype="tabular"/>
             <output name="output_tree" file="output_tree_1.newick" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="classification" value="input_kraken_1.tabular" ftype="tabular"/>
-            <param name="show_zeros" value="True"/>
-            <param name="header_line" value="True"/>
+            <param name="show_zeros_param" value="True"/>
+            <param name="header_line_param" value="True"/>
             <param name="kraken_database" value="test_db"/>
             <param name="otu_name" value=""/>
-            <param name="sanitize_names" value="True"/>
-            <param name="show_rank" value="True"/>
-            <param name="taxonomy" value="True"/>
-            <param name="intermediate" value="True"/>
+            <param name="sanitize_names_param" value="True"/>
+            <param name="rank" value="True"/>
+            <param name="taxo" value="True"/>
+            <param name="intermediate_rank" value="True"/>
             <conditional name="cluster">
-                <param name="cluster" value=""/>
-                <param name="summation" value="False"/>
+                <param name="cluster_param" value=""/>
+                <param name="summ" value="False"/>
             </conditional>
             <param name="tree" value="True"/>
             <output name="output_report" file="output_abundance_2.tabular" ftype="tabular"/>
             <output name="output_tree" file="output_tree_1.newick" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="classification" value="input_kraken_1.tabular" ftype="tabular"/>
-            <param name="show_zeros" value="True"/>
-            <param name="header_line" value="True"/>
+            <param name="show_zeros_param" value="True"/>
+            <param name="header_line_param" value="True"/>
             <param name="kraken_database" value="test_db"/>
             <param name="otu_name" value=""/>
-            <param name="sanitize_names" value="True"/>
-            <param name="show_rank" value="True"/>
-            <param name="taxonomy" value="True"/>
-            <param name="intermediate" value="False"/>
+            <param name="sanitize_names_param" value="True"/>
+            <param name="rank" value="True"/>
+            <param name="taxo" value="True"/>
+            <param name="intermediate_rank" value="False"/>
             <conditional name="cluster">
-                <param name="cluster" value="Species"/>
+                <param name="cluster_param" value="Species"/>
             </conditional>
             <param name="tree" value="True"/>
             <output name="output_report" file="output_abundance_3.tabular" ftype="tabular"/>
             <output name="output_tree" file="output_tree_3.newick" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="classification" value="input_kraken_1.tabular,input_kraken_2.tabular" ftype="tabular"/>
-            <param name="show_zeros" value="True"/>
-            <param name="header_line" value="True"/>
+            <param name="show_zeros_param" value="True"/>
+            <param name="header_line_param" value="True"/>
             <param name="kraken_database" value="test_db"/>
             <param name="otu_name" value=""/>
-            <param name="sanitize_names" value="True"/>
-            <param name="show_rank" value="True"/>
-            <param name="taxonomy" value="True"/>
-            <param name="intermediate" value="False"/>
+            <param name="sanitize_names_param" value="True"/>
+            <param name="rank" value="True"/>
+            <param name="taxo" value="True"/>
+            <param name="intermediate_rank" value="False"/>
             <conditional name="cluster">
-                <param name="cluster" value="Species"/>
+                <param name="cluster_param" value="Species"/>
             </conditional>
             <param name="tree" value="True"/>
             <output name="output_report" file="output_abundance_4.tabular" ftype="tabular"/>