diff NSStats.xml @ 0:ebbbb3265867 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NSStats.xml	Sat Apr 13 16:09:46 2024 +0000
@@ -0,0 +1,50 @@
+<tool id="chewbbaca_nsstats" name="chewBBACA NSStats" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Retrieve basic information about the species and schemas in Chewie-NS</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        chewBBACA.py NSStats
+            -m $mode
+            #if $species_id != ""
+            --sp $species_id 
+            #end if
+            #if $schema_id != ""
+            --sc $schema_id
+            #end if
+            > 'NSStats.txt'
+    ]]></command>
+    <inputs>
+        <param argument="--mode" type="select" label="Mode" optional="false">
+            <option value="species">species</option>
+            <option value="schemas">schemas</option>
+        </param>
+        <param argument="--species-id" type="select" label="Species ID" value="" optional="true">
+            <expand macro="species_id"/>
+        </param>
+        <!-- Currently,the schema id can only be set to 1. Maybe in the next versions other values possible -->
+        <param argument="--schema-id" type="integer" min="1" value="" label="Schema ID" optional="true"/>
+    </inputs>
+    <outputs>
+        <data format="txt" name="NSStats" from_work_dir="NSStats.txt" label="${tool.name}"/>
+    </outputs>
+    <tests>
+        <test expect_exit_code="0">
+            <param name="mode" value="species" />
+            <output name="NSStats">
+                <assert_contents>
+                    <has_text_matching expression="Streptococcus pyogenes\s+1\s+1\s+3044\s+398511"/>
+                    <has_text_matching expression="Clostridium neonatale\s+16\s+1\s+2350\s+13115"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
+
+The NSStats module enables the retrieval of information from the Chewie-NS server. Its main objective is to provide information about the list of species and schemas in Chewie-NS, so that users can quickly identify a schema of interest and download it.
+
+    </help>
+    <expand macro="citations" />
+</tool>
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