# HG changeset patch
# User galaxyp
# Date 1710765264 0
# Node ID e63db1aa82ee5ce67e5d23d7e53b11df25ceb322
# Parent  860429737408522b956d960bbcf49562a2f36b9f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761

diff -r 860429737408 -r e63db1aa82ee macros.xml
--- a/macros.xml	Wed Jun 16 20:00:49 2021 +0000
+++ b/macros.xml	Mon Mar 18 12:34:24 2024 +0000
@@ -1,32 +1,37 @@
 <macros>
     <token name="@TOOL_VERSION@">2.0.2</token>
     <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">metaQuantome</xref>
+        </xrefs>
+    </xml>
     <xml name="requirements">
         <requirements>
-          <requirement type="package" version="@TOOL_VERSION@">metaquantome</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">metaquantome</requirement>
             <yield/>
         </requirements>
     </xml>
     <xml name="db">
-      <param argument="db_tar" type="data" label="Database Archive File"/>
+        <param argument="db_tar" type="data" label="Database Archive File"/>
     </xml>
     <xml name="ONTOLOGY_ARGS">
-      <conditional name="ontology_args">
-        <param name="ontology" type="select" label="Ontology">
-          <option value="go">Gene Ontology (GO terms)</option>
-          <option value="ec">Enzyme Commission (EC) numbers</option>
-          <option value="cog">Clusters of Orthologous Groups (COG categories)</option>
-        </param>
-        <when value="go">
-          <param argument="--slim_down" type="boolean" label="Use slim GO"/>
-        </when>
-        <when value="ec">
-          <!-- do nothing -->
-        </when>
-        <when value="cog">
-          <!-- do nothing -->
-        </when>
-      </conditional>
+        <conditional name="ontology_args">
+            <param name="ontology" type="select" label="Ontology">
+                <option value="go">Gene Ontology (GO terms)</option>
+                <option value="ec">Enzyme Commission (EC) numbers</option>
+                <option value="cog">Clusters of Orthologous Groups (COG categories)</option>
+            </param>
+            <when value="go">
+                <param argument="--slim_down" type="boolean" label="Use slim GO"/>
+            </when>
+            <when value="ec">
+                <!-- do nothing -->
+            </when>
+            <when value="cog">
+                <!-- do nothing -->
+            </when>
+        </conditional>
     </xml>
     <token name="@COMMON_PARAMS@"><![CDATA[
             --samps '$samps'
@@ -40,12 +45,12 @@
     ]]>
     </token>
     <xml name="SAMPS">
-      <param name="samps" type="data" format="tabular" label="Samples file"
-        help="must be created by 'metaQuantome: create samples file'"/>
+        <param name="samps" type="data" format="tabular" label="Samples file" help="must be created by 'metaQuantome: create samples file'"/>
     </xml>
     <xml name="citations">
         <citations>
-            <yield />
+            <citation type="doi">10.1021/ACS.JPROTEOME.0C00960</citation>
+            <yield/>
         </citations>
     </xml>
 </macros>
diff -r 860429737408 -r e63db1aa82ee metaquantome_db.xml
--- a/metaquantome_db.xml	Wed Jun 16 20:00:49 2021 +0000
+++ b/metaquantome_db.xml	Mon Mar 18 12:34:24 2024 +0000
@@ -3,7 +3,8 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         mkdir -p data &&
         #set $database_list = str($databases).split(',')
@@ -14,26 +15,25 @@
         tar --create --file '$outfile' data
     ]]></command>
     <inputs>
-        <param name="databases" type="select" multiple="True" display="checkboxes"
-          label="Databases to Download">
-          <option value="ncbi" selected="true">NCBI Taxonomy Database</option>
-          <option value="go" selected="true">Gene Ontology Database</option>
-          <option value="ec" selected="true">Enzyme Commission (EC) database</option>
+        <param name="databases" type="select" multiple="True" display="checkboxes" label="Databases to Download">
+            <option value="ncbi" selected="true">NCBI Taxonomy Database</option>
+            <option value="go" selected="true">Gene Ontology Database</option>
+            <option value="ec" selected="true">Enzyme Commission (EC) database</option>
         </param>
     </inputs>
     <outputs>
         <data format="tar" name="outfile" label="metaquantome databases"/>
     </outputs>
     <tests>
-      <test>
-        <param name="databases" value="go"/>
-        <output name="outfile">
-          <assert_contents>
-            <has_text text="ontology: go"/>
-            <has_text text="ontology: go/subsets/goslim_metagenomics"/>
-          </assert_contents>
-        </output>
-      </test>
+        <test>
+            <param name="databases" value="go"/>
+            <output name="outfile">
+                <assert_contents>
+                    <has_text text="ontology: go"/>
+                    <has_text text="ontology: go/subsets/goslim_metagenomics"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 <![CDATA[
@@ -69,5 +69,5 @@
 
 Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
 ]]></help>
-    <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>