Mercurial > repos > iuc > metaphlan

diff metaphlan.xml @ 6:2131d7dca455 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
author iuc
date Mon, 27 Feb 2023 07:01:00 +0000
parents 6dee4abadccb
children 1a6cdf55390f
line wrap: on
line diff
--- a/metaphlan.xml	Sat Dec 03 10:43:21 2022 +0000
+++ b/metaphlan.xml	Mon Feb 27 07:01:00 2023 +0000
@@ -263,15 +263,16 @@
                     <option value="history">From history</option>
                 </param>
                 <when value="cached">
-                    <param name="cached_db" label="Cached database with clade-specific marker genes" type="select">
-                        <options from_data_table="metaphlan_database">
-                            <validator message="No MetaPhlAn database is available" type="no_options" />
+                    <param name="cached_db" type="select" label="Cached database with clade-specific marker genes">
+                        <options from_data_table="@IDX_DATA_TABLE@">
+                            <filter type="static_value" column="4" value="@IDX_VERSION@"/>
+                            <validator message="No compatible MetaPhlAn database is available" type="no_options"/>
                         </options>
                     </param>
                 </when>
                 <when value="history">
                     <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/>
-                    <param argument="--mpa_pkl" type="data" format="json" label="Metadata associate to the database with clade-specific marker genes from history"/>
+                    <param argument="--mpa_pkl" type="data" format="json" label="Metadata associated to the database with clade-specific marker genes from history"/>
                 </when>
             </conditional>
         </section>
@@ -435,6 +436,7 @@
                 </assert_contents>
             </output>
             <output_collection name="levels" type="list" >
+            
                 <element name="all" ftype="tabular">
                     <assert_contents>
                         <has_text text="class"/>
@@ -442,21 +444,6 @@
                         <has_n_lines n="1"/>
                     </assert_contents>
                 </element>
-                <element name="kingdom" ftype="tabular">
-                    <assert_contents>
-                        <has_text text="kingdom_id"/>
-                        <has_n_columns n="3"/>
-                        <has_n_lines n="1"/>
-                    </assert_contents>
-                </element>
-                <element name="phylum" ftype="tabular">
-                    <assert_contents>
-                        <has_text text="phylum_id"/>
-                        <not_has_text text="kingdom_id"/>
-                        <has_n_columns n="3"/>
-                        <has_n_lines n="1"/>
-                    </assert_contents>
-                </element>
                 <element name="class" ftype="tabular">
                     <assert_contents>
                         <has_text text="class_id"/>
@@ -465,14 +452,6 @@
                         <has_n_lines n="1"/>
                     </assert_contents>
                 </element>
-                <element name="order" ftype="tabular">
-                    <assert_contents>
-                        <has_text text="order_id"/>
-                        <not_has_text text="class_id"/>
-                        <has_n_columns n="3"/>
-                        <has_n_lines n="1"/>
-                    </assert_contents>
-                </element>
                 <element name="family" ftype="tabular">
                     <assert_contents>
                         <has_text text="family_id"/>
@@ -489,6 +468,29 @@
                         <has_n_lines n="1"/>
                     </assert_contents>
                 </element>
+                <element name="kingdom" ftype="tabular">
+                    <assert_contents>
+                        <has_text text="kingdom_id"/>
+                        <has_n_columns n="3"/>
+                        <has_n_lines n="1"/>
+                    </assert_contents>
+                </element>
+                <element name="order" ftype="tabular">
+                    <assert_contents>
+                        <has_text text="order_id"/>
+                        <not_has_text text="class_id"/>
+                        <has_n_columns n="3"/>
+                        <has_n_lines n="1"/>
+                    </assert_contents>
+                </element>
+                <element name="phylum" ftype="tabular">
+                    <assert_contents>
+                        <has_text text="phylum_id"/>
+                        <not_has_text text="kingdom_id"/>
+                        <has_n_columns n="3"/>
+                        <has_n_lines n="1"/>
+                    </assert_contents>
+                </element>
                 <element name="species" ftype="tabular">
                     <assert_contents>
                         <has_text text="species_id"/>
@@ -588,21 +590,6 @@
                         <has_n_columns n="17"/>
                     </assert_contents>
                 </element>
-                <element name="kingdom" ftype="tabular">
-                    <assert_contents>
-                        <has_text text="kingdom_id"/>
-                        <has_text text="Bacteria"/>
-                        <has_n_columns n="3"/>
-                    </assert_contents>
-                </element>
-                <element name="phylum" ftype="tabular">
-                    <assert_contents>
-                        <has_text text="phylum_id"/>
-                        <not_has_text text="kingdom_id"/>
-                        <has_text text="Firmicutes"/>
-                        <has_n_columns n="3"/>
-                    </assert_contents>
-                </element>
                 <element name="class" ftype="tabular">
                     <assert_contents>
                         <has_text text="class_id"/>
@@ -611,14 +598,6 @@
                         <has_n_columns n="3"/>
                     </assert_contents>
                 </element>
-                <element name="order" ftype="tabular">
-                    <assert_contents>
-                        <has_text text="order_id"/>
-                        <not_has_text text="class_id"/>
-                        <has_text text="Propionibacteriales"/>
-                        <has_n_columns n="3"/>
-                    </assert_contents>
-                </element>
                 <element name="family" ftype="tabular">
                     <assert_contents>
                         <has_text text="family_id"/>
@@ -635,6 +614,29 @@
                         <has_n_columns n="3"/>
                     </assert_contents>
                 </element>
+                <element name="kingdom" ftype="tabular">
+                    <assert_contents>
+                        <has_text text="kingdom_id"/>
+                        <has_text text="Bacteria"/>
+                        <has_n_columns n="3"/>
+                    </assert_contents>
+                </element>
+                <element name="order" ftype="tabular">
+                    <assert_contents>
+                        <has_text text="order_id"/>
+                        <not_has_text text="class_id"/>
+                        <has_text text="Propionibacteriales"/>
+                        <has_n_columns n="3"/>
+                    </assert_contents>
+                </element>
+                <element name="phylum" ftype="tabular">
+                    <assert_contents>
+                        <has_text text="phylum_id"/>
+                        <not_has_text text="kingdom_id"/>
+                        <has_text text="Firmicutes"/>
+                        <has_n_columns n="3"/>
+                    </assert_contents>
+                </element>
                 <element name="species" ftype="tabular">
                     <assert_contents>
                         <has_text text="species_id"/>
@@ -988,20 +990,6 @@
                         <has_n_columns n="9"/>
                     </assert_contents>
                 </element>
-                <element name="kingdom" ftype="tabular">
-                    <assert_contents>
-                        <has_text text="kingdom"/>
-                        <has_text text="Bacteria"/>
-                        <has_n_columns n="2"/>
-                    </assert_contents>
-                </element>
-                <element name="phylum" ftype="tabular">
-                    <assert_contents>
-                        <has_text text="phylum"/>
-                        <has_text text="Firmicutes"/>
-                        <has_n_columns n="2"/>
-                    </assert_contents>
-                </element>
                 <element name="class" ftype="tabular">
                     <assert_contents>
                         <has_text text="class"/>
@@ -1009,13 +997,6 @@
                         <has_n_columns n="2"/>
                     </assert_contents>
                 </element>
-                <element name="order" ftype="tabular">
-                    <assert_contents>
-                        <has_text text="order"/>
-                        <has_text text="Propionibacteriales"/>
-                        <has_n_columns n="2"/>
-                    </assert_contents>
-                </element>
                 <element name="family" ftype="tabular">
                     <assert_contents>
                         <has_text text="family"/>
@@ -1030,6 +1011,27 @@
                         <has_n_columns n="2"/>
                     </assert_contents>
                 </element>
+                <element name="kingdom" ftype="tabular">
+                    <assert_contents>
+                        <has_text text="kingdom"/>
+                        <has_text text="Bacteria"/>
+                        <has_n_columns n="2"/>
+                    </assert_contents>
+                </element>
+                <element name="order" ftype="tabular">
+                    <assert_contents>
+                        <has_text text="order"/>
+                        <has_text text="Propionibacteriales"/>
+                        <has_n_columns n="2"/>
+                    </assert_contents>
+                </element>
+                <element name="phylum" ftype="tabular">
+                    <assert_contents>
+                        <has_text text="phylum"/>
+                        <has_text text="Firmicutes"/>
+                        <has_n_columns n="2"/>
+                    </assert_contents>
+                </element>
                 <element name="species" ftype="tabular">
                     <assert_contents>
                         <has_text text="species"/>