diff humann.xml @ 2:2cd76b089570 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd

--- a/humann.xml	Wed May 19 17:03:51 2021 +0000
+++ b/humann.xml	Tue Feb 07 19:47:50 2023 +0000
@@ -18,7 +18,7 @@
                     </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>
                 <param argument="--prescreen-threshold" type="float" value="0.01" min="0" max="100" label="Minimum percentage of reads matching a species"/>
@@ -29,7 +29,7 @@
             #if $wf.prescreen.metaphlan_db.selector == "history"
             mkdir metaphlan_db
             &&
-            bowtie2-build '$wf.prescreen.metaphlan_db.bowtie2db' 'metaphlan_db/custom_db-v30'
+            bowtie2-build --large-index '$wf.prescreen.metaphlan_db.bowtie2db' 'metaphlan_db/custom_db-v30'
             &&
             python '$__tool_directory__/customizemetadata.py'
                 transform_json_to_pkl
@@ -85,7 +85,7 @@
             mkdir nucleotide_db
             &&
                 #for $f in $wf.nucleotide_search.nucleotide_db.nucleotide_database:
-            ln -s '$f' 'nucleotide_db/${re.sub('[^\w\-_.]', '_', f.element_identifier)}.v296_201901b' &&
+            ln -s '$f' 'nucleotide_db/${re.sub('[^\w\-_.]', '_', f.element_identifier)}.v201901_v31' &&
                 #end for
             #end if
         ]]></token>
@@ -393,6 +393,38 @@
         </data>
     </outputs>
     <tests>
+        <!-- This test refers to the Metaphlan v3 DB format, and hence should fail, which is to be caught gracefully. -->
+        <test expect_exit_code="42" expect_failure="true">
+            <conditional name="in">
+                <!-- raw fasta file -->
+                <param name="selector" value="raw"/>
+                <param name="input" value="demo.fastq.gz"/>
+            </conditional>
+            <conditional name="wf">
+                <!-- full workflow -->
+                <param name="selector" value="none"/>
+                <section name="prescreen">
+                    <conditional name="metaphlan_db">
+                        <param name="selector" value="history"/>
+                        <param name="bowtie2db" value="test-db/metaphlan-db/demo-db-v30.fasta"/>
+                        <param name="mpa_pkl" value="test-db/metaphlan-db/old-structure/demo-db-v30.json"/>
+                    </conditional>
+                    <param name="prescreen_threshold" value="0.01"/>
+                </section>
+                <section name="nucleotide_search">
+                    <conditional name="nucleotide_db">
+                        <param name="selector" value="history"/>
+                        <param name="nucleotide_database">
+                            <collection type="list">
+                                <element name="g__Bacteroides.s__Bacteroides_stercoris.centroids" ftype="fasta.gz" value="test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_dorei.centroids.v201901_v31.ffn.gz" />
+                                <element name="g__Bacteroides.s__Bacteroides_vulgatus.centroids" ftype="fasta.gz" value="test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_vulgatus.centroids.v201901_v31.ffn.gz" />
+                            </collection>
+                        </param>
+                    </conditional>
+                </section>
+            </conditional>
+        </test>
+        <!-- This test refers to the Metaphlan v4 DB format, and hence should be a straight pass. -->
         <test expect_num_outputs="12">
             <conditional name="in">
                 <!-- raw fasta file -->
@@ -415,8 +447,8 @@
                         <param name="selector" value="history"/>
                         <param name="nucleotide_database">
                             <collection type="list">
-                                <element name="g__Bacteroides.s__Bacteroides_stercoris.centroids" ftype="fasta.gz" value="test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_dorei.centroids.v296_201901b.ffn.gz" />
-                                <element name="g__Bacteroides.s__Bacteroides_vulgatus.centroids" ftype="fasta.gz" value="test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_vulgatus.centroids.v296_201901b.ffn.gz" />
+                                <element name="g__Bacteroides.s__Bacteroides_stercoris.centroids" ftype="fasta.gz" value="test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_dorei.centroids.v201901_v31.ffn.gz"/>
+                                <element name="g__Bacteroides.s__Bacteroides_vulgatus.centroids" ftype="fasta.gz" value="test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_vulgatus.centroids.v201901_v31.ffn.gz"/>
                             </collection>
                         </param>
                     </conditional>
@@ -921,6 +953,30 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- This test should fail for as metaphlan v4 is invoked on outdated input DB. -->
+        <test expect_exit_code="1" expect_failure="true">
+            <conditional name="in">
+                <!-- raw fasta file -->
+                <param name="selector" value="raw"/>
+                <param name="input" value="demo.fastq.gz"/>
+            </conditional>
+            <conditional name="wf">
+                <!-- bypass_translated_search -->
+                <param name="selector" value="bypass_translated_search"/>
+                <section name="prescreen">
+                    <conditional name="metaphlan_db">
+                        <param name="selector" value="cached"/>
+                        <param name="cached_db" value="metaphlan-db-old-structure"/>
+                    </conditional>
+                </section>
+                <section name="nucleotide_search">
+                    <conditional name="nucleotide_db">
+                        <param name="selector" value="cached"/>
+                        <param name="nucleotide_database" value="chocophlan-DEMO-20210421"/>
+                    </conditional>
+                </section>
+            </conditional>
+        </test>
     </tests>
     <help><![CDATA[
 @HELP_HEADER@
@@ -975,7 +1031,7 @@
 
 
 HUMAnN uses 3 reference databases
-Locally cached databases have to be downloaded database before using them (using the dedicated tool). Custom databases can also be used after upload.
+Locally cached databases have to be downloaded before using them (using the dedicated tool). Custom databases can also be used after upload.
 
 Outputs
 =======