Add biotools xref to MAFFT (#1342)

* Update macros.xml * Update mafft.xml * Update mafft-add.xml * Increment version suffix * Update mafft-add.xml * Update mafft.xml * fix bug in test3 * adapt test3 to multithreading
bgruening · Oct 31, 2023 · 1570f3a · 1570f3a
1 parent 7dca92b
commit 1570f3a
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diff --git a/tools/mafft/macros.xml b/tools/mafft/macros.xml
@@ -1,7 +1,13 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@VERSION@">0</token>
     <token name="@TOOL_VERSION@">7.508</token>
+    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@PROFILE@">22.01</token>
+    <xml name="biotools">
+        <xrefs>
+            <xref type="bio.tools">MAFFT</xref>
+        </xrefs>
+    </xml>
     <xml name="requirements">
       <requirements>
           <requirement type="package" version="@TOOL_VERSION@">mafft</requirement>

diff --git a/tools/mafft/mafft-add.xml b/tools/mafft/mafft-add.xml
@@ -1,10 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="rbc_mafft_add" name="MAFFT add" version="@TOOL_VERSION@+galaxy@VERSION@">
+<tool id="rbc_mafft_add" name="MAFFT add" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
   <description>Align a sequence,alignment or fragments to an existing alignment.</description>
   <macros>
     <import>macros.xml</import>
   </macros>
-  <expand macro="requirements" />
+  <expand macro="biotools"/>
+  <expand macro="requirements"/>
   <stdio>
     <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
     <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />

diff --git a/tools/mafft/mafft.xml b/tools/mafft/mafft.xml
@@ -1,9 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="rbc_mafft" name="MAFFT" version="@TOOL_VERSION@+galaxy@VERSION@">
-  <description>Multiple alignment program for amino acid or nucleotide sequences</description>
+<tool id="rbc_mafft" name="MAFFT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<description>Multiple alignment program for amino acid or nucleotide sequences</description>
   <macros>
     <import>macros.xml</import>
   </macros>
+  <expand macro="biotools"/>
   <expand macro="requirements" />
   <stdio>
     <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
@@ -229,32 +230,51 @@
       <param name="outputFormat" value="--clustalout"/>
       <output name="outputAlignment" ftype="clustal" file="mafft_nwns_result.aln" lines_diff="2" />
     </test>
+    <!-- WARNING: the results of the following test depends on #threads.
+    The result seems deterministic for single threaded execution, i.e. GALAXY_SLOTS=1 planemo test
+    However, GH CI/CD uses 2 threads and results vary -->
     <test expect_num_outputs="1" >
       <param name="inputSequences" value="sample.fa"/>
       <param name="flavourType" value="custom"/>
-      <param name="matrix_condition" value="BLOSUM"/>
+      <conditional name="matrix_condition">
+        <param name="matrix" value="BLOSUM"/>
+      </conditional>
       <param name="BLOSUM" value="62"/>
       <param name="distance_method" value="--fastapair"/>
       <param name="weighti" value="2.7"/>
       <param name="iterations" value="1000"/>
       <param name="outputFormat" value="--clustalout"/>
-      <output name="outputAlignment" ftype="clustal" file="mafft_custom_result.aln" lines_diff="2" />
+      <output name="outputAlignment" ftype="clustal" file="mafft_custom_result.aln" compare="sim_size">
+        <assert_contents>
+          <has_n_lines n="458" delta="0"/>
+          <has_text text="CLUSTAL format alignment by MAFFT F-INS-i"/>
+          <has_text text="NPIVYGISHPKY"/>
+          <has_text text="1=="/>
+          <has_text text="36=="/>
+          <has_line line="8=opsin,        ------------------------------------------------------------"/>
+        </assert_contents>
+      </output>
     </test>
   </tests>
   <help>    <![CDATA[
       **What it does**
+
       MAFFT is a multiple sequence alignment program for unix-like operating systems.
       It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences),
       FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.
-      From the MAFFT man page, an overview of the different predefined flavours of the tool.
+      From the MAFFT man page, an overview of the different predefined flavours of the tool is as follows:
+
       **Accuracy-oriented methods:**
+
       - L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information):
       - mafft --localpair --maxiterate 1000 input [> output]
       - G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information):
       - mafft --globalpair --maxiterate 1000 input [> output]
       - E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences):
       - mafft --ep 0 --genafpair --maxiterate 1000 input [> output]. For E-INS-i, the --ep 0 option is recommended to allow large gaps.
+
       **Speed-oriented methods:**
+
       - FFT-NS-i (iterative refinement method; two cycles only):
       - mafft --retree 2 --maxiterate 2 input [> output]
       - FFT-NS-i (iterative refinement method; max. 1000 iterations):
@@ -271,23 +291,14 @@
       - mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output]
 
       **Options:**
-      --auto
-      Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data size. Default: off (always FFT-NS-2)
-      --adjustdirection
-      Generate reverse complement sequences, as necessary, and align them together with the remaining sequences. In the case of protein alignment, these options are just ignored.
-      --op
-      Gap opening penalty, default: 1.53
-      --ep
-      Offset (works like gap extension penalty), default: 0.0
-      --maxiterate
-      Maximum number of iterative refinement, default: 0
-      --clustalout
-      Output: clustal format, default: fasta
-      --thread
-      Number of threads (if unsure, --thread -1)
-      --retree number
-      Guide tree is built number times in the progressive stage.
-      Valid with 6mer distance.  Default: 2
+
+      - --auto Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data size. Default: off (always FFT-NS-2)
+      - --adjustdirection Generate reverse complement sequences, as necessary, and align them together with the remaining sequences. In the case of protein alignment, these options are just ignored.
+      - --op Gap opening penalty, default: 1.53
+      - --ep Offset (works like gap extension penalty), default: 0.0
+      - --maxiterate Maximum number of iterative refinement, default: 0
+      - --clustalout Output: clustal format, default: fasta
+      - --retree number Guide tree is built number times in the progressive stage. Valid with 6mer distance. Default: 2
       ]]>
     </help>
   <expand macro="citations" />