cutadapt: make no_match_adapter_wildcards independent

galaxyproject · Nov 6, 2023 · b708043 · b708043
1 parent 439c877
commit b708043
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Showing 5 changed files with 69 additions and 5 deletions.
diff --git a/tools/cutadapt/cutadapt.xml b/tools/cutadapt/cutadapt.xml
@@ -111,6 +111,7 @@ cutadapt
 --overlap=$adapter_options.overlap
 $adapter_options.no_indels
 $adapter_options.match_read_wildcards
+$adapter_options.no_match_adapter_wildcards
 --action=$adapter_options.action
 $adapter_options.revcomp
 
@@ -224,11 +225,8 @@ $read_mod_options.zero_cap
             <param argument="--no-indels" type="boolean" checked="false" truevalue="--no-indels" falsevalue="" label="Do not allow indels (Use ONLY with anchored 5' (front) adapters)." help="Do not allow indels in the alignments. That is, allow only mismatches. This option is currently only supported for anchored 5' adapters ('^ADAPTER') (default: both mismatches and indels are allowed)." />
             <param argument="--times" type="integer" min="1" value="1" label="Match times" help="Try to remove adapters at most COUNT times. Useful when an adapter gets appended multiple times." />
             <param argument="--overlap" type="integer" min="1" value="3" label="Minimum overlap length" help="Minimum overlap length. If the overlap between the adapter and the sequence is shorter than LENGTH, the read is not modified. This reduces the number of bases trimmed purely due to short random adapter matches." />
-                <param name="match_read_wildcards" type="select"  label="Match wildcards" help="Allow 'N's as matches. Default: in the adapters but not in the reads">
-                <option value=" " selected="true">In the adapters but not in the reads</option>
-                <option value="--match-read-wildcards">In the adapters and in the reads</option>
-                <option value="--no-match-adapter-wildcards">Nowhere</option>
-            </param>
+            <param argument="--match-read-wildcards" type="boolean" checked="false" truevalue="--match-read-wildcards" falsevalue="" label="Match wilcards in reads" help="Interpret IUPAC wildcards in reads"/>
+            <param argument="--no-match-adapter-wildcards" type="boolean" checked="true" truevalue="" falsevalue="--no-match-adapter-wildcards" label="Match wilcards in adapters" help="Interpret IUPAC wildcards in adapters."/>
             <param argument="--revcomp" type="boolean" checked="false" truevalue="--revcomp" falsevalue="" label="Look for adapters in the reverse complement" help="Check both the read and its reverse complement for adapter matches. If match is on reverse-complemented version, output that one. Default: check only read." />
         </section>
 
@@ -1268,6 +1266,52 @@ $read_mod_options.zero_cap
                 <has_text text="--max-expected-errors=0.9"/>
             </assert_command>
         </test>
+
+        <!-- https://github.com/marcelm/cutadapt/blob/3407ac0004d04b11ae7157934a6665ecaf82c328/tests/test_commandline.py#L335 -->
+        <test expect_num_outputs="3">
+            <param name="type" value="single" />
+            <param name="input_1" ftype="fasta" value="cutadapt/data/wildcard.fa" />
+            <section name="r1">
+                <repeat name="anywhere_adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="ACGTACGT"/>
+                    </conditional>
+                </repeat>
+            </section>
+            <section name="adapter_options">
+                <param name="match_read_w" value="true"/>
+            </section>
+            <output name="out1" file="cutadapt/cut/wildcard.fa" ftype="fasta"/>
+            <assert_command>
+                <has_text text="--match-read-wildcards"/>
+                <has_text text="-b 'ACGTACGT'"/>
+            </assert_command>
+        </test>
+
+        <!-- https://github.com/marcelm/cutadapt/blob/3407ac0004d04b11ae7157934a6665ecaf82c328/tests/test_commandline.py#L368 -->
+        <test expect_num_outputs="3">
+            <param name="type" value="single" />
+            <param name="input_1" ftype="fasta" value="cutadapt/data/wildcardN.fa" />
+            <section name="r1">
+                <repeat name="anywhere_adapters">
+                    <conditional name="adapter_source">
+                        <param name="adapter_source_list" value="user"/>
+                        <param name="adapter" value="GGGGGGG"/>
+                    </conditional>
+                </repeat>
+            </section>
+            <section name="adapter_options">
+                <param name="match_read_w" value="true"/>
+                <param name="error_rate" value="0"/>
+            </section>
+            <output name="out1" file="cutadapt/cut/wildcardN.fa" ftype="fasta"/>
+            <assert_command>
+                <has_text text="--match-read-wildcards"/>
+                <has_text text="--error-rate 0.0"/>
+                <has_text text="-a 'GGGGGGG'"/>
+            </assert_command>
+        </test>
     </tests>
 
     <help><![CDATA[

diff --git a/tools/cutadapt/test-data/cutadapt/cut/wildcard.fa b/tools/cutadapt/test-data/cutadapt/cut/wildcard.fa
@@ -0,0 +1,4 @@
+>1
+TGCATGCA
+>2
+TGCATGCA
diff --git a/tools/cutadapt/test-data/cutadapt/cut/wildcardN.fa b/tools/cutadapt/test-data/cutadapt/cut/wildcardN.fa
@@ -0,0 +1,6 @@
+>perfect
+TTT
+>withN
+TTT
+>1mism
+TTTGGGGCGG
diff --git a/tools/cutadapt/test-data/cutadapt/data/wildcard.fa b/tools/cutadapt/test-data/cutadapt/data/wildcard.fa
@@ -0,0 +1,4 @@
+>1
+ANGTACGTTGCATGCA
+>2
+ACGTANGTTGCATGCA
diff --git a/tools/cutadapt/test-data/cutadapt/data/wildcardN.fa b/tools/cutadapt/test-data/cutadapt/data/wildcardN.fa
@@ -0,0 +1,6 @@
+>perfect
+TTTGGGGGGG
+>withN
+TTTGGNGGGG
+>1mism
+TTTGGGGCGG