diff generate_sequence_features.xml @ 6:517069eeb0d5 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6

--- a/generate_sequence_features.xml	Sun Aug 10 11:39:49 2025 +0000
+++ b/generate_sequence_features.xml	Tue Oct 28 08:20:21 2025 +0000
@@ -14,7 +14,7 @@
     @BAM_FILES@
 #else:
     #for $e in $input_type_select.mode.abundance:
-        #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
+        #set $identifier = re.sub('[^\s\w\-]', '_', str($e.element_identifier))
         ln -s '$e' '${identifier}.txt' &&
     #end for
 #end if
@@ -23,11 +23,12 @@
 SemiBin2
 #if $input_type_select.mode.select == 'single' or $input_type_select.mode.select == 'co'
     generate_sequence_features_single
+    --input-fasta 'contigs.$input_fasta.ext'
 #else
     generate_sequence_features_multi
     --separator '$separator'
+    --input-fasta 'contigs.fasta'
 #end if
-    --input-fasta 'contigs.fasta'
 #if $input_type_select.input_type == "bam"
     --input-bam *.bam
 #else:
@@ -106,13 +107,70 @@
                     <has_n_lines n="1" delta="1"/>
                 </assert_contents>
             </output>
+        </test><test expect_num_outputs="4">
+            <conditional name="input_type_select">
+                <param name="input_type" value="bam"/>
+                <conditional name="mode">
+                    <param name="select" value="co"/>
+                    <param name="input_fasta" ftype="fasta.bz2" value="input_single.fasta.bz2"/>
+                    <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/>
+                </conditional>
+            </conditional>
+            <conditional name="min_len">
+                <param name="method" value="automatic"/>
+            </conditional>
+            <param name="ml_threshold" value="4000"/>
+            <param name="extra_output" value="coverage"/>
+            <output name="single_data" ftype="csv">
+                <assert_contents>
+                    <has_n_lines n="41"/>
+                    <has_text text="g1k_0"/>
+                    <has_text text="g4k_9"/>
+                </assert_contents>
+            </output>
+            <output name="single_data_split" ftype="csv">
+                <assert_contents>
+                    <has_n_lines n="81"/>
+                    <has_text text="g1k_0_1"/>
+                    <has_text text="g3k_2_2"/>
+                    <has_text text="g4k_7_2"/>
+                </assert_contents>
+            </output>
+            <output_collection name="co_cov" count="5">
+                <element name="0" ftype="csv">
+                    <assert_contents>
+                        <has_n_lines n="41"/>
+                        <has_text text="g1k_0"/>
+                    </assert_contents>
+                </element>
+                <element name="4" ftype="csv">
+                    <assert_contents>
+                        <has_n_lines n="41"/>
+                        <has_text text="g1k_0"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="co_split_cov" count="5">
+                <element name="0" ftype="csv">
+                    <assert_contents>
+                        <has_n_lines n="81"/>
+                        <has_text text="g1k_0_1"/>
+                    </assert_contents>
+                </element>
+                <element name="4" ftype="csv">
+                    <assert_contents>
+                        <has_n_lines n="81"/>
+                        <has_text text="g1k_0_1"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
         </test>
         <test expect_num_outputs="4">
             <conditional name="input_type_select">
                 <param name="input_type" value="bam"/>
                 <conditional name="mode">
                     <param name="select" value="co"/>
-                    <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
+                    <param name="input_fasta" ftype="fasta.gz" value="input_single.fasta.gz"/>
                     <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/>
                 </conditional>
             </conditional>
@@ -324,7 +382,6 @@
                 </element>
             </output_collection>
         </test>
-
         <test expect_num_outputs="2">
             <conditional name="input_type_select">
                 <param name="input_type" value="bam"/>
@@ -334,7 +391,7 @@
                         <param name="select" value="multi"/>
                         <param name="input_fasta" ftype="fasta" value="S1.fasta,S2.fasta,S3.fasta,S4.fasta,S5.fasta,S6.fasta,S7.fasta,S8.fasta,S9.fasta,S10.fasta"/>
                     </conditional>
-                    <param name="input_bam" ftype="bam" value="input_multi_sorted1.bam,input_multi_sorted2.bam,input_multi_sorted3.bam,input_multi_sorted4.bam,input_multi_sorted5.bam,input_multi_sorted6.bam,input_multi_sorted7.bam,input_multi_sorted8.bam,input_multi_sorted9.bam,input_multi_sorted10.bam"/>
+                    <param name="input_bam" ftype="bam" value="input_multi_sorted1_naming.bam,input_multi_sorted2_naming.bam,input_multi_sorted3_naming.bam,input_multi_sorted4_naming.bam,input_multi_sorted5_naming.bam,input_multi_sorted6_naming.bam,input_multi_sorted7_naming.bam,input_multi_sorted8_naming.bam,input_multi_sorted9_naming.bam,input_multi_sorted10_naming.bam"/>
                 </conditional>
             </conditional>
             <conditional name="min_len">
@@ -342,7 +399,7 @@
             </conditional>
             <param name="ml_threshold" value="4000"/>
             <output_collection name="multi_data" count="10">
-                <element name="S1" ftype="csv">
+                <element name="S1_fasta" ftype="csv">
                     <assert_contents>
                         <has_n_lines n="21"/>
                         <has_text text="g1k_0"/>
@@ -350,7 +407,7 @@
                 </element>
             </output_collection>
             <output_collection name="multi_data_split" count="10">
-                <element name="S1" ftype="csv">
+                <element name="S1_fasta" ftype="csv">
                     <assert_contents>
                         <has_n_lines n="41"/>
                         <has_text text="g1k_0_1"/>