diff rnaspades.xml @ 16:001aa495b39a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4

--- a/rnaspades.xml	Mon Mar 03 11:07:13 2025 +0000
+++ b/rnaspades.xml	Wed Mar 12 21:47:16 2025 +0000
@@ -42,11 +42,10 @@
         --ss '$ss'
     #end if
     ## postprocessing
-    @CORRECTED@
     ]]></command>
     <inputs>
-        <expand macro="input_files_all" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTQ RNA-seq file(s)"/>
-        <expand macro="input_additional_files_all" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTQ RNA-seq file(s)"/>
+        <expand macro="input_files_all" format="@INTYPES@" label="FASTQ RNA-seq file(s)"/>
+        <expand macro="input_additional_files_all" format="@INTYPES@" label="FASTQ RNA-seq file(s)"/>
         <section name="arf" title="Additional read files">
             <expand macro="flrna"/>
             <expand macro="nanopore_pacbio"/>
@@ -113,9 +112,17 @@
         <!-- #2 single, separate, fastq, all outputs custom parameters-->
         <test expect_num_outputs="5">
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired"/>
-                <param name="input1" value="ecoli_1K_1.fastq.gz"/>
-                <param name="input2" value="ecoli_1K_2.fastq.gz"/>
+                <param name="sPaired" value="paired_collection"/>
+                <param name="input">
+                    <collection type="list:paired">
+                        <element name="ecoli_1K">
+                            <collection type="paired">
+                                <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
+                                <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
+                            </collection>
+                        </element>
+                    </collection>
+                </param>
             </conditional>
             <param name="phred_offset" value="33"/>
             <param name="ss" value="fr"/>
@@ -142,16 +149,24 @@
             </output>
             <output name="out_l">
                 <assert_contents>
-                    <has_text_matching expression="Thank you for using SPAdes!"/>
+                    <has_text_matching expression="Thank you for using rnaSPAdes!"/>
                 </assert_contents>
             </output>
         </test>
         <!-- #3 single, separate, fasta, default parameters -->
         <test expect_num_outputs="1">
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired"/>
-                <param name="input1" value="ecoli_1K_1.fasta.gz"/>
-                <param name="input2" value="ecoli_1K_2.fasta.gz"/>
+                <param name="sPaired" value="paired_collection"/>
+                <param name="input">
+                    <collection type="list:paired">
+                        <element name="ecoli_1K">
+                            <collection type="paired">
+                                <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
+                                <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
+                            </collection>
+                        </element>
+                    </collection>
+                </param>
             </conditional>
             <output name="out_tr">
                 <assert_contents>
@@ -185,9 +200,17 @@
         <!-- #3 Hibryd assembly -->
         <test expect_num_outputs="1">
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired"/>
-                <param name="input1" value="ecoli_1K_1.fasta.gz"/>
-                <param name="input2" value="ecoli_1K_2.fasta.gz"/>
+                <param name="sPaired" value="paired_collection"/>
+                <param name="input">
+                    <collection type="list:paired">
+                        <element name="ecoli_1K">
+                            <collection type="paired">
+                                <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
+                                <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
+                            </collection>
+                        </element>
+                    </collection>
+                </param>
             </conditional>
             <section name="arf">
                 <param name="nanopore" value="ecoli_1K.fastq.gz"/>