Mercurial > repos > iuc > spades_metaviralspades

diff metaviralspades.xml @ 11:6766a94ef559 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
author iuc
date Wed, 12 Mar 2025 21:47:35 +0000
parents 5b26685e5d3b
children
line wrap: on
line diff
--- a/metaviralspades.xml	Mon Mar 03 11:07:29 2025 +0000
+++ b/metaviralspades.xml	Wed Mar 12 21:47:35 2025 +0000
@@ -43,11 +43,10 @@
     @PIPELINE_OPTIONS@
     ## postprocessing
     @STATS@
-    @CORRECTED@
     ]]></command>
     <inputs>
-        <expand macro="input_files_paired" format="fastq, fastq.gz,fastqsanger.gz" label="FASTQ file(s)"/>
-        <expand macro="input_additional_files_paired" format="fastq,fastq.gz,fastqsanger.gz" label="FASTQ file(s)"/>
+        <expand macro="input_files_paired" format="@FASTQ_INTYPES@" label="FASTQ file(s)"/>
+        <expand macro="input_additional_files_paired" format="@FASTQ_INTYPES@" label="FASTQ file(s)"/>
         <section name="arf" title="Additional read files">
             <expand macro="nanopore_pacbio"/>
             <expand macro="sanger"/>
@@ -88,9 +87,17 @@
         <!-- #1 single, separate, fastq.gz, default parameters -->
          <test expect_num_outputs="2">
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired"/>
-                <param name="input1" value="pl1.fq.gz"/>
-                <param name="input2" value="pl2.fq.gz"/>
+                <param name="sPaired" value="paired_collection"/>
+                <param name="input">
+                    <collection type="list:paired">
+                        <element name="pl">
+                            <collection type="paired">
+                                <element name="forward" value="pl1.fq.gz" ftype="fastqsanger.gz"/>
+                                <element name="reverse" value="pl2.fq.gz" ftype="fastqsanger.gz"/>
+                            </collection>
+                        </element>
+                    </collection>
+                </param>
             </conditional>
             <output name="out_cn">
                 <assert_contents>
@@ -108,9 +115,17 @@
         <!-- #2 single, separate, fastq, custom parameters -->
         <test expect_num_outputs="6">
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired"/>
-                <param name="input1" value="pl1.fq.gz"/>
-                <param name="input2" value="pl2.fq.gz"/>
+                <param name="sPaired" value="paired_collection"/>
+                <param name="input">
+                    <collection type="list:paired">
+                        <element name="pl">
+                            <collection type="paired">
+                                <element name="forward" value="pl1.fq.gz" ftype="fastqsanger.gz"/>
+                                <element name="reverse" value="pl2.fq.gz" ftype="fastqsanger.gz"/>
+                            </collection>
+                        </element>
+                    </collection>
+                </param>
             </conditional>
             <conditional name="kmer_cond">
                 <param name="kmer_sel" value="manual"/>
@@ -132,17 +147,17 @@
                 </assert_contents>
             </output>
             <output_collection name="out_cr" type="list" count="3">
-                <element name="pl1.fq.gz.fastq.00.0_0">
+                <element name="pl1.fastq00.0_0">
                     <assert_contents>
                         <has_size value="71752" delta="1000"/>
                     </assert_contents>
                 </element>
-                <element name="pl2.fq.gz.fastq.00.0_0">
+                <element name="pl2.fastq00.0_0">
                     <assert_contents>
                         <has_size value="71752" delta="1000"/>
                     </assert_contents>
                 </element>
-                <element name="pl_unpaired.00.0_0">
+                <element name="pl_unpaired00.0_0">
                     <assert_contents>
                         <has_size value="423" delta="100"/>
                     </assert_contents>
@@ -163,46 +178,62 @@
             </output>
             <output name="out_l">
                 <assert_contents>
-                    <has_text_matching expression="Thank you for using SPAdes!"/>
+                    <has_text_matching expression="Thank you for using metaviralSPAdes!"/>
                 </assert_contents>
             </output>
         </test>
         <!-- #3 -->
         <test expect_num_outputs="1">
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired"/>
-                <param name="input1" value="pl1.fq.gz"/>
-                <param name="input2" value="pl2.fq.gz"/>
+                <param name="sPaired" value="paired_collection"/>
+                <param name="input">
+                    <collection type="list:paired">
+                        <element name="pl">
+                            <collection type="paired">
+                                <element name="forward" value="pl1.fq.gz" ftype="fastqsanger.gz"/>
+                                <element name="reverse" value="pl2.fq.gz" ftype="fastqsanger.gz"/>
+                            </collection>
+                        </element>
+                    </collection>
+                </param>
             </conditional>
             <param name="operation_mode" value="--only-assembler"/>
             <param name="optional_output" value="l"/>
             <output name="out_l">
                 <assert_contents>
-                    <has_text_matching expression="Thank you for using SPAdes!"/>
+                    <has_text_matching expression="Thank you for using metaviralSPAdes!"/>
                 </assert_contents>
             </output>
         </test>
         <!-- #4, only corrected reads are created as an output -->
         <test expect_num_outputs="2">
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired"/>
-                <param name="input1" value="pl1.fq.gz"/>
-                <param name="input2" value="pl2.fq.gz"/>
+                <param name="sPaired" value="paired_collection"/>
+                <param name="input">
+                    <collection type="list:paired">
+                        <element name="pl">
+                            <collection type="paired">
+                                <element name="forward" value="pl1.fq.gz" ftype="fastqsanger.gz"/>
+                                <element name="reverse" value="pl2.fq.gz" ftype="fastqsanger.gz"/>
+                            </collection>
+                        </element>
+                    </collection>
+                </param>
             </conditional>
             <param name="operation_mode" value="--only-error-correction"/>
             <param name="optional_output" value="cr,l"/>
             <output_collection name="out_cr" type="list" count="3">
-                <element name="pl1.fq.gz.fastq.00.0_0">
+                <element name="pl1.fastq00.0_0">
                     <assert_contents>
                         <has_size value="71752" delta="1000"/>
                     </assert_contents>
                 </element>
-                <element name="pl2.fq.gz.fastq.00.0_0">
+                <element name="pl2.fastq00.0_0">
                     <assert_contents>
                         <has_size value="71752" delta="1000"/>
                     </assert_contents>
                 </element>
-                <element name="pl_unpaired.00.0_0">
+                <element name="pl_unpaired00.0_0">
                     <assert_contents>
                         <has_size value="423" delta="100"/>
                     </assert_contents>
@@ -210,7 +241,7 @@
             </output_collection>
             <output name="out_l">
                 <assert_contents>
-                    <has_text_matching expression="Thank you for using SPAdes!"/>
+                    <has_text_matching expression="Thank you for using metaviralSPAdes!"/>
                 </assert_contents>
             </output>
         </test>