diff quast.xml @ 12:875d0f36d66f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"

--- a/quast.xml	Sat Nov 27 09:45:20 2021 +0000
+++ b/quast.xml	Sun Feb 06 21:02:38 2022 +0000
@@ -190,29 +190,29 @@
             <when value="disabled"/>
 
             <when value="single">
-                <param name="input_1" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file" />
+                <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
             </when>
 
             <when value="paired">
-                <param name="input_1" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file #1" />
-                <param name="input_2" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file #2" />
+                <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" />
+                <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" />
             </when>
 
             <when value="paired_interlaced">
-                <param name="input_1" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file" />
+                <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
             </when>
 
             <when value="mate_paired">
-                <param name="input_1" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file #1" />
-                <param name="input_2" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file #2" />
+                <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" />
+                <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" />
             </when>
 
             <when value="pacbio">
-                <param name="input_1" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file" />
+                <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
             </when>
 
             <when value="nanopore">
-                <param name="input_1" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file" />
+                <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
             </when>
         </conditional>
 
@@ -413,7 +413,7 @@
             </section>
             <param name="output_files" value="html"/>
             <output name="report_html" file="test1_report.html" ftype="html" compare="sim_size"/>
-            <output name="circos_output" file="test1_circos.png" ftype="png"/>
+            <output name="circos_output" file="test1_circos.png" ftype="png" compare="sim_size"/>
         </test>
         <!-- Test 02: all outputs -->
         <test expect_num_outputs="8">
@@ -590,6 +590,26 @@
             <param name="output_files" value="tabular"/>
             <output name="quast_tabular" file="test6.tab" ftype="tabular"/>
         </test>
+        <!-- Test 7: FASTA.gz read files -->
+        <test expect_num_outputs="1">
+            <conditional name="in">
+                <param name="custom" value="true"/>
+                <repeat name="inputs">
+                    <param name="input" value="contigs1.fna"/>
+                    <param name="labels" value="contig1"/>
+                </repeat>
+                <repeat name="inputs">
+                    <param name="input" value="contigs2.fna"/>
+                    <param name="labels" value="contig2"/>
+                </repeat>
+            </conditional>
+            <conditional name="reads">
+                <param name="reads_option" value="single"/>
+                <param name="input_1" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>
+            </conditional>
+            <param name="output_files" value="tabular"/>
+            <output name="quast_tabular" file="test7.tab" ftype="tabular"/>
+        </test>
     </tests>
     <help>
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