diff stacks_kmerfilter.xml @ 3:1544278c272e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"

--- a/stacks_kmerfilter.xml	Thu Jul 16 07:28:45 2020 -0400
+++ b/stacks_kmerfilter.xml	Tue Apr 27 09:32:17 2021 +0000
@@ -107,7 +107,7 @@
     </inputs>
     <outputs>
         <expand macro="out_log"/>
-        <expand macro="fastq_output_filter">
+        <expand macro="fastq_output_filter" format="fastq">
             <filter>not options_kmer_char['k_dist'] and not options_kmer_char['write_k_freq']</filter>
         </expand>
         <data format="tabular" name="kfreq" label="${tool.name} on ${on_string} kmer frequencies">
@@ -136,7 +136,7 @@
             </assert_command>
             <param name="add_log" value="yes"/>
             <output name="output_log"><assert_contents><has_text text="5 retained reads."/></assert_contents></output>
-            <output name="clean" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="kmerfilter/Removed1_0001.1.1.fq.single.gz"/>
+            <output name="clean" compare="diff" ftype="fastq" file="kmerfilter/Removed1_0001.1.1.fq.single"/>
         </test>
         <test expect_num_outputs="7">
             <conditional name="input_type">
@@ -156,12 +156,12 @@
             <param name="add_log" value="yes"/>
             <output name="output_log"><assert_contents><has_text text="8 retained reads."/></assert_contents></output>
             <output_collection name="clean_pair" type="paired">
-                <element name="forward" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="kmerfilter/Removed1_0001.1.1.fq.gz"/>
-                <element name="reverse" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="kmerfilter/Removed2_0001.2.2.fq.gz"/>
+                <element name="forward" compare="diff" ftype="fastq" file="kmerfilter/Removed1_0001.1.1.fq"/>
+                <element name="reverse" compare="diff" ftype="fastq" file="kmerfilter/Removed2_0001.2.2.fq"/>
             </output_collection>
             <output_collection name="discarded_pair" type="paired">
-                <element name="forward" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="kmerfilter/Discarded1_0001.1.1.fq.gz"/>
-                <element name="reverse" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="kmerfilter/Discarded2_0001.2.2.fq.gz"/>
+                <element name="forward" compare="diff" ftype="fastq" file="kmerfilter/Discarded1_0001.1.1.fq"/>
+                <element name="reverse" compare="diff" ftype="fastq" file="kmerfilter/Discarded2_0001.2.2.fq"/>
             </output_collection>
         </test>
         <!-- kfreq output -->