Mercurial > repos > iuc > stacks2_clonefilter

diff stacks_clonefilter.xml @ 3:289b7d6b69a4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
author iuc
date Tue, 27 Apr 2021 09:27:26 +0000
parents 2f1d464ebfd2
children 42201b90e3f4
line wrap: on
line diff
--- a/stacks_clonefilter.xml	Thu Jul 16 07:30:45 2020 -0400
+++ b/stacks_clonefilter.xml	Tue Apr 27 09:27:26 2021 +0000
@@ -65,7 +65,7 @@
     </inputs>
     <outputs>
         <expand macro="out_log"/>
-        <expand macro="fastq_output_filter"/>
+        <expand macro="fastq_output_filter" format="fastqsanger.gz"/>
     </outputs>
     <tests>
         <!-- single end, defaults-->
@@ -76,8 +76,12 @@
             </conditional>
             <param name="oligo_len_1" value="6"/>
             <param name="add_log" value="yes"/>
+            <assert_command>
+                <has_text text="--oligo_len_1 6"/>
+                <not_has_text text="-D"/>
+            </assert_command>
             <output name="output_log" ftype="txt" file="clonefilter/clonefilter.log" lines_diff="8"/>
-            <output name="clean" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/>
+            <output name="clean" compare="diff"  ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/>
         </test>
         <!-- single end, alt BCencoding, capture-->
         <test expect_num_outputs="3">
@@ -86,14 +90,15 @@
                 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz"/>
                 <param name="barcode_encoding" value="--index_null"/>
             </conditional>
-            <param name="capture" value="-D"/>
+            <param name="capture" value="true"/>
             <param name="oligo_len_1" value="6"/>
             <assert_command>
+                <has_text text="--oligo_len_1 6"/>
                 <has_text text="-D"/>
             </assert_command>
             <output name="output_log" ftype="txt"><assert_contents><has_text text="5 pairs of reads input."/></assert_contents></output>
-            <output name="clean"     compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.single-alt.gz"/>
-            <output name="discarded" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Discarded1_0001.1.1.fq.single.gz"/>
+            <output name="clean" compare="diff" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.single-alt.gz"/>
+            <output name="discarded" compare="diff" ftype="fastqsanger.gz" file="clonefilter/Discarded1_0001.1.1.fq.single.gz"/>
         </test>
         <!-- paired end, defaults-->
         <test expect_num_outputs="4">
@@ -107,11 +112,13 @@
                 </param>
             </conditional>
             <param name="oligo_len_1" value="6"/>
+            <assert_command>
+                <has_text text="--oligo_len_1 6"/>
+                <not_has_text text="--oligo_len_2"/>
+                <not_has_text text="-D"/>
+            </assert_command>
             <output name="output_log" ftype="txt"><assert_contents><has_text text="4 pairs of reads input."/></assert_contents></output>
-            <output_collection name="clean_pair" type="paired">
-                <element name="forward" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
-                <element name="reverse" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
-            </output_collection>
+            <output_collection name="clean_pair" type="paired" count="2"/>
         </test>
         <!-- paired end, non defaults -->
         <test expect_num_outputs="7">
@@ -125,20 +132,18 @@
                 </param>
             </conditional>
             <param name="oligo_len_1" value="6"/>
-            <param name="capture" value="-D"/>
-            <param name="retain_oligo" value="--retain_oligo"/>
+            <param name="oligo_len_2" value="6"/>
+            <param name="capture" value="true"/>
+            <param name="retain_oligo" value="true"/>
             <assert_command>
+                <has_text text="--oligo_len_1 6"/>
+                <has_text text="--oligo_len_2 6"/>
+                <has_text text="-D"/>
                 <has_text text="--retain_oligo"/>
             </assert_command>
             <output name="output_log" ftype="txt"><assert_contents><has_text text="4 pairs of reads input."/></assert_contents></output>
-            <output_collection name="clean_pair" type="paired">
-                <element name="forward" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
-                <element name="reverse" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
-            </output_collection>
-            <output_collection name="discarded_pair" type="paired">
-                <element name="forward" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
-                <element name="reverse" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
-            </output_collection>
+            <output_collection name="clean_pair" type="paired" count="2"/>
+            <output_collection name="discarded_pair" type="paired" count="2"/>
         </test>
     </tests>
     <help>