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diff flash.xml @ 6:01a4ebf1f237 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 7e92326c8481e440066c4aabb13d373dec570e2e
author iuc
date Wed, 06 Jul 2022 13:27:05 +0000
parents a27654fc4270
children
line wrap: on
line diff
--- a/flash.xml	Wed Apr 03 19:49:20 2019 -0400
+++ b/flash.xml	Wed Jul 06 13:27:05 2022 +0000
@@ -1,6 +1,8 @@
-<?xml version="1.0"?>
-<tool id="flash" name="FLASH" version="@VERSION@.4">
+<tool id="flash" name="FLASH" version="@VERSION@.4" profile="21.05">
     <description>adjust length of short reads</description>
+    <xrefs>
+        <xref type="bio.tools">flash</xref>
+    </xrefs>
     <macros>
         <token name="@VERSION@">1.2.11</token>
     </macros>
@@ -97,15 +99,15 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="5">
             <param name="select_layout" value="individual" />
             <param name="forward" value="flash_forward_in1.fastqsanger" ftype="fastqsanger" />
             <param name="reverse" value="flash_reverse_in1.fastqsanger" ftype="fastqsanger" />
             <param name="generate_histogram" value="false" />
             <param name="save_log" value="true" />
-            <output name="merged_paired_reads" file="flash_merged_out1.fastqsanger" ftype="fastqsanger" />
-            <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out1.fastqsanger" ftype="fastqsanger" />
-            <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out1.fastqsanger" ftype="fastqsanger" />
+            <output name="merged_paired_reads" file="flash_merged_out1.fastqsanger" ftype="fastqsanger" sort="true" />
+            <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out1.fastqsanger" ftype="fastqsanger" sort="true" />
+            <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out1.fastqsanger" ftype="fastqsanger" sort="true" />
             <output name="hist" file="flash_hist_out1.tabular" />
             <output name="log">
               <assert_contents>
@@ -113,16 +115,16 @@
               </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="10">
             <param name="select_layout" value="individual" />
             <param name="forward" value="flash_forward_in2.fastqsanger" ftype="fastqsanger" />
             <param name="reverse" value="flash_reverse_in2.fastqsanger" ftype="fastqsanger" />
             <param name="allow_outies" value="true" />
             <param name="generate_histogram" value="true" />
             <param name="save_log" value="true" />            
-            <output name="merged_paired_reads" file="flash_merged_out2.fastqsanger" ftype="fastqsanger" />
-            <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out2.fastqsanger" ftype="fastqsanger" />
-            <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out2.fastqsanger" ftype="fastqsanger" />
+            <output name="merged_paired_reads" file="flash_merged_out2.fastqsanger" ftype="fastqsanger" sort="true" />
+            <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out2.fastqsanger" ftype="fastqsanger" sort="true" />
+            <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out2.fastqsanger" ftype="fastqsanger" sort="true" />
             <output name="hist" file="flash_hist_out2.tabular" />
             <output name="histogram" file="flash_hist_out2.txt" />
             <output name="hist_in" file="flash_hist_in_out2.tabular" />
@@ -135,7 +137,7 @@
               </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="5">
             <param name="select_layout" value="collection" />
             <param name="generate_histogram" value="false" />
             <param name="reads">
@@ -144,12 +146,12 @@
                     <element name="reverse" value="flash_reverse_in3.fastqillumina" ftype="fastqillumina" />
                 </collection>
             </param>
-            <output name="merged_reads" file="flash_merged_out3.fastqillumina" ftype="fastqillumina" />
-            <output name="unmerged_reads_f" file="flash_unmerged_f_out3.fastqillumina" ftype="fastqillumina" />
-            <output name="unmerged_reads_r" file="flash_unmerged_r_out3.fastqillumina" ftype="fastqillumina" />
+            <output name="merged_reads" file="flash_merged_out3.fastqillumina" ftype="fastqillumina" sort="true" />
+            <output name="unmerged_reads_f" file="flash_unmerged_f_out3.fastqillumina" ftype="fastqillumina" sort="true" />
+            <output name="unmerged_reads_r" file="flash_unmerged_r_out3.fastqillumina" ftype="fastqillumina" sort="true" />
             <output name="hist" file="flash_hist_out3.tabular" />
         </test>
-        <test>
+        <test expect_num_outputs="5">
             <param name="select_layout" value="individual" />
             <param name="forward" value="flash_forward_in4.fastqsanger.gz" ftype="fastqsanger.gz" />
             <param name="reverse" value="flash_reverse_in4.fastqsanger.gz" ftype="fastqsanger.gz" />
@@ -164,7 +166,7 @@
               </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="5">
             <param name="select_layout" value="collection" />
             <param name="generate_histogram" value="false" />
             <param name="reads">