Mercurial > repos > iuc > medaka_consensus_pipeline

diff medaka_consensus.xml @ 3:35666d44fe7a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
author iuc
date Tue, 01 Sep 2020 03:08:04 -0400
parents 6a87478ed985
children a1b70f038b4a
line wrap: on
line diff
--- a/medaka_consensus.xml	Thu Jun 18 05:07:32 2020 -0400
+++ b/medaka_consensus.xml	Tue Sep 01 03:08:04 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="medaka_consensus_pipeline" name="medaka: Consensus pipeline" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="medaka_consensus_pipeline" name="medaka: Consensus pipeline" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
     <description>Assembly polishing via neural networks</description>
     <macros>
         <import>macros.xml</import>
@@ -19,7 +19,7 @@
 -i '$i'
 -d '$d'
 
-|& tee '$out_log'
+2>&1 | tee '$out_log'
     ]]></command>
     <inputs>
         <param argument="-i" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select basecalls"/>
@@ -76,12 +76,14 @@
             </output>
             <output name="out_probs">
                 <assert_contents>
-                    <has_size value="192187" delta="100"/>
+                    <!-- <has_size value="192187" delta="100"/> -->
+                    <has_size value="165271" delta="100"/>
                 </assert_contents>
             </output>
             <output name="out_calls">
                 <assert_contents>
-                    <has_size value="533242" delta="100"/>
+                    <!-- <has_size value="533242" delta="100"/> -->
+                    <has_size value="343197" delta="100"/>
                 </assert_contents>
             </output>
         </test>
@@ -96,24 +98,29 @@
                 <assert_contents>
                     <has_n_lines n="65"/>
                     <has_line line=">4 length=3792 depth=114.52x circular=true"/>
-                    <has_line line="CATCTCTTT"/>
+                    <has_line line="ATCTCTTT"/>
                 </assert_contents>
             </output>
             <output name="out_probs">
                 <assert_contents>
-                    <has_size value="192710" delta="100"/>
+                    <has_size value="166251" delta="100"/>
+                    <!-- <has_size value="192710" delta="100"/> -->
                 </assert_contents>
             </output>
             <output name="out_calls">
                 <assert_contents>
-                    <has_size value="533163" delta="100"/>
+                    <has_size value="343197" delta="100"/>
+                    <!-- <has_size value="533163" delta="100"/> -->
                 </assert_contents>
             </output>
             <output name="out_draft">
                 <assert_contents>
-                    <has_n_lines n="6"/>
-                    <has_line line="chain 3789 4 3792 + 0 3792 4 3789 + 0 3789 1"/>
-                    <has_line line="1204"/>
+                    <has_line line="chain 3788 4 3792 + 0 3792 4 3788 + 0 3788 1"/>
+                    <has_line line="1409 1 0"/>
+                    <has_line line="440 1 0"/>
+                    <has_line line="736 1 0"/>
+                    <has_line line="853 1 0"/>
+                    <has_line line="350"/>
                 </assert_contents>
             </output>
             <output name="out_polished">