Mercurial > repos > bgruening > trim_galore

diff trim_galore.xml @ 13:b6c00b82f623 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit be11349529528f508eb05073396e80c3d1cbed4d
author bgruening
date Thu, 01 Jun 2017 08:59:04 -0400
parents 1bf4789584dc
children 949f01671246
line wrap: on
line diff
--- a/trim_galore.xml	Tue May 16 09:34:00 2017 -0400
+++ b/trim_galore.xml	Thu Jun 01 08:59:04 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="trim_galore" name="Trim Galore!" version="0.4.3.0" profile="17.01">
+<tool id="trim_galore" name="Trim Galore!" version="0.4.3.1" profile="17.01">
     <!-- Wrapper compatible with Trim Galore! version 0.4.3 -->
     <description>Quality and adapter trimmer of reads</description>
     <macros>
@@ -48,7 +48,7 @@
     <version_command>
         trim_galore --version
     </version_command>
-    <command detect_errors="exit_code"><![CDATA[
+    <command detect_errors="aggressive"><![CDATA[
         #set compressed = 'no'
         #if $singlePaired.sPaired == "single":
             #if $singlePaired.input_singles.is_of_type("fastq.gz"):
@@ -132,7 +132,6 @@
         #end if
 
         --output_dir ./
-        --suppress_warn
 
         #if $params.settingsType == "custom" and not $params.report:
             --no_report_file
@@ -385,8 +384,8 @@
             <param name="sPaired" value="paired" />
             <param name="settingsType" value="custom" />
             <param name="report" value="true" />
-            <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
-            <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
+            <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="30"/>
+            <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="30"/>
             <output name="report_file" file="paired_example_results2gz.txt" ftype="txt" lines_diff="24" />
         </test>
 
@@ -431,13 +430,13 @@
             <output name="report_file" file="paired_collection_example_results3gz.txt" ftype="txt" lines_diff="25" />
 
             <output_collection name="trimmed_reads_paired_collection" type="paired">
-                <element name="forward" file="paired_collection_example_pair1_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
-                <element name="reverse" file="paired_collection_example_pair2_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
+                <element name="forward" file="paired_collection_example_pair1_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="30"/>
+                <element name="reverse" file="paired_collection_example_pair2_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="30"/>
             </output_collection>
 
             <output_collection name="trimmed_reads_unpaired_collection" type="paired">
-                <element name="forward" file="paired_collection_example_unpair1_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
-                <element name="reverse" file="paired_collection_example_unpair2_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
+                <element name="forward" file="paired_collection_example_unpair1_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="30"/>
+                <element name="reverse" file="paired_collection_example_unpair2_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="30"/>
             </output_collection>
         </test>
     </tests>