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changeset 6:a935cbdf1c0e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15
author iuc
date Thu, 23 Aug 2018 02:53:34 -0400
parents 3e2551a37201
children 6c2351178f8d
files fastp.xml
diffstat 1 files changed, 12 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/fastp.xml	Fri Aug 10 19:40:07 2018 -0400
+++ b/fastp.xml	Thu Aug 23 02:53:34 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="fastp" name="fastp" version="@WRAPPER_VERSION@.2">
+<tool id="fastp" name="fastp" version="@WRAPPER_VERSION@.3">
     <description>- fast all-in-one preprocessing for FASTQ files</description>
     <macros>
         <import>macros.xml</import>
@@ -154,7 +154,7 @@
 
 #if $read_mod_options.polyx_tail_trimming.polyx_trimming_select == '-x':
     $read_mod_options.polyx_tail_trimming.polyx_trimming_select
-    #if str($read_mod_options.polyg_tail_trimming.poly_g_min_len):
+    #if str($read_mod_options.polyx_tail_trimming.poly_x_min_len):
         --poly_x_min_len $read_mod_options.polyx_tail_trimming.poly_x_min_len
     #end if
 #end if
@@ -260,7 +260,7 @@
         <!-- Read Modification Options -->
          <section name="read_mod_options" title="Read Modification Options">
             <conditional name="polyg_tail_trimming">
-                <param name="trimming_select" type="select" label="PolyG tail trimming" help="Useful for NextSeq/NovaSeq data">
+                <param name="trimming_select" type="select" label="PolyG tail trimming" help="This feature is enabled for NextSeq/NovaSeq data by default. NextSeq/NovaSeq data is detected by the machine ID in the FASTQ records.">
                     <option value="" selected="true">Automatic trimming for Illumina NextSeq/NovaSeq data</option>
                     <option value="-g">Force polyG tail trimming</option>
                     <option value="-G">Disable polyG tail trimming</option>
@@ -444,6 +444,15 @@
             <param name="poly_g_min_len" value="10"/>
             <output name="out1" ftype="fastq.gz" decompress="True" file="out1.fq.gz"/>
         </test>
+        <!-- Ensure polyX trimming works -->
+        <test expect_num_outputs="2">
+            <param name="in1" ftype="fastq.gz" value="R1.fq.gz"/>
+            <param name="single_paired_selector" value="single"/>
+            <param name="trimming_select" value="-G"/>
+            <param name="polyx_trimming_select" value="-x"/>
+            <param name="poly_x_min_len" value="10"/>
+            <output name="out1" ftype="fastq.gz" decompress="True" file="out1.fq.gz"/>
+        </test>
     </tests>
     <help><![CDATA[
 .. class:: infomark