Mercurial > repos > lparsons > cutadapt

diff cutadapt.xml @ 28:c053d4cad713 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 9ec830a98da45d5fb2f92a817c7cd0376504be90"
author iuc
date Sat, 27 Nov 2021 10:09:14 +0000
parents de6cebe3c043
children 48f587c13075
line wrap: on
line diff
--- a/cutadapt.xml	Mon Nov 01 12:14:05 2021 +0000
+++ b/cutadapt.xml	Sat Nov 27 10:09:14 2021 +0000
@@ -134,7 +134,7 @@
 #if str($filter_options.max_expected_errors):
     --max-expected-errors=$filter_options.max_expected_errors
 #end if
-
+$filter_options.discard_cassava
 
 #if str($read_mod_options.quality_cutoff) != '0':
    --quality-cutoff=$read_mod_options.quality_cutoff
@@ -143,6 +143,9 @@
     --nextseq-trim=$read_mod_options.nextseq_trim
 #end if
 $read_mod_options.trim_n
+#if $read_mod_options.strip_suffix != ''
+    --strip-suffix $read_mod_options.strip_suffix
+#end if
 #if str($read_mod_options.shorten_options.shorten_values) == 'True':
     #if str($read_mod_options.shorten_options.shorten_end) == '3prime'
         --length=$read_mod_options.shorten_options.length
@@ -505,11 +508,9 @@
                     </conditional>
                 </repeat>
             </section>
-            <param name="output_filtering" value="filter"/>
             <section name="filter_options">
                 <param name="discard_trimmed" value="True"/>
             </section>
-            <param name="read_modification" value="none"/>
             <output name="out1" file="cutadapt_discard.out" ftype="fastq"/>
             <assert_command>
                 <has_text text="--discard-trimmed"/>
@@ -526,8 +527,6 @@
                     </conditional>
                 </repeat>
             </section>
-            <param name="output_filtering" value="default"/>
-            <param name="read_modification" value="none"/>
             <param name="output_selector" value="rest_file,json_stats"/>
             <output name="out1" file="cutadapt_rest.out" ftype="fasta"/>
             <output name="json_stats" file="cutadapt_rest.json" ftype="json"/>
@@ -545,7 +544,6 @@
                     </conditional>
                 </repeat>
             </section>
-            <param name="read_modification" value="modify"/>
             <param name="nextseq_trim" value="20" />
             <output name="out1" decompress="True" file="cutadapt_nextseq_out.fq.gz" ftype="fastq.gz"/>
         </test>