# HG changeset patch
# User nick
# Date 1527887269 14400
# Node ID 7ee4030173eaef4a86ea0ea78884e5d6b4e0aa08
# Parent  9d28b4509c02eda52fcccd2f3f6cea270d78e6d7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'230f018da2c0bc4eedc72e0f70eac0df1e85ebdb\n'-dirty

diff -r 9d28b4509c02 -r 7ee4030173ea trimmer.xml
--- a/trimmer.xml	Fri Jun 01 16:51:02 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,84 +0,0 @@
-<tool id="sequence_content_trimmer" version="0.1" name="Sequence Content Trimmer">
-  <description>trim reads based on certain bases</description>
-  <command interpreter="python">
-  trimmer.py $input1
-  #if $paired.is_paired:
-    $input2 $output1 $output2
-    #if ('fasta' in $input1.extension and 'fastq' in $input2.extension) or ('fastq' in $input1.extension and 'fasta' in $input2.extension)
-      --error 'Both input files must be either fastq or fasta (no mixing the two).'
-    #end if
-  #end if
-  #if $input1.extension == 'fastq' or $input1.extension == 'fastqsanger' or $input1.extension == 'fastqillumina' or $input1.extension == 'fastqsolexa'
-    -f fastq
-  #elif $input1.extension == 'fasta'
-    -f fasta
-  #else
-    -f $input1.extension
-  #end if
-  -b $bases -t $thres -w $win_len $invert
-  #if $min_len.has_min_len:
-    -m $min_len.value
-  #end if
-  #if not $paired.is_paired:
-    &gt; $output1
-  #end if
-  </command>
-  <inputs>
-    <conditional name="paired">
-      <param name="is_paired" type="select" label="Paired reads?">
-        <option value="" selected="True">Unpaired</option>
-        <option value="true">Paired</option>
-      </param>
-      <when value="true">
-        <param name="input1" type="data" format="fasta,fastq" label="Input reads (mate 1)"/>
-        <param name="input2" type="data" format="fasta,fastq" label="Input reads (mate 2)"/>
-      </when>
-      <when value="">
-        <param name="input1" type="data" format="fasta,fastq" label="Input reads"/>
-      </when>
-    </conditional>
-    <param name="bases" type="text" value="N" label="Bases to filter on"/>
-    <param name="thres" type="float" value="0.5" min="0" max="1" label="Frequency threshold" help="Trim when the frequency of filter bases (or non-filter bases, if inverting) exceeds this value."/>
-    <param name="win_len" type="integer" value="10" min="1" label="Size of the window"/>
-    <param name="invert" type="boolean" truevalue="--invert" falsevalue="" checked="False" label="Invert filter bases" help="Trim when the frequency of bases NOT in the &quot;filter bases&quot; list exceeds the threshold."/>
-    <conditional name="min_len">
-      <param name="has_min_len" type="boolean" truevalue="true" falsevalue="" checked="False" label="Set a minimum read length"/>
-      <when value="true"> 
-        <param name="value" type="integer" value="10" min="0" label="Minimum read length" help="Reads trimmed to less than this length will be omitted from the output. Pairs will be preserved: both must exceed this threshold to be kept."/>
-      </when>
-    </conditional>
-  </inputs>
-  <outputs>
-    <data name="output1" format_source="input1"/>
-    <data name="output2" format_source="input2">
-      <filter>paired['is_paired']</filter>
-    </data>
-  </outputs>
-
-  <help>
-
-.. class:: infomark
-
-**What it does**
-
-This tool trims the 3' ends of reads based on the presence of the given bases. For instance, trim when N's are encountered or when the GC content exceeds a certain frequency.
-
-
-.. class:: infomark
-
-**How it works**
-
-This will slide along the read with a window, and trim once the frequency of filter bases exceeds the frequency threshold (unless "Invert filter bases" is enabled, in which case it will trim once non-filter bases exceed the threshold).
-
-The trim point will be just before the first (leftmost) filter base in the final window (the one where the frequency exceeded the threshold).
-
-
-.. class:: infomark
-
-**Input**
-
-The inputs can be in the following formats: fasta, fastq, fastqsanger, fastqillumina, and fastqsolexa. Both must be either a fasta or fastq type (no mixing fastq and fasta).
-
-  </help>
-
-</tool>