diff trimmer.xml @ 1:7ef568cbf13b draft

"planemo upload commit 9a5d91c35d21411a0733cd233ca588ff358aabd8-dirty"

--- a/trimmer.xml	Tue Dec 01 21:11:51 2015 -0500
+++ b/trimmer.xml	Fri May 27 22:44:01 2022 +0000
@@ -1,27 +1,31 @@
-<tool id="sequence_content_trimmer" version="0.1" name="Sequence Content Trimmer">
+<?xml version="1.0"?>
+<tool id="sequence_content_trimmer" version="0.2.1" 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).'
+  <command detect_errors="exit_code"><![CDATA[
+  #if $paired.is_paired and (('fasta' in $input1.extension and 'fastq' in $input2.extension) or \
+      ('fastq' in $input1.extension and 'fasta' in $input2.extension))
+    echo 'Both input files must be either fastq or fasta (no mixing the two).' >&2
+  #else
+    trimmer.py $input1
+    #if $paired.is_paired:
+      $input2 $output1 $output2
+    #end if
+    #if $input1.extension in ('fastq', 'fastqsanger', 'fastqillumina', '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:
+      > $output1
     #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; $output1
-  #end if
+  ]]>
   </command>
   <inputs>
     <conditional name="paired">
@@ -38,7 +42,7 @@
       </when>
     </conditional>
     <param name="bases" type="text" value="N" label="Bases to filter on"/>
-    <param name="thres" type="float" value="0.5" min="0" max="1" label="Frequency threshold" help="trim when the frequency of filter bases (or non-filter bases, if inverting) exceeds this value."/>
+    <param name="thres" type="float" value="0.5" min="0" max="1" label="Frequency threshold" help="Trim when the frequency of filter bases (or non-filter bases, if inverting) exceeds this value."/>
     <param name="win_len" type="integer" value="10" min="1" label="Size of the window"/>
     <param name="invert" type="boolean" truevalue="--invert" falsevalue="" checked="False" label="Invert filter bases" help="Trim when the frequency of bases NOT in the &quot;filter bases&quot; list exceeds the threshold."/>
     <conditional name="min_len">
@@ -49,8 +53,8 @@
     </conditional>
   </inputs>
   <outputs>
-    <data name="output1" format_source="input1"/>
-    <data name="output2" format_source="input2">
+    <data name="output1" format_source="input1" label="$tool.name on $on_string"/>
+    <data name="output2" format_source="input2" label="$tool.name on $on_string (mate 2)">
       <filter>paired['is_paired']</filter>
     </data>
   </outputs>
@@ -66,6 +70,15 @@
 
 .. 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).