Mercurial > repos > nick > sequence_content_trimmer

comparison trimmer.xml @ 1:464aee13e2df draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 8e52aac4afce4ab7c4d244e2b70f205f70c16749-dirty"
author nick
date Fri, 27 May 2022 23:29:45 +0000
parents 7f170cb06e2e
children
comparison
equal deleted inserted replaced
0:7f170cb06e2e 1:464aee13e2df
1 <tool id="sequence_content_trimmer" version="0.1" name="Sequence Content Trimmer"> 1 <?xml version="1.0"?>
2 <tool id="sequence_content_trimmer" version="0.2.3" name="Sequence Content Trimmer">
2 <description>trim reads based on certain bases</description> 3 <description>trim reads based on certain bases</description>
3 <command interpreter="python"> 4 <command detect_errors="exit_code"><![CDATA[
4 trimmer.py $input1 5 #if $paired.is_paired and (('fasta' in $input1.extension and 'fastq' in $input2.extension) or \
5 #if $paired.is_paired: 6 ('fastq' in $input1.extension and 'fasta' in $input2.extension))
6 $input2 $output1 $output2 7 echo 'Both input files must be either fastq or fasta (no mixing the two).' >&2
7 #if ('fasta' in $input1.extension and 'fastq' in $input2.extension) or ('fastq' in $input1.extension and 'fasta' in $input2.extension) 8 #else
8 --error 'Both input files must be either fastq or fasta (no mixing the two).' 9 python '$__tool_directory__/trimmer.py' '$input1'
10 #if $paired.is_paired:
11 '$input2' '$output1' '$output2'
12 #end if
13 #if $input1.extension in ('fastq', 'fastqsanger', 'fastqillumina', 'fastqsolexa')
14 -f fastq
15 #elif $input1.extension == 'fasta'
16 -f fasta
17 #else
18 -f '$input1.extension'
19 #end if
20 -b '$bases' -t '$thres' -w '$win_len' $invert
21 #if $min_len.has_min_len:
22 -m '$min_len.value'
23 #end if
24 #if not $paired.is_paired:
25 > '$output1'
9 #end if 26 #end if
10 #end if 27 #end if
11 #if $input1.extension == 'fastq' or $input1.extension == 'fastqsanger' or $input1.extension == 'fastqillumina' or $input1.extension == 'fastqsolexa' 28 ]]>
12 -f fastq
13 #elif $input1.extension == 'fasta'
14 -f fasta
15 #else
16 -f $input1.extension
17 #end if
18 -b $bases -t $thres -w $win_len $invert
19 #if $min_len.has_min_len:
20 -m $min_len.value
21 #end if
22 #if not $paired.is_paired:
23 &gt; $output1
24 #end if
25 </command> 29 </command>
26 <inputs> 30 <inputs>
27 <conditional name="paired"> 31 <conditional name="paired">
28 <param name="is_paired" type="select" label="Paired reads?"> 32 <param name="is_paired" type="select" label="Paired reads?">
29 <option value="" selected="True">Unpaired</option> 33 <option value="" selected="True">Unpaired</option>
47 <param name="value" type="integer" value="10" min="0" label="Minimum read length" help="Reads trimmed to less than this length will be omitted from the output. Pairs will be preserved: both must exceed this threshold to be kept."/> 51 <param name="value" type="integer" value="10" min="0" label="Minimum read length" help="Reads trimmed to less than this length will be omitted from the output. Pairs will be preserved: both must exceed this threshold to be kept."/>
48 </when> 52 </when>
49 </conditional> 53 </conditional>
50 </inputs> 54 </inputs>
51 <outputs> 55 <outputs>
52 <data name="output1" format_source="input1"/> 56 <data name="output1" format_source="input1" label="$tool.name on $on_string"/>
53 <data name="output2" format_source="input2"> 57 <data name="output2" format_source="input2" label="$tool.name on $on_string (mate 2)">
54 <filter>paired['is_paired']</filter> 58 <filter>paired['is_paired']</filter>
55 </data> 59 </data>
56 </outputs> 60 </outputs>
57 61
58 <help> 62 <help>
66 70
67 .. class:: infomark 71 .. class:: infomark
68 72
69 **How it works** 73 **How it works**
70 74
71 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, when it will trim once non-filter bases exceed the threshold). 75 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).
72 76
73 The trim point will be just before the first (leftmost) filter base in the final window (the one where the frequency exceeded the threshold). 77 The trim point will be just before the first (leftmost) filter base in the final window (the one where the frequency exceeded the threshold).
74 78
75 79
76 .. class:: infomark 80 .. class:: infomark