Mercurial > repos > nick > sequence_content_trimmer
comparison trimmer.xml @ 3:d8b86dc67f84 draft default tip
"planemo upload commit 8e52aac4afce4ab7c4d244e2b70f205f70c16749-dirty"
| author | nick |
|---|---|
| date | Fri, 27 May 2022 23:27:43 +0000 |
| parents | a8fd651dcbd9 |
| children |
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| 2:a8fd651dcbd9 | 3:d8b86dc67f84 |
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| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool id="sequence_content_trimmer" version="0.2.2" name="Sequence Content Trimmer"> | 2 <tool id="sequence_content_trimmer" version="0.2.3" name="Sequence Content Trimmer"> |
| 3 <description>trim reads based on certain bases</description> | 3 <description>trim reads based on certain bases</description> |
| 4 <command detect_errors="exit_code"><![CDATA[ | 4 <command detect_errors="exit_code"><![CDATA[ |
| 5 #if $paired.is_paired and (('fasta' in $input1.extension and 'fastq' in $input2.extension) or \ | 5 #if $paired.is_paired and (('fasta' in $input1.extension and 'fastq' in $input2.extension) or \ |
| 6 ('fastq' in $input1.extension and 'fasta' in $input2.extension)) | 6 ('fastq' in $input1.extension and 'fasta' in $input2.extension)) |
| 7 echo 'Both input files must be either fastq or fasta (no mixing the two).' >&2 | 7 echo 'Both input files must be either fastq or fasta (no mixing the two).' >&2 |
| 8 #else | 8 #else |
| 9 trimmer.py $input1 | 9 python '$__tool_directory__/trimmer.py' '$input1' |
| 10 #if $paired.is_paired: | 10 #if $paired.is_paired: |
| 11 $input2 $output1 $output2 | 11 '$input2' '$output1' '$output2' |
| 12 #end if | 12 #end if |
| 13 #if $input1.extension in ('fastq', 'fastqsanger', 'fastqillumina', 'fastqsolexa') | 13 #if $input1.extension in ('fastq', 'fastqsanger', 'fastqillumina', 'fastqsolexa') |
| 14 -f fastq | 14 -f fastq |
| 15 #elif $input1.extension == 'fasta' | 15 #elif $input1.extension == 'fasta' |
| 16 -f fasta | 16 -f fasta |
| 17 #else | 17 #else |
| 18 -f $input1.extension | 18 -f '$input1.extension' |
| 19 #end if | 19 #end if |
| 20 -b '$bases' -t $thres -w $win_len $invert | 20 -b '$bases' -t '$thres' -w '$win_len' $invert |
| 21 #if $min_len.has_min_len: | 21 #if $min_len.has_min_len: |
| 22 -m $min_len.value | 22 -m '$min_len.value' |
| 23 #end if | 23 #end if |
| 24 #if not $paired.is_paired: | 24 #if not $paired.is_paired: |
| 25 > $output1 | 25 > '$output1' |
| 26 #end if | 26 #end if |
| 27 #end if | 27 #end if |
| 28 ]]> | 28 ]]> |
| 29 </command> | 29 </command> |
| 30 <inputs> | 30 <inputs> |