Mercurial > repos > artbio > yac_clipper

comparison yac.xml @ 4:f7947c5a18b8 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 48768de9d682fb80c4981cd52ef724fdf8f6961e
author artbio
date Mon, 08 Apr 2019 07:26:41 -0400
parents 94d67b195acd
children 6bfb7e333280
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3:94d67b195acd 4:f7947c5a18b8
1 <tool id="yac" name="Clip adapter" version="2.2.0"> 1 <tool id="yac" name="Clip adapter" version="2.3.0">
2 <description /> 2 <description />
3 <command detect_errors="exit_code"><![CDATA[ 3 <command detect_errors="exit_code"><![CDATA[
4 python $__tool_directory__/yac.py 4 python $__tool_directory__/yac.py
5 --input $input 5 --input $input
6 --output 'clip.tmp' 6 --output 'clip.tmp'
17 #if ($out_format == 'fastagz') or ($out_format == 'fastqgz'): 17 #if ($out_format == 'fastagz') or ($out_format == 'fastqgz'):
18 gzip -c 'clip.tmp' > $output 18 gzip -c 'clip.tmp' > $output
19 #else 19 #else
20 mv clip.tmp $output 20 mv clip.tmp $output
21 #end if 21 #end if
22 22
23 ]]></command> 23 ]]></command>
24 <inputs> 24 <inputs>
25 <param format="fasta,fastq" label="Source file" name="input" type="data" /> 25 <param format="fasta,fastq" label="Source file" name="input" type="data" />
26 <param label="min size" name="min" size="4" type="integer" value="15" /> 26 <param label="min size" name="min" size="4" type="integer" value="15" />
27 <param label="max size" name="max" size="4" type="integer" value="36" /> 27 <param label="max size" name="max" size="4" type="integer" value="36" />
123 <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" /> 123 <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" />
124 <param name="Nmode" value="accept" /> 124 <param name="Nmode" value="accept" />
125 <param name="out_format" value="fastagz" /> 125 <param name="out_format" value="fastagz" />
126 <output file="out.fasta.gz" name="output" decompress="True" /> 126 <output file="out.fasta.gz" name="output" decompress="True" />
127 </test> 127 </test>
128 <test>
129 <param ftype="fastqsanger.gz" name="input" value="yac_with_empty_reads.fastqsanger.gz" />
130 <param name="min" value="18" />
131 <param name="max" value="30" />
132 <param name="clip_source_list" value="prebuilt" />
133 <param name="clip_sequence" value="TGGAATTCTCGGGTGCCAAG" />
134 <param name="Nmode" value="accept" />
135 <param name="out_format" value="fastagz" />
136 <output file="out_with_empty_reads.fasta.gz" name="output" decompress="True" />
137 </test>
128 </tests> 138 </tests>
129 <help> 139 <help>
130 140
131 **What it does** 141 **What it does**
132 142