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comparison flye.xml @ 1:cd256484eb1a draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 6cd5f829f985631f0e8360d66a73206389101171
author bgruening
date Fri, 28 Sep 2018 19:18:54 -0400
parents d9f4c141d88a
children 156e0da5b917
comparison
equal deleted inserted replaced
0:d9f4c141d88a 1:cd256484eb1a
7 <version_command>flye --version</version_command> 7 <version_command>flye --version</version_command>
8 <command detect_errors="exit_code"> 8 <command detect_errors="exit_code">
9 <![CDATA[ 9 <![CDATA[
10 10
11 #for $counter, $input in enumerate($inputs): 11 #for $counter, $input in enumerate($inputs):
12 ln -s '$input' ./input_${counter}.${input.ext} && 12
13 #if $input.is_of_type('fastqsanger', 'fastq'):
14 #set $ext = 'fastq'
15 #elif $input.is_of_type('fastqsanger.gz'):
16 #set $ext = 'fastq.gz'
17 #elif $input.is_of_type('fasta.gz'):
18 #set $ext = 'fasta.gz'
19 #elif $input.is_of_type('fasta'):
20 #set $ext = 'fasta'
21 #end if
22 ln -s '$input' ./input_${counter}.${ext} &&
13 #end for 23 #end for
14 24
15 flye 25 flye
16 $mode 26 $mode
17 #for $counter, $input in enumerate($inputs): 27 #for $counter, $input in enumerate($inputs):
26 -m '$m' 36 -m '$m'
27 #end if 37 #end if
28 2>&1 38 2>&1
29 ]]></command> 39 ]]></command>
30 <inputs> 40 <inputs>
31 <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz" multiple="true" label="Input reads" /> 41 <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger.gz,fastqsanger" multiple="true" label="Input reads" />
32 <param name="mode" type="select" label="Mode"> 42 <param name="mode" type="select" label="Mode">
33 <option value="--nano-raw">Nanopore raw</option> 43 <option value="--nano-raw">Nanopore raw</option>
34 <option value="--nano-corr">Nanopore corrected</option> 44 <option value="--nano-corr">Nanopore corrected</option>
35 <option value="--pacbio-raw">PacBio raw</option> 45 <option value="--pacbio-raw">PacBio raw</option>
36 <option value="--pacbio-corr">PacBio corrected</option> 46 <option value="--pacbio-corr">PacBio corrected</option>