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comparison MIRUReader.xml @ 2:f9422a33e9c1 draft default tip

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author dcouvin
date Fri, 03 Sep 2021 19:52:01 +0000
parents 1a7d6584e1ec
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1:1a7d6584e1ec 2:f9422a33e9c1
1 <tool id="mirureader" name="mirureader" version="1.0.0"> 1 <tool id="mirureader" name="mirureader" version="1.0.0">
2 <description> MIRUReader allows to perform in-silico MIRU-VNTR typing using long reads or assembled genome </description> 2 <description> MIRUReader allows to perform in-silico MIRU-VNTR typing using assembled genomes (FASTA format)</description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.2.0">python3-openid</requirement> 5 <requirement type="package" version="3.2.0">python3-openid</requirement>
6 <requirement type="package" version="6.6.0">emboss</requirement> 6 <requirement type="package" version="6.6.0">emboss</requirement>
7 <requirement type="package" version="1.3.2">pandas</requirement> 7 <requirement type="package" version="1.3.2">pandas</requirement>
15 ## Creates symlinks for each input file based on the Galaxy 'element_identifier' 15 ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
16 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat') 16 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
17 17
18 ## Add single quotes around each input file identifier 18 ## Add single quotes around each input file identifier
19 #set $_input_file = "'{}'".format($input.element_identifier) 19 #set $_input_file = "'{}'".format($input.element_identifier)
20 #set $_input_file = $_input_file + '.fasta' 20
21 ln -s '${input}' ${_input_file} && 21
22 22 ln -s '${input}' "${_input_file}" &&
23 python3 $__tool_directory__/MIRUReader/MIRUReader.py -r $_input_file -p $_input_file > $output 23 cp "$_input_file" input.fasta &&
24 python3 $__tool_directory__/MIRUReader/MIRUReader.py -r input.fasta -p $_input_file > $output
24 25
25 26
26 27
27 28
28 ]]></command> 29 ]]></command>
30
31 <!-- #set $var = ${_input_file//[^[:alnum:]]/}
32 #set var = ${f//:()/}
33 #set $_input_file = $_input_file + '.fasta'
34 $_input_file="${_input_file// /_}" && -->
29 35
30 <!-- for element in `echo $named_input_files`; do python3 MIRUReader.py -r $element -p $element;done > $output 36 <!-- for element in `echo $named_input_files`; do python3 MIRUReader.py -r $element -p $element;done > $output
31 sudo python3 '$__tool_directory__/MIRUReader/MIRUReader.py' '-r' $named_input_files '-p' $named_input_files > $output --> 37 sudo python3 '$__tool_directory__/MIRUReader/MIRUReader.py' '-r' $named_input_files '-p' $named_input_files > $output -->
32 38
33 <inputs> 39 <inputs>
34 <!-- 40 <!--
35 <param format="fasta" name="input_files" type="data" label="fasta files :" multiple="true" display="checkboxes"/> 41 <param format="fasta" name="input_files" type="data" label="fasta files :" multiple="true" display="checkboxes"/>
36 --> 42 -->
37 <param format="fasta" name="input" type="data" label="Fasta file"/> 43 <param format="fasta" name="input" type="data" label="FASTA file"/>
38 </inputs> 44 </inputs>
39 45
40 <outputs> 46 <outputs>
41 <data format="tabular" name="output" label="MIRUReader output"/> 47 <data format="tabular" name="output" label="MIRUReader output"/>
42 <!--<data format="txt" name="logfile" label="LogFile"/>--> 48 <!--<data format="txt" name="logfile" label="LogFile"/>-->