Mercurial > repos > dcouvin > mirureader

comparison MIRUReader.xml @ 0:f0e3646a4e45 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author dcouvin
date Tue, 17 Aug 2021 19:15:15 +0000
parents
children 1a7d6584e1ec
comparison
equal deleted inserted replaced
-1:000000000000 0:f0e3646a4e45
1 <tool id="mirutool" name="mirureader" version="6.6.0">
2 <description> MIRUReader.... </description>
3
4 <requirements>
5 <requirement type="package" version="3.2.0">python3-openid</requirement>
6 <requirement type="package" version="6.6.0">emboss</requirement>
7 <requirement type="package" version="1.3.2">pandas</requirement>
8 </requirements>
9
10 <command>cp $input input.fasta; python3 $__tool_directory__/MIRUReader/MIRUReader.py -r input.fasta -p name 1> $output 2>$logfile</command>
11 <!--
12 <command interpreter="bash" detect_errors="aggressive"><![CDATA[
13
14 #import re
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')
17 #set $named_input_files = ''
18 #for $input_file in $input_files
19 ## Add single quotes around each input file identifier
20 #set $_input_file = "'{}'".format($input_file.element_identifier)
21 ln -s '${input_file}' ${_input_file} &&
22 #set $named_input_files = $named_input_files + ' ' + $_input_file
23 #end for
24
25 #for $element in $named_input_files
26 sudo python3 '$__tool_directory__/MIRUReader/MIRUReader.py' '-r' $element '-p' $element > $output
27 #end for
28
29
30
31 ]]></command>
32 -->
33
34 <!-- for element in `echo $named_input_files`; do python3 MIRUReader.py -r $element -p $element;done > $output
35 sudo python3 '$__tool_directory__/MIRUReader/MIRUReader.py' '-r' $named_input_files '-p' $named_input_files > $output -->
36
37 <inputs>
38 <!--
39 <param format="fasta" name="input_files" type="data" label="fasta files :" multiple="true" display="checkboxes"/>
40 -->
41 <param format="fasta" name="input" type="data" label="Fasta file"/>
42 </inputs>
43
44 <outputs>
45 <data format="tabular" name="output" label="MIRUreader output"/>
46 <data format="txt" name="logfile" label="Logfile"/>
47 </outputs>
48
49 <help>
50 -Git:https://github.com/phglab/MIRUReader.git
51 </help>
52
53 <citations>
54 <citation type="doi">10.1093/bioinformatics/btz771</citation>
55 </citations>
56 </tool>