Mercurial > repos > thanhlv > biotradis
comparison biotradis_tradis_comparison.xml @ 6:5506c4307812 draft
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 312fa79eebd5a3da99506d18deba55e6824f3956-dirty
author | thanhlv |
---|---|
date | Wed, 23 Oct 2019 10:40:28 -0400 |
parents | |
children | 09c1f97a5bcc |
comparison
equal
deleted
inserted
replaced
5:bf790f407b1b | 6:5506c4307812 |
---|---|
1 <tool id="tradis_comparison" name="tradis comparison" version="@VERSION@"> | |
2 <description>Compares two experimental conditions</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 #for $counter, $input in enumerate($control): | |
9 ln -s '$input' $input.element_identifier && | |
10 echo ./$new_name >> control && | |
11 #end for | |
12 | |
13 #for $counter, $input in enumerate($conditions): | |
14 ln -s '$input' $input.element_identifier && | |
15 echo ./$new_name >> conditions && | |
16 #end for | |
17 | |
18 tradis_comparison.R | |
19 --controls control | |
20 --conditions conditions | |
21 -o output.csv | |
22 -p plot.pdf | |
23 #if str($filter.filter_selector)=="yes": | |
24 -f | |
25 -t $filter.cutoff | |
26 #end if | |
27 ]]> </command> | |
28 <inputs> | |
29 <param name="control" type="data" format="csv" multiple="true" label="Control list"/> | |
30 <param name="conditions" type="data" format="csv" multiple="true" label="Condition list"/> | |
31 <conditional name="filter"> | |
32 <param name="filter_selector" type="select" label="Filter"> | |
33 <option value="yes">Yes</option> | |
34 <option value="no" selected="true" >No</option> | |
35 </param> | |
36 <when value="yes"> | |
37 <param name="cutoff" type="integer" value="" label="Cut-off value"/> | |
38 </when> | |
39 <when value="no"/> | |
40 </conditional> | |
41 | |
42 </inputs> | |
43 | |
44 <outputs> | |
45 <data name="output" format="txt" label="${tool.name} on ${on_string} Log" from_work_dir="output.csv"/> | |
46 <data name="plot" format="pdf" label="${tool.name} on ${on_string} Plot" from_work_dir="plot.pdf" /> | |
47 </outputs> | |
48 | |
49 <tests> | |
50 <test> | |
51 </test> | |
52 </tests> | |
53 <help><![CDATA[ | |
54 Adds transposon sequence and quality tags to the read strings and | |
55 outputs a BAM. | |
56 | |
57 Usage: add_tags -b file.bam [options] | |
58 | |
59 Options: | |
60 -b : bam file with tradis tags | |
61 -v : verbose debugging output | |
62 ]]> </help> | |
63 | |
64 </tool> |