Mercurial > repos > vimalkumarvelayudhan > riboplot
comparison riboplot.xml @ 0:ca58e9466cbf
First commit
author | Vimalkumar Velayudhan <vimal@biotechcoder.com> |
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date | Mon, 29 Jun 2015 16:38:36 +0100 |
parents | |
children | 1e9797878349 |
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1 <tool id="riboplot" name="riboplot" version="0.1.0"> | |
2 <description>Plot and output read counts for a single transcript in an alignment (BAM) | |
3 </description> | |
4 <requirements> | |
5 <requirement type="package" version="1.2.1">matplotlib</requirement> | |
6 <requirement type="package" version="0.7.7">pysam</requirement> | |
7 <requirement type="package" version="0.1.18">samtools</requirement> | |
8 </requirements> | |
9 <stdio> | |
10 <exit_code range="1:" level="fatal" description="Error" /> | |
11 </stdio> | |
12 <command interpreter="python">./riboplot/riboplot.py | |
13 --ribo_file "${ribo_file}" | |
14 --transcriptome_fasta "${transcriptome_fasta}" | |
15 --transcript_name "${transcript_name}" | |
16 #if $rnacov.rnacov_select=="yes" | |
17 --rna_file "${rna_file}" | |
18 #end if | |
19 --read_length "${read_length}" | |
20 --read_offset "${read_offset}" | |
21 --html_file "${html_file}" | |
22 --output_path "${html_file.files_path}" | |
23 ## --debug | |
24 </command> | |
25 <inputs> | |
26 <param name="ribo_file" type="data" format="bam" label="Ribo-Seq alignment file in BAM format"/> | |
27 <param name="transcriptome_fasta" type="data" format="fasta" label="FASTA format file of the transcriptome"/> | |
28 <param name="transcript_name" type="text" label="Name of the transcript to plot (as in FASTA)" size="40"> | |
29 <validator type="expression" message="Please input a single transcript name">len(value.split(',')) == 1</validator> | |
30 <validator type="empty_field" message="Field requires a value"/> | |
31 <sanitizer> | |
32 <valid> | |
33 <add value="|"/> | |
34 </valid> | |
35 </sanitizer> | |
36 </param> | |
37 <conditional name="rnacov"> | |
38 <param name="rnacov_select" type="select" label="Include RNA Coverage"> | |
39 <option value="no">No</option> | |
40 <option value="yes">Yes</option> | |
41 </param> | |
42 <when value="yes"> | |
43 <param name="rna_file" type="data" format="bam" label="RNA-Seq alignment file in BAM format"/> | |
44 </when> | |
45 </conditional> | |
46 <param name="read_length" type="integer" label="Read length to consider" value="28"/> | |
47 <param name="read_offset" type="integer" label="Offset" value="0"/> | |
48 </inputs> | |
49 <outputs> | |
50 <data format="html" name="html_file" label="riboplot (HTML report)"/> | |
51 </outputs> | |
52 <help> | |
53 </help> | |
54 </tool> |