Mercurial > repos > vimalkumarvelayudhan > riboplot
comparison riboplot.xml @ 4:1901dcdc12ff
Move galaxy xml wrappers to top level
author | Vimalkumar Velayudhan <vimal@biotechcoder.com> |
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date | Wed, 12 Aug 2015 09:44:36 +0100 |
parents | galaxy/riboplot.xml@8e1efafa6277 |
children | 844eb8c36f32 |
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3:8e1efafa6277 | 4:1901dcdc12ff |
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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="0.8.3">pysam</requirement> | |
7 </requirements> | |
8 <stdio> | |
9 <exit_code range="1:" level="fatal" description="Error" /> | |
10 </stdio> | |
11 <command interpreter="python">riboplot/riboplot.py | |
12 --ribo_file "${ribo_file}" | |
13 --transcriptome_fasta "${transcriptome_fasta}" | |
14 --transcript_name "${transcript_name}" | |
15 #if $rnacov.rnacov_select=="yes" | |
16 --rna_file "${rna_file}" | |
17 #end if | |
18 --read_length "${read_length}" | |
19 --read_offset "${read_offset}" | |
20 --html_file "${html_file}" | |
21 --output_path "${html_file.files_path}" | |
22 ## --debug | |
23 </command> | |
24 <inputs> | |
25 <param name="ribo_file" type="data" format="bam" label="Ribo-Seq alignment file in BAM format"/> | |
26 <param name="transcriptome_fasta" type="data" format="fasta" label="FASTA format file of the transcriptome"/> | |
27 <param name="transcript_name" type="text" label="Name of the transcript to plot (as in FASTA)" size="40"> | |
28 <validator type="expression" message="Please input a single transcript name">len(value.split(',')) == 1</validator> | |
29 <validator type="empty_field" message="Field requires a value"/> | |
30 <sanitizer> | |
31 <valid> | |
32 <add value="|"/> | |
33 </valid> | |
34 </sanitizer> | |
35 </param> | |
36 <conditional name="rnacov"> | |
37 <param name="rnacov_select" type="select" label="Include RNA Coverage"> | |
38 <option value="no">No</option> | |
39 <option value="yes">Yes</option> | |
40 </param> | |
41 <when value="yes"> | |
42 <param name="rna_file" type="data" format="bam" label="RNA-Seq alignment file in BAM format"/> | |
43 </when> | |
44 <when value="no" /> | |
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> |