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comparison ribocount.xml @ 30:b26c8f3b5aa6

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Use latest version of riboplot from PyPI (0.2.1)
author Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
date Fri, 16 Oct 2015 17:19:33 +0100
parents fb64b970da25
children 69f43f4144df
comparison
equal deleted inserted replaced
29:fb64b970da25 30:b26c8f3b5aa6
1 <tool id="ribocount" name="ribocount" version="0.1.0"> 1 <tool id="ribocount" name="ribocount" version="0.2.0">
2 <description>Get read counts for all transcripts in an alignment (BAM) 2 <description>Get read counts for all transcripts in an alignment (BAM)
3 </description> 3 </description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="0.1.1">riboplot</requirement> 5 <requirement type="package" version="0.2.1">riboplot</requirement>
6 </requirements> 6 </requirements>
7 <stdio> 7 <stdio>
8 <exit_code range="1:" level="fatal" description="Error" /> 8 <exit_code range="1:" level="fatal" description="Error" />
9 </stdio> 9 </stdio>
10 <command>python \${RIBOPLOT_PATH}/ribocount 10 <command>python \${RIBOPLOT_PATH}/ribocount
11 --ribo_file "${ribo_file}" 11 --ribo_file "${ribo_file}"
12 --transcriptome_fasta "${transcriptome_fasta}" 12 --transcriptome_fasta "${transcriptome_fasta}"
13 --read_length "${read_length}" 13 --read_length "${read_length}"
14 --read_offset "${read_offset}" 14 --read_offset "${read_offset}"
15 #if (str($region_select) == 'five_prime'):
16 --count_five
17 #elif (str($region_select) == 'three_prime'):
18 --count_three
19 #end if
15 --html_file "${html_file}" 20 --html_file "${html_file}"
16 --output_path "${html_file.files_path}" 21 --output_path "${html_file.files_path}"
17 ## --debug 22 ## --debug
18 </command> 23 </command>
19 <inputs> 24 <inputs>
20 <param name="ribo_file" type="data" format="bam" label="Ribo-Seq alignment file in BAM format"/> 25 <param name="ribo_file" type="data" format="bam" label="Ribo-Seq alignment file in BAM format"/>
21 <param name="transcriptome_fasta" type="data" format="fasta" label="FASTA format file of the transcriptome"/> 26 <param name="transcriptome_fasta" type="data" format="fasta" label="FASTA format file of the transcriptome"/>
22 <param name="read_length" type="integer" label="Read length to consider" value="28"/> 27 <param name="read_length" type="integer" label="Read length to consider" value="28" help="If specified, only reads of this length will be considered.
28 A read length of 0 will output counts for all reads"/>
23 <param name="read_offset" type="integer" label="Offset" value="0"/> 29 <param name="read_offset" type="integer" label="Offset" value="0"/>
30 <param name="region_select" type="select" label="Which read counts to output?"
31 help="Output read counts for the entire transcript or restrict read counts to the region 5' or 3' of the longest ORF">
32 <option value="all_reads">All reads</option>
33 <option value="five_prime">5' of the longest ORF</option>
34 <option value="three_prime">3' of the longest ORF</option>
35 </param>
24 </inputs> 36 </inputs>
25 <outputs> 37 <outputs>
26 <data format="html" name="html_file" label="ribocount (HTML report)"/> 38 <data format="html" name="html_file" label="ribocount on ${ribo_file.name} ($region_select.value_label)"/>
27 </outputs> 39 </outputs>
28 <help> 40 <help>
29 **RiboCount** 41 **RiboCount**
30 42
31 Output read counts for all transcripts in an alignment. 43 Output read counts for all transcripts in an alignment.
52 64
53 4. Offset [optional] (Integer - 0 or greater) 65 4. Offset [optional] (Integer - 0 or greater)
54 66
55 If this option is provided, this offset is added to the read alignment positions. 67 If this option is provided, this offset is added to the read alignment positions.
56 68
69 5. Restrict read counts
70
71 Choose whether to output read counts for the entire transcript or restrict read counts to the 5' or 3' region of the longest ORF.
72 Default start (ATG) and stop codons ('TAG', 'TGA', 'TAA') are used to identify the longest ORF in 3 frames.
73
57 ---- 74 ----
58 75
59 **Output** 76 **Output**
60 77
61 Read counts for all transcripts in the alignment (ZIP) 78 Read counts for all transcripts in the alignment (ZIP)