Mercurial > repos > vimalkumarvelayudhan > riboplot
comparison ribocount.xml @ 30:b26c8f3b5aa6
Use latest version of riboplot from PyPI (0.2.1)
author | Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> |
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date | Fri, 16 Oct 2015 17:19:33 +0100 |
parents | fb64b970da25 |
children | 69f43f4144df |
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29:fb64b970da25 | 30:b26c8f3b5aa6 |
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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) |