annotate ribocount.xml @ 36:3985e058fd63 default tip

Use latest version of riboplot from PyPI (0.2.4)
author Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
date Wed, 25 Nov 2015 13:04:01 +0000
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1 <tool id="ribocount" name="ribocount" version="0.2.4">
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2 <description>Get read counts for all transcripts in an alignment (BAM)
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3 </description>
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4 <requirements>
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5 <requirement type="package" version="0.2.4">riboplot</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" level="fatal" description="Error" />
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9 </stdio>
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10 <command>python \${RIBOPLOT_PATH}/ribocount
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11 --ribo_file "${ribo_file}"
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12 --transcriptome_fasta "${transcriptome_fasta}"
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13 --read_length "${read_length}"
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14 --read_offset "${read_offset}"
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15 #if (str($region_select) == 'five_prime'):
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16 --count_five
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17 #elif (str($region_select) == 'three_prime'):
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18 --count_three
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19 #end if
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20 --html_file "${html_file}"
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21 --output_path "${html_file.files_path}"
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22 ## --debug
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23 </command>
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24 <inputs>
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25 <param name="ribo_file" type="data" format="bam" label="Ribo-Seq alignment file in BAM format"/>
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26 <param name="transcriptome_fasta" type="data" format="fasta" label="FASTA format file of the transcriptome"/>
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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.
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28 A read length of 0 will output counts for all reads"/>
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29 <param name="read_offset" type="integer" label="Offset" value="0"/>
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30 <param name="region_select" type="select" label="Which read counts to output?"
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31 help="Output read counts for the entire transcript or restrict read counts to the region 5' or 3' of the longest ORF">
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32 <option value="all_reads">All reads</option>
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33 <option value="five_prime">5' of the longest ORF</option>
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34 <option value="three_prime">3' of the longest ORF</option>
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35 </param>
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36 </inputs>
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37 <outputs>
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38 <data format="html" name="html_file" label="ribocount on ${ribo_file.name} ($region_select.value_label)"/>
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39 </outputs>
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40 <help>
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41 **RiboCount**
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43 Output read counts for all transcripts in an alignment.
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45 ----
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47 **Parameters**
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49 1. Ribo-Seq alignment file (Sorted BAM file)
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51 A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM
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52 file should be sorted. This can be done using one of the following methods.
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53
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54 1. RiboGalaxy -> Sort Data -> Sort BAM dataset.
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55 2. ``samtools sort input.bam inputsorted``
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57 2. Transcriptome (FASTA)
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59 A FASTA format file with sequences of the transcripts.
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61 3. Read lengths to consider [optional] (Integer - 0 or greater)
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63 If this option is provided, only Ribo-Seq data of the given length is considered.
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65 4. Offset [optional] (Integer - 0 or greater)
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67 If this option is provided, this offset is added to the read alignment positions.
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68
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69 5. Restrict read counts
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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.
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72 Default start (ATG) and stop codons ('TAG', 'TGA', 'TAA') are used to identify the longest ORF in 3 frames.
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74 ----
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75
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76 **Output**
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78 Read counts for all transcripts in the alignment (ZIP)
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80 The output file ``ribocount_output.zip`` should first be uncompressed. This will generate
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81 a folder called ``ribocount_output``. Open ``index.html`` in a web browser to view the results of ribocount.
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83 Total reads for each transcript will be displayed in a table along with the name of the transcript and a link
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84 to the CSV file containing the read counts in 3 frames for each position in the transcript.
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85
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86 .. image:: images/ribocount.png
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87
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88 </help>
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89 </tool>