Mercurial > repos > vimalkumarvelayudhan > riboseqr_wrapper
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| author | Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> |
|---|---|
| date | Tue, 27 Oct 2015 12:29:39 +0000 |
| parents | d7ce95ccf54f |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="riboseqr_triplet_periodicity" name="Triplet Periodicity" |
| 2 version="0.4.0"> | |
| 3 <description> | |
| 4 (Step 2) Plot triplet periodicity for different read lengths. | |
| 5 </description> | |
| 6 <requirements> | |
| 7 <requirement type="package" version="3.1.2">R</requirement> | |
| 8 <requirement type="package" version="6.2">readline</requirement> | |
| 9 <requirement type="package" version="2.3.10">rpy2</requirement> | |
| 10 <requirement type="package" version="0.4.0">riboseqr_wrapper_deps</requirement> | |
| 11 </requirements> | |
| 12 <stdio> | |
| 13 <exit_code range="1:" level="fatal" description="Error" /> | |
| 14 </stdio> | |
| 15 <command interpreter="python">riboseqr/triplet.py | |
| 16 --rdata_load "$rdata_load" | |
| 17 --fasta_file "$fasta_file" | |
| 18 --start_codons "$start_codons" | |
| 19 --stop_codons "$stop_codons" | |
| 20 --include_lengths "$include_lengths" | |
| 21 --analyze_plot_lengths "$analyze_plot_lengths" | |
| 22 --text_legend "$text_legend" | |
| 23 --rdata_save "$rdata_save" | |
| 24 --html_file "$html_file" | |
| 25 --output_path "$html_file.files_path" | |
| 26 </command> | |
| 27 <inputs> | |
|
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d7ce95ccf54f
Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents:
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diff
changeset
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28 <param name="rdata_load" type="data" format="RData" |
| 0 | 29 label="Select prepared riboSeqR input (R data file)" |
| 30 multiple="false" optional="false" | |
| 31 help="<br><h4><font color="#666666">findCDS | |
| 32 parameters</font></h4>"> | |
| 33 <validator type="expression" | |
| 34 message="Please check if the correct RDA file is selected">value.name == "Prepare riboSeqR input (R data file)"</validator> | |
| 35 </param> | |
| 36 | |
| 37 <param format="fasta" name="fasta_file" type="data" | |
| 38 label="Select FASTA file of the reference transcriptome" | |
| 39 help="This Fasta file is used to find start (ATG) and | |
| 40 stop codons(TAG, TAA, TGA) in frame with one another. If no files | |
| 41 are listed, you will need to upload a FASTA file of the reference | |
| 42 transcriptome. Please note that the FASTA header of the transcriptome | |
| 43 sequences must match the sequence names from the SAM file."> | |
| 44 <validator type="empty_field" message="Field requires a value"/> | |
| 45 </param> | |
| 46 | |
| 47 <param name="start_codons" type="text" size="15" value="ATG" | |
| 48 label="Start codon(s) to use" | |
| 49 help="Default is ATG. Multiple values must be comma-separated."> | |
| 50 <validator type="empty_field" message="Field requires a value"/> | |
| 51 </param> | |
| 52 | |
| 53 <param name="stop_codons" type="text" size="15" value="TAG, TAA, TGA" | |
| 54 label="Stop codon(s) to use" | |
| 55 help="Default is TAG, TAA, TGA. Multiple values must be comma-separated. | |
| 56 <h4><font color="#666666">frameCounting | |
| 57 parameters</font></h4>"> | |
| 58 <validator type="empty_field" message="Field requires a value"/> | |
| 59 </param> | |
| 60 | |
| 61 <param name="include_lengths" type="text" | |
| 62 label="Lengths of ribosome footprints | |
| 63 to be included" | |
| 64 help="Here, you can specify the lengths of ribosome footprints to | |
| 65 be included in the riboData object. <br>For example 25:30. | |
| 66 Range, semi-colon separated. <h4><font color="#666666">readingFrame | |
| 67 parameters</font></h4>" value="25:30"/> | |
| 68 | |
| 69 <param name="analyze_plot_lengths" type="text" | |
| 70 label="Lengths of reads to be analysed for frame-shift, or to be plotted" | |
| 71 help="[Optional] If omitted, all lengths will be plotted. | |
| 72 <br>For example 26:30. Range, semi-colon separated. | |
| 73 <h4><font color="#666666">plotFS | |
| 74 parameters</font></h4>" value="26:30"/> | |
| 75 | |
| 76 <param name="text_legend" type="text" size="30" | |
| 77 value='Frame 0, Frame 1, Frame 2' | |
| 78 label="Text for legend used in the | |
| 79 plot" help="Comma-separated values."/> | |
| 80 </inputs> | |
| 81 <outputs> | |
|
3
d7ce95ccf54f
Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents:
2
diff
changeset
|
82 <data format="RData" name="rdata_save" |
| 0 | 83 label="Triplet periodicity (R data file)"/> |
| 84 <data format="html" name="html_file" | |
| 85 label="Triplet periodicity (HTML report)"/> | |
| 86 </outputs> | |
|
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d7ce95ccf54f
Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents:
2
diff
changeset
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87 <!--<tests>--> |
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d7ce95ccf54f
Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents:
2
diff
changeset
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88 <!--<test>--> |
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d7ce95ccf54f
Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents:
2
diff
changeset
|
89 <!--<param name="rdata_load" value="Prepare riboSeqR input (R data file)" ftype="RData" />--> |
|
d7ce95ccf54f
Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents:
2
diff
changeset
|
90 <!--<param name="fasta_file" value="rsem_chlamy236_deNovo.transcripts.fa" />--> |
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d7ce95ccf54f
Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents:
2
diff
changeset
|
91 <!--<param name="include_lengths" value="25:30" />--> |
|
d7ce95ccf54f
Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents:
2
diff
changeset
|
92 <!--<param name="analyze_plot_lengths" value="26:30" />--> |
|
d7ce95ccf54f
Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents:
2
diff
changeset
|
93 <!--<output name="rdata_save" file="Triplet periodicity (R data file)" ftype="RData" />--> |
|
d7ce95ccf54f
Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents:
2
diff
changeset
|
94 <!--<output name="html_file" file="Triplet_periodicity_(HTML_report).html">--> |
|
d7ce95ccf54f
Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents:
2
diff
changeset
|
95 <!--<extra_files type="file" name="Periodicity-plot.png" value="Periodicity-plot.png" ftype="png" />--> |
|
d7ce95ccf54f
Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents:
2
diff
changeset
|
96 <!--<extra_files type="file" name="Periodicity-plot.pdf" value="Periodicity-plot.pdf" ftype="pdf" />--> |
|
d7ce95ccf54f
Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents:
2
diff
changeset
|
97 <!--</output>--> |
|
d7ce95ccf54f
Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents:
2
diff
changeset
|
98 <!--</test>--> |
|
d7ce95ccf54f
Change R data file format in xml wrappers (rda -> RData)
Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
parents:
2
diff
changeset
|
99 <!--</tests>--> |
| 0 | 100 <help> |
| 101 Triplet Periodicity | |
| 102 ------------------- | |
| 103 riboSeqR version: ``1.0.5``. | |
| 104 | |
| 105 This tool can be used to plot triplet periodicity for different read lengths. | |
| 106 The inputs for this program are: | |
| 107 | |
| 108 #. Prepare riboSeqR input (R data file) from the previous step. | |
| 109 #. FASTA format file of the reference transcriptome. | |
| 110 | |
|
2
b2eb07000039
Fix spacing in environment_variables in tool_dependencies (breaks env.sh)
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
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diff
changeset
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111 .. class:: infomark |
| 0 | 112 |
|
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b2eb07000039
Fix spacing in environment_variables in tool_dependencies (breaks env.sh)
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
0
diff
changeset
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113 Please note that the FASTA header of the transcriptome sequences must |
|
b2eb07000039
Fix spacing in environment_variables in tool_dependencies (breaks env.sh)
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
0
diff
changeset
|
114 match the sequence names from the SAM file. |
| 0 | 115 |
| 116 How to use? | |
| 117 ----------- | |
| 118 Inputs | |
| 119 ...... | |
| 120 Select prepared R data file from the previous step. | |
| 121 | |
| 122 Select FASTA format file of the reference transcriptome, review/change other | |
| 123 options if necessary and execute program. | |
| 124 | |
| 125 Outputs | |
| 126 ....... | |
| 127 The following files will be generated on completion: | |
| 128 | |
| 129 #. Triplet periodicity (HTML report) | |
| 130 | |
|
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
0
diff
changeset
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131 A HTML file with results and links to other output files - triplet |
|
b2eb07000039
Fix spacing in environment_variables in tool_dependencies (breaks env.sh)
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
0
diff
changeset
|
132 periodicity plot (PDF) and R script used for the session. |
| 0 | 133 |
| 134 #. Triplet periodicity (R data file) | |
| 135 | |
|
2
b2eb07000039
Fix spacing in environment_variables in tool_dependencies (breaks env.sh)
Vimalkumar Velayudhan <vimal@biotechcoder.com>
parents:
0
diff
changeset
|
136 Used as input for the next step - *Metagene analysis*. |
| 0 | 137 |
| 138 riboSeqR functions used | |
| 139 ....................... | |
| 140 ``findCDS``, ``frameCounting``, ``readingFrame`` and ``plotFS``. | |
| 141 | |
| 142 For detailed description of the functions and the options used, please consult | |
| 143 the riboSeqR documentation. | |
| 144 | |
| 145 Links | |
| 146 ..... | |
| 147 `riboSeqR <http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html>`_. | |
| 148 | |
| 149 </help> | |
| 150 <citations> | |
| 151 <citation type="bibtex"> | |
| 152 @Manual{, | |
| 153 title = {riboSeqR: Analysis of sequencing data from ribosome | |
| 154 profiling experiments.}, | |
| 155 author = {Thomas J. Hardcastle}, | |
| 156 year = {2014}, | |
| 157 note = {R package version 1.0.5}, | |
| 158 } | |
| 159 </citation> | |
| 160 </citations> | |
| 161 </tool> |