Mercurial > repos > iuc > dexseq

annotate dexseq_count.xml @ 0:4ca0e679f21e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
author iuc
date Thu, 08 Oct 2015 16:52:01 -0400
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4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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1 <tool id="dexseq_count" name="DEXSeq-Count" version="1.0">
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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2 <description>Prepare and count exon abundancies from RNA-seq data</description>
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3 <requirements>
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4 <requirement type="package" version="1.14">dexseq</requirement>
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5 <requirement type="package" version="0.6.1">htseq</requirement>
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6 <requirement type="package" version="0.7.7">pysam</requirement>
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7 </requirements>
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8 <stdio>
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9 <!-- Anything other than zero is an error -->
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10 <exit_code range="1:" />
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11 <exit_code range=":-1" />
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12 <!-- In case the return code has not been set propery check stderr too -->
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13 <regex match="Error:" />
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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14 <regex match="Exception:" />
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15 </stdio>
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16 <command>
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17 <![CDATA[
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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18 #if $mode.mode_select == "prepare":
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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19 python \$DEXSEQ_ROOT/python_scripts/dexseq_prepare_annotation.py
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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20 -r $mode.aggregate
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21 $mode.gtffile
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22 $flattened_gtf_out
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23 #elif $mode.mode_select == "count":
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24 python \$DEXSEQ_ROOT/python_scripts/dexseq_count.py
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25 -f bam
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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26 -p $mode.paired
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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27 -s $mode.stranded
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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28 -a $mode.qual
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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29 -r $mode.order
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30 $mode.flattened_gtf_in
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31 $mode.bamfile
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32 $counts_file
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33 #end if
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34 ]]>
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35 </command>
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36 <inputs>
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37 <conditional name="mode">
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38 <param name="mode_select" type="select" label="Mode of operation">
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39 <option value="prepare">Prepare annotation</option>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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40 <option value="count">Count reads</option>
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41 </param>
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42 <when value="prepare">
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43 <param name="gtffile" type="data" format="gff" label="GTF file"/>
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44 <param name="aggregate" type="boolean" checked="True" truevalue="yes" falsevalue="no"
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45 label="Aggretare genes with exons?"
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46 help="Indicates whether two or more genes sharing an exon should be merged into an 'aggregate gene'. If 'no', the exons that can not be assiged to a single gene are ignored."/>
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47 </when>
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48 <when value="count">
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49 <param name="bamfile" type="data" format="bam" label="Input bam file"/>
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50 <param name="flattened_gtf_in" type="data" format="gff" label="DEXSeq compatible GTF file" help="Created by prepare mode"/>
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51 <param name="paired" type="boolean" checked="True" truevalue="yes" falsevalue="no" label="Is libray paired end?"/>
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52 <param name="stranded" type="select" label="Is library strand specific?">
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53 <option value="no">No</option>
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54 <option value="yes">Yes</option>
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55 <option value="reverse">Yes, but reverse</option>
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56 </param>
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57 <param name="qual" type="integer" value="10" label="Skip all reads with alignment quality lower than the given minimum value"/>
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58 <param name="order" type="select" label="Sorting order of alignments" help="If you generated your alignments using tophat, they are by default position sorted. Ignored for single-end data">
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59 <option value="pos">By position</option>
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60 <option value="name">By name</option>
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61 </param>
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62 </when>
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63 </conditional>
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64 </inputs>
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65
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66 <outputs>
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67 <data format="tabular" name="counts_file" label="DEXSeq count reads on ${on_string}">
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68 <filter>mode['mode_select'] == 'count'</filter>
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69 </data>
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70 <data format="gtf" name="flattened_gtf_out" label="DEXSeq prepare annotation on ${on_string}">
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71 <filter>mode['mode_select'] == 'prepare'</filter>
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72 </data>
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73 </outputs>
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74
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75 <tests>
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76 <test>
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77 <param name="mode_select" value="prepare" />
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78 <param name="gtffile" ftype="gff" value="original.gtf"/>
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79 <param name="aggregate" value="True"/>
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80 <output name="flattened_gtf_out" file="flattened.gtf" ftype="gtf"/>
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81 </test>
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82 </tests>
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83
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84 <help>
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85 <![CDATA[
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86 .. class:: infomark
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87
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88 **What it does**
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89
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90 The main goal of this tol is to count the number of reads/fragments per exon of each gene in RNA-seq sample. In addition it also prepares your annotation gtf file compatible for counting.
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91
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92
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93 **Inputs**
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94
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95 Mode-preprare: Takes a normal gtf file as input. For example from ensembl database.
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96 Mode-count: Inputs are flattened gtf file and BAM file. The flattened gtf file can be generated from 'prepare' mode of this tool.
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97
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98 **Output**
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99
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100 Mode-preprare: Flattened gtf file that contains only exons with corresponding gene ids from given gtf file. Sometimes two or more genes sharing an exon will be merged into an 'aggregate gene' if the aggregate option was used.
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101 Mode-count: Two column tab-delimeted file with exon ids and their read counts.
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102
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103 .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html
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104
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105 ]]>
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106 </help>
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107 <citations>
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108 <citation type="doi">10.1101/gr.133744.111</citation>
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109 </citations>
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110 </tool>