Mercurial > repos > fubar > htseq_bams_to_count_matrix
annotate htseqsams2mx.xml @ 59:57841366f112 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
| author | iuc |
|---|---|
| date | Mon, 04 May 2015 22:47:20 -0400 |
| parents | 9b59cd40f20d |
| children | d300bc688e95 |
| rev | line source |
|---|---|
| 56 | 1 <tool id="htseqsams2mxlocal" name="SAM/BAM to count matrix" version="0.5"> |
| 2 <description>using HTSeq code</description> | |
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57841366f112
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
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3 <requirements> |
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57841366f112
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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4 <requirement type="package" version="0.7.6">pysam</requirement> |
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57841366f112
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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5 <requirement type="package" version="1.2.1">matplotlib</requirement> |
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57841366f112
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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6 <requirement type="package" version="0.5.4p3">htseq</requirement> |
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57841366f112
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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7 </requirements> |
| 56 | 8 <stdio> |
| 9 <regex match=".*" source="both" level="warning" description="chatter from HTSeq:"/> | |
| 10 </stdio> | |
| 11 <command interpreter="python"> | |
| 12 htseqsams2mx.py -g "$gfffile" -o "$outfile" -m "$model" --id_attribute "$id_attr" --feature_type "$feature_type" | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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13 --mapqMin $mapqMin |
| 56 | 14 #for $s in $samfiles: |
| 15 #if $s.ext != 'data': | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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16 --samf "'${s}','${s.name}','${s.ext}','${s.metadata.bam_index}'" |
| 56 | 17 #end if |
| 18 #end for | |
| 19 #if $filter_extras: | |
| 20 --filter_extras "$filter_extras" | |
| 21 #end if | |
| 22 </command> | |
| 23 <inputs> | |
| 24 <param format="gtf" name="gfffile" type="data" label="Gene model (GFF) file to count reads over from your current history" size="100" /> | |
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57841366f112
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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25 <param name="mapqMin" label="Filter reads with mapq below than this value" |
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57841366f112
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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26 help="0 to count any mapping quality read. Otherwise only reads at or above specified mapq will be counted" |
| 56 | 27 type="integer" value="5"/> |
| 28 <param name="title" label="Name for this job's output file" type="text" size="80" value="bams to DGE count matrix"/> | |
| 29 <param name="stranded" value="false" type="boolean" label="Reads are stranded - use strand in counting" display="checkbox" | |
| 30 truevalue="yes" falsevalue="no" checked="no" help="Check this ONLY if you know your sequences are strand specific" /> | |
| 31 <param name="model" type="select" label="Model for counting reads over the supplied gene model- see HTSeq docs" | |
| 32 help="If in doubt, union is a reasonable default but intersection-strict avoids double counting over overlapping exons"> | |
| 33 <option value="union" selected="true">union</option> | |
| 34 <option value="intersection-strict">intersection-strict</option> | |
| 35 <option value="intersection-nonempty">intersection-nonempty</option> | |
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57841366f112
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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36 </param> |
| 56 | 37 <param name="id_attr" type="select" label="GTF attribute to output as the name for each contig - see HTSeq docs" |
| 38 help="If in doubt, use gene name or if you need the id in your GTF, gene id"> | |
| 39 <option value="gene_name" selected="true">gene name</option> | |
| 40 <option value="gene_id">gene id</option> | |
| 41 <option value="transcript_id">transcript id</option> | |
| 42 <option value="transcript_name">transcript name</option> | |
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57841366f112
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
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diff
changeset
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43 </param> |
| 56 | 44 <param name="feature_type" type="select" label="GTF feature type for counting reads over the supplied gene model- see HTSeq docs" |
| 45 help="GTF feature type to count over - exon is a good choice with gene name as the contig to count over"> | |
| 46 <option value="exon" selected="true">exon</option> | |
| 47 <option value="CDS">CDS</option> | |
| 48 <option value="UTR">UTR</option> | |
| 49 <option value="transcript">transcript</option> | |
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57841366f112
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
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50 </param> |
| 56 | 51 <param name="filter_extras" type="select" label="Filter any read with one or more flags" |
| 52 help="eg the XS tag created by bowtie for multiple reads" optional="true" mutliple="true"> | |
| 53 <option value="">None</option> | |
| 54 <option value="XS">XS:i > 0 - More than one mapping position Bowtie</option> | |
| 55 <option value="XS:A">Might be useful for tophat</option> | |
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57841366f112
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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56 </param> |
| 56 | 57 |
| 58 <param name="samfiles" type="data" label="bam/sam file from your history" format="sam,bam" size="100" multiple="true"/> | |
| 59 </inputs> | |
| 60 <outputs> | |
| 61 <data format="tabular" name="outfile" label="${title}_htseqsams2mx.xls" /> | |
| 62 </outputs> | |
| 63 <tests> | |
| 64 <test> | |
| 65 <param name="feature_type" value="exon" /> | |
| 66 <param name="gfffile" value="rn4_chr20_100k.gtf" /> | |
| 67 <param name="samfiles" value="rn4chr20test1.bam,rn4chr20test2.bam" ftype="bam"/> | |
| 68 <param name="id_attr" value="gene_name" /> | |
| 69 <param name="model" value="union" /> | |
| 70 <param name="stranded" value="no" /> | |
| 71 <param name="title" value="htseqtest" /> | |
| 72 <param name="mapqMin" value="0" /> | |
| 73 | |
| 74 <output name="outfile" file="htseqsams2mx_test1_out.xls" lines_diff="1"/> | |
| 75 </test> | |
| 76 </tests> | |
| 77 <help> | |
| 78 | |
| 79 **What this tool does** | |
| 80 | |
| 81 Counts reads in multiple sam/bam format mapped files and generates a matrix ideal for edgeR and other count based tools | |
| 82 It uses HTSeq to count your sam reads over a gene model supplied as a GTF file | |
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57841366f112
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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83 The output is a tabular text (columnar - spreadsheet) file containing the |
| 56 | 84 count matrix for downstream processing. Each row contains the counts from each sample for each |
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57841366f112
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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changeset
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85 of the non-emtpy GTF input file contigs matching the GTF attribute choice above. |
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57841366f112
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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86 You probably want to use gene level GTF output attribute and count reads that overlap |
| 56 | 87 GTF exons for RNA-seq. Or you can count over exons by using transcript level output names or ids. Etc. |
| 88 | |
| 89 ---- | |
| 90 | |
| 91 **Author's plea on replicates** | |
| 92 | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
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93 If you want to interpret the downstream p values in terms of rejecting or accepting the null hypothesis |
| 56 | 94 under random sampling with replacement from the universe of possible biological/experimental replicates from which your data was derived, |
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57841366f112
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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95 which is what published p values are often assumed to do, then you need biological |
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57841366f112
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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96 (or for cell culture material experimental) replicates. |
| 56 | 97 |
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57841366f112
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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98 Using technical or no replicates means the downstream p values are not interpretable the way most people would assume |
| 56 | 99 they are - ie as the probability of obtaining a result as or more extreme as your experimental data |
| 100 in millions of experiments conducted using the same methods under the null hypothesis. | |
| 101 | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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102 There is no way around this and it is scientific fraud to ignore this issue and publish bogus p values derived from |
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57841366f112
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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103 technical or no replicates without making the lack of biological or experimental error in the p value calculations |
| 56 | 104 clear to your readers so they can adjust their expectations. However, the buck stops here at higher level inference. |
| 105 If you have no replicates, you must not use this tool as the p values are uninterpretable. So there. | |
| 106 | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
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107 See your stats 101 notes on the central limit theorem and test statistics for a refresher or talk to a |
| 56 | 108 statistician if this makes no sense please. |
| 109 | |
| 110 **Attribution** | |
| 111 | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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112 This Galaxy tool relies on HTSeq_ from http://www-huber.embl.de/users/anders/HTSeq/doc/index.html |
| 56 | 113 for the tricky work of counting. That code includes the following attribution: |
| 114 | |
| 115 ## Written by Simon Anders (sanders@fs.tum.de), European Molecular Biology | |
| 116 ## Laboratory (EMBL). (c) 2010. Released under the terms of the GNU General | |
| 117 ## Public License v3. Part of the 'HTSeq' framework, version HTSeq-0.5.4p3 | |
| 118 | |
| 119 It will be automatically installed if you use the toolshed as in general, you probably should. | |
| 120 HTSeq_ must be installed with this tool if you install manually. | |
| 121 | |
| 122 Otherwise, all code and documentation comprising this tool including the requirement | |
| 123 for more than one sample bam | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
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124 was written by Ross Lazarus and is |
| 56 | 125 licensed to you under the LGPL_ like other rgenetics artefacts |
| 126 | |
| 127 Sorry, I don't use readgroups so had no reason to code read groups. Contributions welcome. Send code | |
| 128 | |
| 129 .. _LGPL: http://www.gnu.org/copyleft/lesser.html | |
| 130 .. _HTSeq: http://www-huber.embl.de/users/anders/HTSeq/doc/index.html | |
| 131 </help> | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
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132 <citations> |
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57841366f112
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq commit 344140b8df53b8b7024618bb04594607a045c03a
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133 </citations> |
| 56 | 134 </tool> |