Mercurial > repos > fubar > htseq_bams_to_count_matrix

--- a/htseq_bams_to_count_matrix/htseqsams2mx.xml~	Thu Aug 08 08:11:22 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,145 +0,0 @@
-<tool id="htseqsams2mx" name="SAM/BAM to count matrix" version="0.2">
- <description>using HTSeq code</description>
-  <stdio>
-     <exit_code range="666"   level="warning"
-       description="Exit code 666 encountered" />
-  </stdio>
-  <requirements>
-      <requirement type="package" version="1.7.1">numpy</requirement>
-      <requirement type="package" version="2.4.11">freetype</requirement>
-      <requirement type="package" version="1.2.1">matplotliblite</requirement>
-      <requirement type="package" version="0.5.4p3">htseq</requirement>
-  </requirements>
-  <command interpreter="python">
-    htseqsams2mx.py -g "$gfffile" -o "$outfile" -m "$model" --id_attribute "$id_attr" --feature_type "$feature_type"
-    --samf "'$firstsamf','${firstsamf.name}'"
-    #if $secondsamf:
-    --samf "'$secondsamf','${secondsamf.name}'"
-    #end if
-    #if $thirdsamf:
-    --samf "'$thirdsamf','${thirdsamf.name}'"
-    #end if
-    #if $fourthsamf:
-    --samf "'$fourthsamf','${fourthsamf.name}'"
-    #end if
-    #for $s in $samfiles:
-      #if $s.samf:
-        --samf "'${s.samf}','${s.samf.name}'"
-      #end if
-    #end for
-  </command>
-  <inputs>
-    <param format="gtf" name="gfffile" type="data" label="Gene model (GFF) file to count reads over from your current history" size="100" />
-    <param name="mapqMin" label="Filter reads with mapq below than this value"
-    help="0 to count any mapping quality read. Otherwise only reads at or above specified mapq will be counted"
-    type="integer" value="5"/>
-    <param name="title" label="Name for this job's output file" type="text" size="80" value="bams to DGE count matrix"/>
-    <param name="stranded" value="false" type="boolean" label="Reads are stranded - use strand in counting" display="checkbox"
-      truevalue="yes" falsevalue="no" checked="no" help="Check this ONLY if you know your sequences are strand specific" />
-    <param name="model"  type="select" label="Model for counting reads over the supplied gene model- see HTSeq docs"
-        help="If in doubt, union is a reasonable default but intersection-strict avoids double counting over overlapping exons">
-        <option value="union" selected="true">union</option>
-        <option value="intersection-strict">intersection-strict</option>
-        <option value="intersection-nonempty">intersection-nonempty</option>
-    </param>
-    <param name="id_attr" type="select" label="GTF attribute to output as the name for each contig - see HTSeq docs"
-        help="If in doubt, use gene name or if you need the id in your GTF, gene id">
-        <option value="gene_name" selected="true">gene name</option>
-        <option value="gene_id">gene id</option>
-        <option value="transcript_id">transcript id</option>
-        <option value="transcript_name">transcript name</option>
-    </param>
-    <param name="feature_type" type="select" label="GTF feature type for counting reads over the supplied gene model- see HTSeq docs"
-        help="GTF feature type to count over - exon is a good choice with gene name as the contig to count over">
-        <option value="exon" selected="true">exon</option>
-        <option value="CDS">CDS</option>
-        <option value="UTR">UTR</option>
-        <option value="transcript">transcript</option>
-    </param>
-    <param name="firstsamf" type="data" label="First bam/sam file from your history to count reads overlapping gene model regions"
-          format="sam,bam" optional="false"/>
-    <param name="secondsamf" type="data" label="Another bam/sam file from your history to count reads overlapping gene model regions"
-          format="sam,bam" optional="false"/>
-    <param name="thirdsamf" type="data" label="Another bam/sam file from your history to count reads overlapping gene model regions"
-          format="sam,bam" optional="true"/>
-    <param name="fourthsamf" type="data" label="Another bam/sam file from your history to count reads overlapping gene model regions"
-          format="sam,bam" optional="true"/>
-    <repeat name="samfiles" title="Use this to add all needed additional bam/sam files from your history to count reads overlapping gene model regions">
-        <param name="samf" type="data" label="Additional bam/sam file from your history" format="sam,bam" size="100" optional="true"/>
-    </repeat>
-  </inputs>
-  <outputs>
-    <data format="tabular" name="outfile" label="${title}_htseqsams2mx.xls" />
-  </outputs>
-  <tests>
-    <test>
-      <param name="feature_type" value="exon" />
-      <param name="gfffile" value="rn4_chr20_100k.gtf" />
-      <param name="firstsamf" value="rn4chr20test1.bam" label="rn4chr20test1.bam"/>
-      <param name="secondsamf" value="rn4chr20test2.bam" label="rn4chr20test2.bam" />
-      <param name="id_attr" value="gene_name" />
-      <param name="model" value="union" />
-      <param name="stranded" value="no" />
-      <param name="title" value="htseqtest" />
-      <param name="mapqMin" value="0" />
-
-      <output name="outfile" file="htseqsams2mx_test1_out.xls" lines_diff="1"/>
-    </test>
-  </tests>
-  <help>
-
-**What this tool does**
-
-Counts reads in multiple sam/bam format mapped files and generates a matrix ideal for edgeR and other count based tools
-It uses HTSeq to count your sam reads over a gene model supplied as a GTF file
-The output is a tabular text (columnar - spreadsheet) file containing the
-count matrix for downstream processing. Each row contains the counts from each sample for each
-of the non-emtpy GTF input file contigs matching the GTF attribute choice above.
-You probably want to use gene level GTF output attribute and count reads that overlap
-GTF exons for RNA-seq. Or you can count over exons by using transcript level output names or ids. Etc.
-
-----
-
-**Author's plea on replicates**
-
-If you want to interpret the downstream p values in terms of rejecting or accepting the null hypothesis
-under random sampling with replacement from the universe of possible biological/experimental replicates from which your data was derived,
-which is what published p values are often assumed to do, then you need biological
-(or for cell culture material experimental) replicates.
-
-Using technical or no replicates means the downstream p values are not interpretable the way most people would assume
-they are - ie as the probability of obtaining a result as or more extreme as your experimental data
-in millions of experiments conducted using the same methods under the null hypothesis.
-
-There is no way around this and it is scientific fraud to ignore this issue and publish bogus p values derived from
-technical or no replicates without making the lack of biological or experimental error in the p value calculations
-clear to your readers so they can adjust their expectations. However, the buck stops here at higher level inference.
-If you have no replicates, you must not use this tool as the p values are uninterpretable. So there.
-
-See your stats 101 notes on the central limit theorem and test statistics for a refresher or talk to a
-statistician if this makes no sense please.
-
-**Attribution**
-
-This Galaxy tool relies on HTSeq_ from http://www-huber.embl.de/users/anders/HTSeq/doc/index.html
-for the tricky work of counting. That code includes the following attribution:
-
-## Written by Simon Anders (sanders@fs.tum.de), European Molecular Biology
-## Laboratory (EMBL). (c) 2010. Released under the terms of the GNU General
-## Public License v3. Part of the 'HTSeq' framework, version HTSeq-0.5.4p3
-
-It will be automatically installed if you use the toolshed as in general, you probably should.
-HTSeq_ must be installed with this tool if you install manually.
-
-Otherwise, all code and documentation comprising this tool including the requirement
-for more than one sample bam
-was written by Ross Lazarus and is
-licensed to you under the LGPL_ like other rgenetics artefacts
-
-Sorry, don't use so can't be buggered with read groups - contributions welcome - send code
-
-.. _LGPL: http://www.gnu.org/copyleft/lesser.html
-.. _HTSeq: http://www-huber.embl.de/users/anders/HTSeq/doc/index.html
-  </help>
-
-</tool>