htseq_count: htseq-count.xml annotate

annotate htseq-count.xml @ 25:88cea300225a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit da411ad3afa5b8fb7d28fdb1b13a777854e87212

author	iuc
date	Tue, 17 Jan 2017 09:26:25 -0500
parents	0c01ed8d0e60
children	d8c5761a8ba7

rev	line source
25 88cea300225a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit da411ad3afa5b8fb7d28fdb1b13a777854e87212 iuc parents: 24 diff changeset	1 <tool id="htseq_count" name="htseq-count" version="0.6.1galaxy3" profile="16.04">
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	2 <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	3 <requirements>
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	4 <requirement type="package" version="0.6.1.post1">htseq</requirement>
25 88cea300225a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit da411ad3afa5b8fb7d28fdb1b13a777854e87212 iuc parents: 24 diff changeset	5 <requirement type="package" version="1.3.1">samtools</requirement>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	6 </requirements>
18 737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	7
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	8 <stdio>
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	9 <exit_code range="1:" level="fatal" description="Unknown error occurred" />
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	10 <regex match="htseq-count: (command ){0,1}not found" source="stderr" level="fatal" description="The HTSeq python package is not properly installed, contact Galaxy administrators" />
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	11 <regex match="samtools: (command ){0,1}not found" source="stderr" level="fatal" description="The samtools package is not properly installed, contact Galaxy administrators" />
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	12 <regex match="Error: Feature (.+) does not contain a '(.+)' attribute" source="both" level="fatal" description="Error parsing the GFF file, at least one feature of the specified 'Feature type' does not have a value for the specified 'ID Attribute'" />
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	13 <regex match="Error occured in line (\d+) of file" source="stderr" level="fatal" description="Unknown error parsing the GFF file" />
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	14 <regex match="Error" source="stderr" level="fatal" description="Unknown error occured" />
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	15 <regex match="Warning: Read (.+) claims to have an aligned mate which could not be found. $Is the SAM file properly sorted\?$" source="stderr" level="warning" description="PAIRED DATA MISSING OR NOT PROPERLY SORTED. Try reruning and selecting the option to 'Force sorting of SAM/BAM file by NAME'. See stderr output of this dataset for more information." />
18 737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	16 </stdio>
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	17
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	18 <version_command>htseq-count -h \| grep version \| sed 's/^$.$$version .*$\./\2/'</version_command>
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	19
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	20 <command><![CDATA[
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	21 ##set up input files
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	22 #set $reference_fasta_filename = "localref.fa"
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	23 #if $samout_conditional.samout == "Yes":
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	24 #if str( $samout_conditional.reference_source.reference_source_selector ) == "history":
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	25 ln -s "${samout_conditional.reference_source.ref_file}" "${reference_fasta_filename}" &&
25 88cea300225a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit da411ad3afa5b8fb7d28fdb1b13a777854e87212 iuc parents: 24 diff changeset	26 samtools faidx '${reference_fasta_filename}' 2>&1 \|\| echo "Error running samtools faidx for htseq-count" >&2 &&
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	27 #else:
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	28 #set $reference_fasta_filename = str( $samout_conditional.reference_source.ref_file.fields.path )
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	29 #end if
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	30 #end if
25 88cea300225a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit da411ad3afa5b8fb7d28fdb1b13a777854e87212 iuc parents: 24 diff changeset	31
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	32 #if $force_sort == "True":
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	33 #if $samfile.extension == 'bam':
25 88cea300225a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit da411ad3afa5b8fb7d28fdb1b13a777854e87212 iuc parents: 24 diff changeset	34 samtools sort -n -o 'name_sorted_alignment.bam' '$samfile' &&
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	35 #else
25 88cea300225a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit da411ad3afa5b8fb7d28fdb1b13a777854e87212 iuc parents: 24 diff changeset	36 samtools view -Su -t '${reference_fasta_filename}.fai' '$samfile' \| samtools sort -n -o 'name_sorted_alignment.bam' - &&
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	37 #end if
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	38 #end if
25 88cea300225a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit da411ad3afa5b8fb7d28fdb1b13a777854e87212 iuc parents: 24 diff changeset	39
18 737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	40 htseq-count
24 0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	41 --mode=$mode
0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	42 --stranded=$stranded
0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	43 --minaqual=$minaqual
25 88cea300225a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit da411ad3afa5b8fb7d28fdb1b13a777854e87212 iuc parents: 24 diff changeset	44 --type='$featuretype'
88cea300225a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit da411ad3afa5b8fb7d28fdb1b13a777854e87212 iuc parents: 24 diff changeset	45 --idattr='$idattr'
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	46 #if $samout_conditional.samout == "Yes":
24 0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	47 --samout='$__new_file_path__/${samoutfile.id}_tmp'
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	48 #end if
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	49 #if $force_sort == "True":
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	50 --order=name
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	51 --format=bam
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	52 name_sorted_alignment.bam
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	53 #else
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	54 --order=pos
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	55 --format=$samfile.extension
24 0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	56 '$samfile'
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	57 #end if
25 88cea300225a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit da411ad3afa5b8fb7d28fdb1b13a777854e87212 iuc parents: 24 diff changeset	58
24 0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	59 "$gfffile" \| awk '{if ($1 ~ "no_feature\|ambiguous\|too_low_aQual\|not_aligned\|alignment_not_unique") print $0 \| "cat 1>&2"; else print $0}'
0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	60 > '$counts'
0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	61 2> '$othercounts'
25 88cea300225a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit da411ad3afa5b8fb7d28fdb1b13a777854e87212 iuc parents: 24 diff changeset	62
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	63 #if $samout_conditional.samout == "Yes":
24 0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	64 && samtools view -Su
25 88cea300225a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit da411ad3afa5b8fb7d28fdb1b13a777854e87212 iuc parents: 24 diff changeset	65 -t '${reference_fasta_filename}.fai'
88cea300225a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit da411ad3afa5b8fb7d28fdb1b13a777854e87212 iuc parents: 24 diff changeset	66 '$__new_file_path__/${samoutfile.id}_tmp'
88cea300225a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit da411ad3afa5b8fb7d28fdb1b13a777854e87212 iuc parents: 24 diff changeset	67 \| samtools sort -o '$samoutfile' -
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	68 #end if
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	69 ]]>
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	70 </command>
18 737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	71
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	72 <inputs>
13 256d3114ce31 Fix input format string and change dependency owners to devteam lparsons parents: 12 diff changeset	73 <param format="sam,bam" name="samfile" type="data" label="Aligned SAM/BAM File"/>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	74 <param format="gff" name="gfffile" type="data" label="GFF File"/>
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	75 <param name="mode" type="select" label="Mode" argument="(--mode)">
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	76 <help>Mode to handle reads overlapping more than one feature.</help>
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	77 <option value="union" selected="True">Union</option>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	78 <option value="intersection-strict">Intersection (strict)</option>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	79 <option value="intersection-nonempty">Intersection (nonempty)</option>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	80 </param>
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	81 <param name="stranded" type="select" label="Stranded" argument="(--stranded)">
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	82 <help>Specify whether the data is from a strand-specific assay. 'Reverse' means yes with reversed strand interpretation.</help>
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	83 <option value="yes" selected="True">Yes</option>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	84 <option value="no">No</option>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	85 <option value="reverse">Reverse</option>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	86 </param>
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	87 <param name="minaqual" type="integer" value="10" label="Minimum alignment quality" argument="--minaqual">
b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	88 <help>Skip all reads with alignment quality lower than the given minimum value.</help>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	89 </param>
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	90 <param name="featuretype" type="text" value="exon" label="Feature type" argument="--type">
b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	91 <help>Feature type (3rd column in GFF file) to be used. All features of other types are ignored. The default, suitable for RNA-Seq and Ensembl GTF files, is exon.</help>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	92 </param>
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	93 <param name="idattr" type="text" value="gene_id" label="ID Attribute" argument="--idattr">
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	94 <help>GFF attribute to be used as feature ID. Several GFF lines with the same feature ID will be considered as parts of the same feature. The feature ID is used to identity the counts in the output table. All features of the specified type MUST have a value for this attribute. The default, suitable for RNA-Seq and Ensembl GTF files, is gene_id.</help>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	95 </param>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	96 <conditional name="samout_conditional">
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	97 <param name="samout" type="select" label="Additional BAM Output">
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	98 <help>Write out all SAM alignment records into an output BAM file, annotating each line with its assignment to a feature or a special counter (as an optional field with tag ‘XF’).</help>
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	99 <option value="No" selected="True">Do not output additional BAM file</option>
b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	100 <option value="Yes">Output additional BAM file</option>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	101 </param>
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	102 <when value="Yes">
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	103 <conditional name="reference_source">
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	104 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	105 <option value="cached">Locally cached</option>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	106 <option value="history">History</option>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	107 </param>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	108 <when value="cached">
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	109 <param name="ref_file" type="select" label="Using reference genome">
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	110 <options from_data_table="sam_fa_indexes">
5 0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	111 <filter type="data_meta" key="dbkey" ref="samfile" column="1"/>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	112 </options>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	113 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	114 </param>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	115 </when>
24 0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	116 <when value="history">
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	117 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	118 </when>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	119 </conditional>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	120 </when>
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	121 <when value="No">
b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	122 <!-- Do nothing -->
b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	123 </when>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	124 </conditional>
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	125 <param name="force_sort" type="boolean" value="False" truevalue="True" falsevalue="False" label="Force sorting of SAM/BAM file by NAME">
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	126 <help>This option can be used for for paired-end data that has many unmapped mates. Use this if you get the warning about paired end data missing or not being properly sorted.</help>
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	127 </param>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	128 </inputs>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	129
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	130 <outputs>
24 0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	131 <data format="tabular" name="counts" metadata_source="samfile" label="${tool.name} on ${on_string}">
0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	132 <actions>
0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	133 <action name="column_names" type="metadata" default="Geneid,${samfile.name}" />
0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	134 </actions>
0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	135 </data>
5 0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	136 <data format="tabular" name="othercounts" metadata_source="samfile" label="${tool.name} on ${on_string} (no feature)"/>
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	137 <data format="bam" name="samoutfile" metadata_source="samfile" label="${tool.name} on ${on_string} (BAM)">
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	138 <filter>samout_conditional['samout'] == "Yes"</filter>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	139 </data>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	140 </outputs>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	141
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	142 <tests>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	143 <test>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	144 <param name="samfile" value="htseq-test.sam" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	145 <param name="gfffile" value="htseq-test.gff" />
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	146 <param name="samout" value="No" />
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	147 <output name="counts" file="htseq-test_counts.tsv" />
5 0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	148 <output name="othercounts" file="htseq-test_othercounts.tsv" />
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	149 </test>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	150 <test>
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	151 <param name="samfile" value="htseq-test.sam" />
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	152 <param name="gfffile" value="htseq-test.gff" />
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	153 <param name="samout" value="No" />
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	154 <param name="force_sort" value="True" />
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	155 <output name="counts" file="htseq-test_counts.tsv" />
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	156 <output name="othercounts" file="htseq-test_othercounts.tsv" />
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	157 </test>
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	158 <test>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	159 <param name="samfile" value="htseq-test.bam" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	160 <param name="gfffile" value="htseq-test.gff" />
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	161 <param name="samout" value="No" />
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	162 <output name="counts" file="htseq-test_counts.tsv" />
5 0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	163 <output name="othercounts" file="htseq-test_othercounts.tsv" />
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	164 </test>
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	165 <test>
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	166 <param name="samfile" value="htseq-test-paired.bam" />
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	167 <param name="singlepaired" value="paired" />
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	168 <param name="gfffile" value="htseq-test.gff" />
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	169 <param name="samout" value="No" />
5 0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	170 <output name="counts" file="htseq-test-paired_counts.tsv" />
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	171 <output name="othercounts" file="htseq-test-paired_othercounts.tsv" />
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	172 </test>
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	173 <test>
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	174 <param name="samfile" value="htseq-test-paired.bam" />
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	175 <param name="singlepaired" value="paired" />
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	176 <param name="gfffile" value="htseq-test.gff" />
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	177 <param name="samout" value="No" />
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	178 <param name="force_sort" value="True" />
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	179 <output name="counts" file="htseq-test-paired_counts.tsv" />
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	180 <output name="othercounts" file="htseq-test-paired_othercounts.tsv" />
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	181 </test>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	182 <test>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	183 <param name="samfile" value="htseq-test.sam" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	184 <param name="gfffile" value="htseq-test.gff" />
24 0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	185 <param name="samout" value="Yes" />
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	186 <param name="reference_source_selector" value="history" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	187 <param name="ref_file" value="htseq-test_reference.fasta" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	188 <output name="counts" file="htseq-test_counts.tsv" />
5 0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	189 <output name="othercounts" file="htseq-test_othercounts.tsv" />
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	190 <output name="samoutfile" file="htseq-test_samout.bam" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	191 </test>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	192 </tests>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	193
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	194 <help>
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	195 <![CDATA[
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	196 Overview
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	197 --------
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	198
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	199 This tool takes an alignment file in SAM or BAM format and feature file in GFF format
18 737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	200 and calculates the number of reads mapping to each feature. It uses the htseq-count
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	201 script that is part of the HTSeq python module. See
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	202 http://www-huber.embl.de/users/anders/HTSeq/doc/count.html for details.
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	203
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	204 A feature is an interval (i.e., a range of positions) on a chromosome or a union of
18 737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	205 such intervals. In the case of RNA-Seq, the features are typically genes, where
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	206 each gene is considered here as the union of all its exons. One may also consider
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	207 each exon as a feature, e.g., in order to check for alternative splicing. For
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	208 comparative ChIP-Seq, the features might be binding regions from a pre-determined
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	209 list.
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	210
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	211
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	212 Overlap Modes
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	213 -------------
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	214
18 737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	215 Special care must be taken to decide how to deal with reads that overlap more than one feature.
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	216
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	217 The htseq-count script allows to choose between three modes: union, intersection-strict, and intersection-nonempty.
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	218
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	219 The following figure illustrates the effect of these three modes:
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	220
14 c1db55359a86 Fix image path and size lparsons parents: 13 diff changeset	221 .. image:: count_modes.png
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	222
6 08a11d1eaec6 Updated HTSEQ package to version 0.5.4p1, attempted to fix galaxy install where lib64 directory does not exist lparsons parents: 5 diff changeset	223
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	224 Strandedness
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	225 ------------
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	226
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	227 Important: The default for strandedness is yes. If your RNA-Seq data has not been made with a strand-specific protocol, this causes half of the reads to be lost. Hence, make sure to set the option Stranded to 'No' unless you have strand-specific data!
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	228
6 08a11d1eaec6 Updated HTSEQ package to version 0.5.4p1, attempted to fix galaxy install where lib64 directory does not exist lparsons parents: 5 diff changeset	229
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	230 Output
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	231 ------
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	232
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	233 The script outputs a table with counts for each feature, followed by the special counters, which count reads that were not counted for any feature for various reasons, namely
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	234
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	235 - no_feature: reads which could not be assigned to any feature (set S as described above was empty).
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	236
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	237 - ambiguous: reads which could have been assigned to more than one feature and hence were not counted for any of these (set S had mroe than one element).
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	238
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	239 - too_low_aQual: reads which were not counted due to the -a option, see below
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	240
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	241 - not_aligned: reads in the SAM file without alignment
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	242
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	243 - alignment_not_unique: reads with more than one reported alignment. These reads are recognized from the NH optional SAM field tag. (If the aligner does not set this field, multiply aligned reads will be counted multiple times.)
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	244
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	245
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	246 Options Summary
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	247 ---------------
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	248
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	249 Usage: htseq-count [options] sam_file gff_file
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	250
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	251 This script takes an alignment file in SAM format and a feature file in GFF
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	252 format and calculates for each feature the number of reads mapping to it. See
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	253 http://www-huber.embl.de/users/anders/HTSeq/doc/count.html for details.
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	254
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	255 Options:
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	256 -h, --help show this help message and exit
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	257 -m MODE, --mode=MODE mode to handle reads overlapping more than one
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	258 feature(choices: union, intersection-strict,
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	259 intersection-nonempty; default: union)
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	260 -s STRANDED, --stranded=STRANDED
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	261 whether the data is from a strand-specific assay.
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	262 Specify 'yes', 'no', or 'reverse' (default: yes).
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	263 'reverse' means 'yes' with reversed strand
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	264 interpretation
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	265 -a MINAQUAL, --minaqual=MINAQUAL
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	266 skip all reads with alignment quality lower than the
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	267 given minimum value (default: 0)
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	268 -t FEATURETYPE, --type=FEATURETYPE
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	269 feature type (3rd column in GFF file) to be used, all
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	270 features of other type are ignored (default, suitable
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	271 for Ensembl GTF files: exon)
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	272 -i IDATTR, --idattr=IDATTR
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	273 GFF attribute to be used as feature ID (default,
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	274 suitable for Ensembl GTF files: gene_id)
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	275 -o SAMOUT, --samout=SAMOUT
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	276 write out all SAM alignment records into an output SAM
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	277 file called SAMOUT, annotating each line with its
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	278 feature assignment (as an optional field with tag
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	279 'XF')
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	280 -q, --quiet suppress progress report and warnings
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	281
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	282 Written by Simon Anders (sanders@fs.tum.de), European Molecular Biology
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	283 Laboratory (EMBL). (c) 2010. Released under the terms of the GNU General
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	284 Public License v3. Part of the 'HTSeq' framework.
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	285 ]]>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	286 </help>
18 737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	287 <citations>
24 0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	288 <citation type="doi">10.1093/bioinformatics/btu638</citation>
18 737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	289 </citations>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	290 </tool>

Mercurial > repos > lparsons > htseq_count

annotate htseq-count.xml @ 25:88cea300225a draft