htseq_count: htseq-count.xml annotate

annotate htseq-count.xml @ 23:b638ba24d9fb draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314

author	iuc
date	Tue, 20 Sep 2016 17:56:25 -0400
parents	dee20b55f360
children	0c01ed8d0e60

rev	line source
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	1 <tool id="htseq_count" name="htseq-count" version="0.6.1galaxy2">
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>
8 65c91537862c Updated to HTSeq 0.5.4p5, use tool shed repository dependencies lparsons parents: 7 diff changeset	5 <requirement type="package" version="0.1.19">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}" "${reference_fasta_filename}" &&
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	26 samtools faidx "${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
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	31 #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	32 #if $samfile.extension == 'bam':
21 19e80c732870 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 20 diff changeset	33 samtools sort -n "$samfile" "name_sorted_alignment" &&
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	34 #else
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	35 samtools view -Su -t "${reference_fasta_filename}.fai" "$samfile" \| samtools sort -n - "name_sorted_alignment" &&
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	36 #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	37 #end if
18 737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	38 htseq-count
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	39 --mode=$mode
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	40 --stranded=$stranded
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	41 --minaqual=$minaqual
21 19e80c732870 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 20 diff changeset	42 --type="$featuretype"
19e80c732870 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 20 diff changeset	43 --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	44 #if $samout_conditional.samout == "Yes":
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	45 --samout=$__new_file_path__/${samoutfile.id}_tmp
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	46 #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	47 #if $force_sort == "True":
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	48 --order=name
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	49 --format=bam
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	50 name_sorted_alignment.bam
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	51 #else
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	52 --order=pos
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	53 --format=$samfile.extension
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	54 $samfile
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	55 #end if
21 19e80c732870 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 20 diff changeset	56 "$gfffile"
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 \| awk '{if ($1 ~ "no_feature\|ambiguous\|too_low_aQual\|not_aligned\|alignment_not_unique") print $0 \| "cat 1>&2"; else print $0}' > $counts 2>$othercounts
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	58 #if $samout_conditional.samout == "Yes":
b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	59 && samtools view -Su -t "${reference_fasta_filename}.fai" "$__new_file_path__/${samoutfile.id}_tmp" \| samtools sort -o - sorted > "$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	60 #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	61 ]]>
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	62 </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	63
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	64 <inputs>
13 256d3114ce31 Fix input format string and change dependency owners to devteam lparsons parents: 12 diff changeset	65 <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	66 <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	67 <param name="mode" type="select" label="Mode" argument="(--mode)">
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	68 <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	69 <option value="union" selected="True">Union</option>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	70 <option value="intersection-strict">Intersection (strict)</option>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	71 <option value="intersection-nonempty">Intersection (nonempty)</option>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	72 </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	73 <param name="stranded" type="select" label="Stranded" argument="(--stranded)">
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	74 <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	75 <option value="yes" selected="True">Yes</option>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	76 <option value="no">No</option>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	77 <option value="reverse">Reverse</option>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	78 </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	79 <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	80 <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	81 </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	82 <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	83 <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	84 </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	85 <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	86 <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	87 </param>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	88 <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	89 <param name="samout" type="select" label="Additional BAM Output">
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	90 <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	91 <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	92 <option value="Yes">Output additional BAM file</option>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	93 </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	94 <when value="Yes">
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	95 <conditional name="reference_source">
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	96 <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	97 <option value="cached">Locally cached</option>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	98 <option value="history">History</option>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	99 </param>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	100 <when value="cached">
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	101 <param name="ref_file" type="select" label="Using reference genome">
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	102 <options from_data_table="sam_fa_indexes">
5 0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	103 <filter type="data_meta" key="dbkey" ref="samfile" column="1"/>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	104 </options>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	105 <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	106 </param>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	107 </when>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	108 <when value="history"> <!-- FIX ME!!!! -->
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	109 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	110 </when>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	111 </conditional>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	112 </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	113 <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	114 <!-- 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	115 </when>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	116 </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	117 <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	118 <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	119 </param>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	120 </inputs>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	121
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	122 <outputs>
5 0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	123 <data format="tabular" name="counts" metadata_source="samfile" label="${tool.name} on ${on_string}"/>
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	124 <data format="tabular" name="othercounts" metadata_source="samfile" label="${tool.name} on ${on_string} (no feature)"/>
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	125 <data format="bam" name="samoutfile" metadata_source="samfile" label="${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	126 <filter>samout_conditional['samout'] == "Yes"</filter>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	127 </data>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	128 </outputs>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	129
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	130 <tests>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	131 <test>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	132 <param name="samfile" value="htseq-test.sam" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	133 <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	134 <param name="samout" value="No" />
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	135 <output name="counts" file="htseq-test_counts.tsv" />
5 0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	136 <output name="othercounts" file="htseq-test_othercounts.tsv" />
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	137 </test>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	138 <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	139 <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	140 <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	141 <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	142 <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	143 <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	144 <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	145 </test>
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	146 <test>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	147 <param name="samfile" value="htseq-test.bam" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	148 <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	149 <param name="samout" value="No" />
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	150 <output name="counts" file="htseq-test_counts.tsv" />
5 0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	151 <output name="othercounts" file="htseq-test_othercounts.tsv" />
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	152 </test>
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	153 <test>
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	154 <param name="samfile" value="htseq-test-paired.bam" />
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	155 <param name="singlepaired" value="paired" />
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	156 <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	157 <param name="samout" value="No" />
5 0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	158 <output name="counts" file="htseq-test-paired_counts.tsv" />
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	159 <output name="othercounts" file="htseq-test-paired_othercounts.tsv" />
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	160 </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	161 <test>
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	162 <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	163 <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	164 <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	165 <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	166 <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	167 <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	168 <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	169 </test>
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	170
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	171 <!-- Seems to be an issue setting the $reference_fasta_filename variable during test
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	172 <test>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	173 <param name="samfile" value="htseq-test.sam" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	174 <param name="gfffile" value="htseq-test.gff" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	175 <param name="samout" value="True" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	176 <param name="reference_source_selector" value="history" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	177 <param name="ref_file" value="htseq-test_reference.fasta" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	178 <output name="counts" file="htseq-test_counts.tsv" />
5 0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	179 <output name="othercounts" file="htseq-test_othercounts.tsv" />
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	180 <output name="samoutfile" file="htseq-test_samout.bam" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	181 </test>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	182 -->
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	183 </tests>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	184
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	185 <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	186 <![CDATA[
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	187 Overview
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	188 --------
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	189
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	190 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	191 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	192 script that is part of the HTSeq python module. See
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	193 http://www-huber.embl.de/users/anders/HTSeq/doc/count.html for details.
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	194
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	195 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	196 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	197 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	198 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	199 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	200 list.
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	201
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	202
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	203 Overlap Modes
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	204 -------------
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	205
18 737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	206 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	207
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	208 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	209
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	210 The following figure illustrates the effect of these three modes:
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	211
14 c1db55359a86 Fix image path and size lparsons parents: 13 diff changeset	212 .. image:: count_modes.png
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	213
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	214
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	215 Strandedness
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	216 ------------
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	217
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	218 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	219
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	220
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	221 Output
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	222 ------
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	223
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	224 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	225
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	226 - 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	227
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	228 - 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	229
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	230 - 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	231
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	232 - not_aligned: reads in the SAM file without alignment
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	233
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	234 - 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	235
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	236
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	237 Options Summary
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	238 ---------------
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	239
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	240 Usage: htseq-count [options] sam_file gff_file
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	241
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	242 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	243 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	244 http://www-huber.embl.de/users/anders/HTSeq/doc/count.html for details.
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:
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	247 -h, --help show this help message and exit
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	248 -m MODE, --mode=MODE mode to handle reads overlapping more than one
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	249 feature(choices: union, intersection-strict,
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	250 intersection-nonempty; default: union)
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	251 -s STRANDED, --stranded=STRANDED
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	252 whether the data is from a strand-specific assay.
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	253 Specify 'yes', 'no', or 'reverse' (default: yes).
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	254 'reverse' means 'yes' with reversed strand
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	255 interpretation
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	256 -a MINAQUAL, --minaqual=MINAQUAL
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	257 skip all reads with alignment quality lower than the
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	258 given minimum value (default: 0)
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	259 -t FEATURETYPE, --type=FEATURETYPE
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	260 feature type (3rd column in GFF file) to be used, all
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	261 features of other type are ignored (default, suitable
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	262 for Ensembl GTF files: exon)
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	263 -i IDATTR, --idattr=IDATTR
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	264 GFF attribute to be used as feature ID (default,
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	265 suitable for Ensembl GTF files: gene_id)
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	266 -o SAMOUT, --samout=SAMOUT
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	267 write out all SAM alignment records into an output SAM
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	268 file called SAMOUT, annotating each line with its
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	269 feature assignment (as an optional field with tag
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	270 'XF')
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	271 -q, --quiet suppress progress report and warnings
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	272
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	273 Written by Simon Anders (sanders@fs.tum.de), European Molecular Biology
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	274 Laboratory (EMBL). (c) 2010. Released under the terms of the GNU General
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	275 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	276 ]]>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	277 </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	278
18 737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	279 <citations>
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	280 <citation type="bibtex">
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	281 @article{anders_htseqpython_2015,
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	282 title = {{HTSeq}—a {Python} framework to work with high-throughput sequencing data},
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	283 volume = {31},
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	284 issn = {1367-4803, 1460-2059},
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	285 url = {http://bioinformatics.oxfordjournals.org/content/31/2/166},
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	286 doi = {10.1093/bioinformatics/btu638},
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	287 abstract = {Motivation: A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard workflows, custom scripts are needed.
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	288 Results: We present HTSeq, a Python library to facilitate the rapid development of such scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data, such as genomic coordinates, sequences, sequencing reads, alignments, gene model information and variant calls, and provides data structures that allow for querying via genomic coordinates. We also present htseq-count, a tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes.
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	289 Availability and implementation: HTSeq is released as an open-source software under the GNU General Public Licence and available from http://www-huber.embl.de/HTSeq or from the Python Package Index at https://pypi.python.org/pypi/HTSeq.
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	290 Contact: sanders\{at\}fs.tum.de},
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	291 language = {en},
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	292 number = {2},
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	293 urldate = {2015-04-21},
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	294 journal = {Bioinformatics},
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	295 author = {Anders, Simon and Pyl, Paul Theodor and Huber, Wolfgang},
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	296 month = jan,
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	297 year = {2015},
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	298 pmid = {25260700},
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	299 pages = {166--169},
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	300 }
18 737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	301 }
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	302 </citation>
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	303 </citations>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	304 </tool>

Mercurial > repos > lparsons > htseq_count

annotate htseq-count.xml @ 23:b638ba24d9fb draft