htseq_count: htseq-count.xml annotate

annotate htseq-count.xml @ 21:19e80c732870 draft

planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23

author	lparsons
date	Mon, 22 Jun 2015 16:57:03 -0400
parents	6b61ba6dd9e2
children	dee20b55f360

rev	line source
20 6b61ba6dd9e2 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 0ad2d616320c8741d762750d19ab3ea812516007 lparsons parents: 19 diff changeset	1 <tool id="htseq_count" name="htseq-count" version="0.6.1galaxy1">
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>
12 c86659f03e98 Uploaded test version lparsons parents: 8 diff changeset	4 <requirement type="package" version="0.6.1">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>
16 c9bacde2356c Added missing dependency lparsons parents: 14 diff changeset	6 <requirement type="package" version="0.7.7">pysam</requirement>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	7 </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	8
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	9 <stdio>
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	10 <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	11 <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	12 <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	13 <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	14 <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	15 <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	16 <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	17 </stdio>
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	18
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	19 <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	20
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	21 <command><![CDATA[
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	22 ##set up input files
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	23 #set $reference_fasta_filename = "localref.fa"
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	24 #if $samout_conditional.samout:
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	25 #if str( $samout_conditional.reference_source.reference_source_selector ) == "history":
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	26 ln -s "${samout_conditional.reference_source.ref_file}" "${reference_fasta_filename}" &&
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	27 samtools faidx "${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	28 #else:
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	29 #set $reference_fasta_filename = str( $samout_conditional.reference_source.ref_file.fields.path )
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	30 #end if
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	31 #end if
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 $force_sort:
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 $samfile.extension == 'bam':
21 19e80c732870 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 20 diff changeset	34 samtools sort -n "$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	35 #else
21 19e80c732870 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 20 diff changeset	36 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	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
18 737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	39 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	40 --mode=$mode
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	41 --stranded=$stranded
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	42 --minaqual=$minaqual
21 19e80c732870 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 20 diff changeset	43 --type="$featuretype"
19e80c732870 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 20 diff changeset	44 --idattr="$idattr"
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	45 #if $samout_conditional.samout:
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	46 --samout=$__new_file_path__/${samoutfile.id}_tmp
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	47 #end if
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 #if $force_sort:
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	49 --order=name
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	50 --format=bam
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	51 name_sorted_alignment.bam
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	52 #else
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	53 --order=pos
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	54 --format=$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	55 $samfile
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	56 #end if
21 19e80c732870 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 20 diff changeset	57 "$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	58 \| 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
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	59 #if $samout_conditional.samout:
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 && samtools view -Su -t ${reference_fasta_filename}.fai $__new_file_path__/${samoutfile.id}_tmp \| samtools sort -o - sorted > $samoutfile
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	61 #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	62 ]]>
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	63 </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	64
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	65 <inputs>
13 256d3114ce31 Fix input format string and change dependency owners to devteam lparsons parents: 12 diff changeset	66 <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	67 <param format="gff" name="gfffile" type="data" label="GFF File"/>
21 19e80c732870 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 20 diff changeset	68 <param name="mode" type="select" label="Mode" help="(--mode)">
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	69 <help>Mode to handle reads overlapping more than one feature.</help>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	70 <option value="union" selected="true">Union</option>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	71 <option value="intersection-strict">Intersection (strict)</option>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	72 <option value="intersection-nonempty">Intersection (nonempty)</option>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	73 </param>
21 19e80c732870 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 20 diff changeset	74 <param name="stranded" type="select" label="Stranded" help="(--stranded)">
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	75 <help>Specify whether the data is from a strand-specific assay. 'Reverse' means yes with reversed strand interpretation.</help>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	76 <option value="yes" selected="true">Yes</option>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	77 <option value="no">No</option>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	78 <option value="reverse">Reverse</option>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	79 </param>
12 c86659f03e98 Uploaded test version lparsons parents: 8 diff changeset	80 <param name="minaqual" type="integer" value="10" label="Minimum alignment quality">
21 19e80c732870 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 20 diff changeset	81 <help>Skip all reads with alignment quality lower than the given minimum value. (-minaqual)</help>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	82 </param>
5 0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	83 <param name="featuretype" type="text" value="exon" label="Feature type">
21 19e80c732870 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 20 diff changeset	84 <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. (--type)</help>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	85 </param>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	86 <param name="idattr" type="text" value="gene_id" label="ID Attribute">
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	87 <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	88 </param>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	89 <conditional name="samout_conditional">
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	90 <param name="samout" type="boolean" value="False" truevalue="True" falsevalue="False" label="Additional BAM Output">
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	91 <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>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	92 </param>
18 737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	93 <when value="True">
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	94 <conditional name="reference_source">
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	95 <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	96 <option value="cached">Locally cached</option>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	97 <option value="history">History</option>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	98 </param>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	99 <when value="cached">
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	100 <param name="ref_file" type="select" label="Using reference genome">
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	101 <options from_data_table="sam_fa_indexes">
5 0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	102 <filter type="data_meta" key="dbkey" ref="samfile" column="1"/>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	103 </options>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	104 <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	105 </param>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	106 </when>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	107 <when value="history"> <!-- FIX ME!!!! -->
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	108 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	109 </when>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	110 </conditional>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	111 </when>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	112 </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	113 <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	114 <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	115 </param>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	116 </inputs>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	117
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	118 <outputs>
5 0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	119 <data format="tabular" name="counts" metadata_source="samfile" label="${tool.name} on ${on_string}"/>
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	120 <data format="tabular" name="othercounts" metadata_source="samfile" label="${tool.name} on ${on_string} (no feature)"/>
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	121 <data format="bam" name="samoutfile" metadata_source="samfile" label="${tool.name} on ${on_string} (BAM)">
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	122 <filter>samout_conditional['samout']</filter>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	123 </data>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	124 </outputs>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	125
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	126 <tests>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	127 <test>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	128 <param name="samfile" value="htseq-test.sam" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	129 <param name="gfffile" value="htseq-test.gff" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	130 <param name="samout" value="False" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	131 <output name="counts" file="htseq-test_counts.tsv" />
5 0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	132 <output name="othercounts" file="htseq-test_othercounts.tsv" />
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	133 </test>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	134 <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	135 <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	136 <param name="gfffile" value="htseq-test.gff" />
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	137 <param name="samout" value="False" />
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	138 <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	139 <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	140 <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	141 </test>
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	142 <test>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	143 <param name="samfile" value="htseq-test.bam" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	144 <param name="gfffile" value="htseq-test.gff" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	145 <param name="samout" value="False" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	146 <output name="counts" file="htseq-test_counts.tsv" />
5 0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	147 <output name="othercounts" file="htseq-test_othercounts.tsv" />
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	148 </test>
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	149 <test>
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	150 <param name="samfile" value="htseq-test-paired.bam" />
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	151 <param name="singlepaired" value="paired" />
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	152 <param name="gfffile" value="htseq-test.gff" />
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	153 <param name="samout" value="False" />
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	154 <output name="counts" file="htseq-test-paired_counts.tsv" />
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	155 <output name="othercounts" file="htseq-test-paired_othercounts.tsv" />
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	156 </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	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 <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	159 <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	160 <param name="gfffile" value="htseq-test.gff" />
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	161 <param name="samout" value="False" />
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="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	163 <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	164 <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	165 </test>
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	166
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	167 <!-- Seems to be an issue setting the $reference_fasta_filename variable during test
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	168 <test>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	169 <param name="samfile" value="htseq-test.sam" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	170 <param name="gfffile" value="htseq-test.gff" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	171 <param name="samout" value="True" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	172 <param name="reference_source_selector" value="history" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	173 <param name="ref_file" value="htseq-test_reference.fasta" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	174 <output name="counts" file="htseq-test_counts.tsv" />
5 0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	175 <output name="othercounts" file="htseq-test_othercounts.tsv" />
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	176 <output name="samoutfile" file="htseq-test_samout.bam" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	177 </test>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	178 -->
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	179 </tests>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	180
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	181 <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	182 <![CDATA[
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	183 Overview
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	184 --------
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	185
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	186 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	187 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	188 script that is part of the HTSeq python module. See
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	189 http://www-huber.embl.de/users/anders/HTSeq/doc/count.html for details.
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	190
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	191 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	192 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	193 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	194 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	195 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	196 list.
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 Overlap Modes
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	200 -------------
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	201
18 737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	202 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	203
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	204 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	205
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	206 The following figure illustrates the effect of these three modes:
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	207
14 c1db55359a86 Fix image path and size lparsons parents: 13 diff changeset	208 .. image:: count_modes.png
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	209
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	210
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	211 Strandedness
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	212 ------------
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	213
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	214 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	215
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	216
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	217 Output
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	218 ------
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	219
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	220 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	221
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	222 - 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	223
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	224 - 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	225
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	226 - 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	227
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	228 - not_aligned: reads in the SAM file without alignment
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	229
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	230 - 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	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 Options Summary
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	234 ---------------
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	235
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	236 Usage: htseq-count [options] sam_file gff_file
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	237
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	238 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	239 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	240 http://www-huber.embl.de/users/anders/HTSeq/doc/count.html for details.
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	241
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	242 Options:
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	243 -h, --help show this help message and exit
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	244 -m MODE, --mode=MODE mode to handle reads overlapping more than one
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	245 feature(choices: union, intersection-strict,
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	246 intersection-nonempty; default: union)
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	247 -s STRANDED, --stranded=STRANDED
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	248 whether the data is from a strand-specific assay.
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	249 Specify 'yes', 'no', or 'reverse' (default: yes).
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	250 'reverse' means 'yes' with reversed strand
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	251 interpretation
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	252 -a MINAQUAL, --minaqual=MINAQUAL
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	253 skip all reads with alignment quality lower than the
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	254 given minimum value (default: 0)
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	255 -t FEATURETYPE, --type=FEATURETYPE
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	256 feature type (3rd column in GFF file) to be used, all
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	257 features of other type are ignored (default, suitable
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	258 for Ensembl GTF files: exon)
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	259 -i IDATTR, --idattr=IDATTR
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	260 GFF attribute to be used as feature ID (default,
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	261 suitable for Ensembl GTF files: gene_id)
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	262 -o SAMOUT, --samout=SAMOUT
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	263 write out all SAM alignment records into an output SAM
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	264 file called SAMOUT, annotating each line with its
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	265 feature assignment (as an optional field with tag
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	266 'XF')
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	267 -q, --quiet suppress progress report and warnings
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	268
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	269 Written by Simon Anders (sanders@fs.tum.de), European Molecular Biology
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	270 Laboratory (EMBL). (c) 2010. Released under the terms of the GNU General
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	271 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	272 ]]>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	273 </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	274
18 737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	275 <citations>
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	276 <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	277 @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	278 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	279 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	280 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	281 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	282 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	283 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	284 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	285 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	286 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	287 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	288 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	289 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	290 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	291 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	292 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	293 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	294 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	295 pages = {166--169},
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	296 file = {Full Text PDF:/Users/lparsons/Library/Application Support/Firefox/Profiles/thd2t4je.default/zotero/storage/84XQB8V6/Anders et al. - 2015 - HTSeq—a Python framework to work with high-through.pdf:application/pdf;Snapshot:/Users/lparsons/Library/Application Support/Firefox/Profiles/thd2t4je.default/zotero/storage/JKUAUCKB/166.html:text/html}
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	297 }
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	298 </citation>
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	299 </citations>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	300 </tool>

Mercurial > repos > lparsons > htseq_count

annotate htseq-count.xml @ 21:19e80c732870 draft