htseq_count: htseq-count.xml annotate

annotate htseq-count.xml @ 20:3b3601a2a7c7 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 17:01:05 -0400
parents	d5edaf8dc974
children	a6dcb86af112

rev	line source
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	1 <tool id="htseq_count" name="htseq-count" version="0.6.1galaxy1">
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	2 <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	3 <requirements>
16 227f9d3f0e32 Updated HTSeq package to version 0.6.1, fixed input format string, updated dependency definitions lparsons parents: 15 diff changeset	4 <requirement type="package" version="0.6.1">htseq</requirement>
13 30bb8acb77a4 Updated to v0.5.4p5, use repository dependencies. lparsons parents: 12 diff changeset	5 <requirement type="package" version="0.1.19">samtools</requirement>
17 d5edaf8dc974 Fixed test output, added missing pysam dependency lparsons parents: 16 diff changeset	6 <requirement type="package" version="0.7.7">pysam</requirement>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	7 </requirements>
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	8
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	9 <stdio>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	10 <exit_code range="1:" level="fatal" description="Unknown error occurred" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 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" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 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" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 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'" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 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" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	15 <regex match="Error" source="stderr" level="fatal" description="Unknown error occured" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 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." />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	17 </stdio>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	18
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	19 <version_command>htseq-count -h \| grep version \| sed 's/^$.$$version .*$\./\2/'</version_command>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	21 <command><![CDATA[
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	22 ##set up input files
3fdeebd7e710 Initial commit lparsons parents: diff changeset	23 #set $reference_fasta_filename = "localref.fa"
3fdeebd7e710 Initial commit lparsons parents: diff changeset	24 #if $samout_conditional.samout:
3fdeebd7e710 Initial commit lparsons parents: diff changeset	25 #if str( $samout_conditional.reference_source.reference_source_selector ) == "history":
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	26 ln -s "${samout_conditional.reference_source.ref_file}" "${reference_fasta_filename}" &&
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	27 samtools faidx "${reference_fasta_filename}" 2>&1 \|\| echo "Error running samtools faidx for htseq-count" >&2 &&
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	28 #else:
3fdeebd7e710 Initial commit lparsons parents: diff changeset	29 #set $reference_fasta_filename = str( $samout_conditional.reference_source.ref_file.fields.path )
3fdeebd7e710 Initial commit lparsons parents: diff changeset	30 #end if
3fdeebd7e710 Initial commit lparsons parents: diff changeset	31 #end if
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	32 #if $force_sort:
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	33 #if $samfile.extension == 'bam':
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	34 samtools sort -n "$samfile" "name_sorted_alignment" &&
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	35 #else
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	36 samtools view -Su -t ${reference_fasta_filename}.fai "$samfile" \| samtools sort -n - "name_sorted_alignment" &&
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	37 #end if
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	38 #end if
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	39 htseq-count
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	40 --mode=$mode
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	41 --stranded=$stranded
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	42 --minaqual=$minaqual
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	43 --type="$featuretype"
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	44 --idattr="$idattr"
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	45 #if $samout_conditional.samout:
3fdeebd7e710 Initial commit lparsons parents: diff changeset	46 --samout=$__new_file_path__/${samoutfile.id}_tmp
3fdeebd7e710 Initial commit lparsons parents: diff changeset	47 #end if
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	48 #if $force_sort:
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	49 --order=name
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	50 --format=bam
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	51 name_sorted_alignment.bam
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	52 #else
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	53 --order=pos
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	54 --format=$samfile.extension
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	55 $samfile
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	56 #end if
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	57 "$gfffile"
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 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 3fdeebd7e710 Initial commit lparsons parents: diff changeset	59 #if $samout_conditional.samout:
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	60 && samtools view -Su -t ${reference_fasta_filename}.fai $__new_file_path__/${samoutfile.id}_tmp \| samtools sort -o - sorted > $samoutfile
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	61 #end if
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	62 ]]>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	63 </command>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	64
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	65 <inputs>
16 227f9d3f0e32 Updated HTSeq package to version 0.6.1, fixed input format string, updated dependency definitions lparsons parents: 15 diff changeset	66 <param format="sam,bam" name="samfile" type="data" label="Aligned SAM/BAM File"/>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	67 <param format="gff" name="gfffile" type="data" label="GFF File"/>
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	68 <param name="mode" type="select" label="Mode" help="(--mode)">
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	69 <help>Mode to handle reads overlapping more than one feature.</help>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	70 <option value="union" selected="true">Union</option>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	71 <option value="intersection-strict">Intersection (strict)</option>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	72 <option value="intersection-nonempty">Intersection (nonempty)</option>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	73 </param>
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	74 <param name="stranded" type="select" label="Stranded" help="(--stranded)">
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	75 <help>Specify whether the data is from a strand-specific assay. 'Reverse' means yes with reversed strand interpretation.</help>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	76 <option value="yes" selected="true">Yes</option>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	77 <option value="no">No</option>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	78 <option value="reverse">Reverse</option>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	79 </param>
16 227f9d3f0e32 Updated HTSeq package to version 0.6.1, fixed input format string, updated dependency definitions lparsons parents: 15 diff changeset	80 <param name="minaqual" type="integer" value="10" label="Minimum alignment quality">
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	81 <help>Skip all reads with alignment quality lower than the given minimum value. (-minaqual)</help>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	82 </param>
6 2861eb44fbbf Fix issue with workflows (type->featuretype) and general error check Lance Parsons <lparsons@princeton.edu> parents: 5 diff changeset	83 <param name="featuretype" type="text" value="exon" label="Feature type">
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 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 3fdeebd7e710 Initial commit lparsons parents: diff changeset	85 </param>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	86 <param name="idattr" type="text" value="gene_id" label="ID Attribute">
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 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 3fdeebd7e710 Initial commit lparsons parents: diff changeset	88 </param>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	89 <conditional name="samout_conditional">
3fdeebd7e710 Initial commit lparsons parents: diff changeset	90 <param name="samout" type="boolean" value="False" truevalue="True" falsevalue="False" label="Additional BAM Output">
3fdeebd7e710 Initial commit lparsons 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>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	92 </param>
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	93 <when value="True">
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	94 <conditional name="reference_source">
3fdeebd7e710 Initial commit lparsons parents: diff changeset	95 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
3fdeebd7e710 Initial commit lparsons parents: diff changeset	96 <option value="cached">Locally cached</option>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	97 <option value="history">History</option>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	98 </param>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	99 <when value="cached">
3fdeebd7e710 Initial commit lparsons parents: diff changeset	100 <param name="ref_file" type="select" label="Using reference genome">
3fdeebd7e710 Initial commit lparsons parents: diff changeset	101 <options from_data_table="sam_fa_indexes">
9 971e20519fb8 Fix for dbkey column check when output additional bam is selected lparsons parents: 8 diff changeset	102 <filter type="data_meta" key="dbkey" ref="samfile" column="1"/>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	103 </options>
3fdeebd7e710 Initial commit lparsons 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"/>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	105 </param>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	106 </when>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	107 <when value="history"> <!-- FIX ME!!!! -->
3fdeebd7e710 Initial commit lparsons parents: diff changeset	108 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
3fdeebd7e710 Initial commit lparsons parents: diff changeset	109 </when>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	110 </conditional>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	111 </when>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	112 </conditional>
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	113 <param name="force_sort" type="boolean" value="False" truevalue="True" falsevalue="False" label="Force sorting of SAM/BAM file by NAME">
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 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>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	115 </param>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	116 </inputs>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	117
3fdeebd7e710 Initial commit lparsons parents: diff changeset	118 <outputs>
10 5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools) lparsons parents: 9 diff changeset	119 <data format="tabular" name="counts" metadata_source="samfile" label="${tool.name} on ${on_string}"/>
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools) lparsons parents: 9 diff changeset	120 <data format="tabular" name="othercounts" metadata_source="samfile" label="${tool.name} on ${on_string} (no feature)"/>
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools) lparsons parents: 9 diff changeset	121 <data format="bam" name="samoutfile" metadata_source="samfile" label="${tool.name} on ${on_string} (BAM)">
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	122 <filter>samout_conditional['samout']</filter>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	123 </data>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	124 </outputs>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	125
3fdeebd7e710 Initial commit lparsons parents: diff changeset	126 <tests>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	127 <test>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	128 <param name="samfile" value="htseq-test.sam" />
3fdeebd7e710 Initial commit lparsons parents: diff changeset	129 <param name="gfffile" value="htseq-test.gff" />
3fdeebd7e710 Initial commit lparsons parents: diff changeset	130 <param name="samout" value="False" />
3fdeebd7e710 Initial commit lparsons parents: diff changeset	131 <output name="counts" file="htseq-test_counts.tsv" />
3 f7a5b54a8d4f Split feature and non-feature counts, removed tool_dependencies.xml (for now) Lance Parsons <lparsons@princeton.edu> parents: 0 diff changeset	132 <output name="othercounts" file="htseq-test_othercounts.tsv" />
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	133 </test>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	134 <test>
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	135 <param name="samfile" value="htseq-test.sam" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	136 <param name="gfffile" value="htseq-test.gff" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	137 <param name="samout" value="False" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	138 <param name="force_sort" value="True" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	139 <output name="counts" file="htseq-test_counts.tsv" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	140 <output name="othercounts" file="htseq-test_othercounts.tsv" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	141 </test>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	142 <test>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	143 <param name="samfile" value="htseq-test.bam" />
3fdeebd7e710 Initial commit lparsons parents: diff changeset	144 <param name="gfffile" value="htseq-test.gff" />
3fdeebd7e710 Initial commit lparsons parents: diff changeset	145 <param name="samout" value="False" />
3fdeebd7e710 Initial commit lparsons parents: diff changeset	146 <output name="counts" file="htseq-test_counts.tsv" />
3 f7a5b54a8d4f Split feature and non-feature counts, removed tool_dependencies.xml (for now) Lance Parsons <lparsons@princeton.edu> parents: 0 diff changeset	147 <output name="othercounts" file="htseq-test_othercounts.tsv" />
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	148 </test>
10 5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools) lparsons parents: 9 diff changeset	149 <test>
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools) lparsons parents: 9 diff changeset	150 <param name="samfile" value="htseq-test-paired.bam" />
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools) lparsons parents: 9 diff changeset	151 <param name="singlepaired" value="paired" />
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools) lparsons parents: 9 diff changeset	152 <param name="gfffile" value="htseq-test.gff" />
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools) lparsons parents: 9 diff changeset	153 <param name="samout" value="False" />
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools) lparsons parents: 9 diff changeset	154 <output name="counts" file="htseq-test-paired_counts.tsv" />
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools) lparsons parents: 9 diff changeset	155 <output name="othercounts" file="htseq-test-paired_othercounts.tsv" />
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools) lparsons parents: 9 diff changeset	156 </test>
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	157 <test>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	158 <param name="samfile" value="htseq-test-paired.bam" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	159 <param name="singlepaired" value="paired" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	160 <param name="gfffile" value="htseq-test.gff" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	161 <param name="samout" value="False" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	162 <param name="force_sort" value="True" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	163 <output name="counts" file="htseq-test-paired_counts.tsv" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	164 <output name="othercounts" file="htseq-test-paired_othercounts.tsv" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	165 </test>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	166
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	167 <!-- Seems to be an issue setting the $reference_fasta_filename variable during test
3fdeebd7e710 Initial commit lparsons parents: diff changeset	168 <test>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	169 <param name="samfile" value="htseq-test.sam" />
3fdeebd7e710 Initial commit lparsons parents: diff changeset	170 <param name="gfffile" value="htseq-test.gff" />
3fdeebd7e710 Initial commit lparsons parents: diff changeset	171 <param name="samout" value="True" />
3fdeebd7e710 Initial commit lparsons parents: diff changeset	172 <param name="reference_source_selector" value="history" />
3fdeebd7e710 Initial commit lparsons parents: diff changeset	173 <param name="ref_file" value="htseq-test_reference.fasta" />
3fdeebd7e710 Initial commit lparsons parents: diff changeset	174 <output name="counts" file="htseq-test_counts.tsv" />
3 f7a5b54a8d4f Split feature and non-feature counts, removed tool_dependencies.xml (for now) Lance Parsons <lparsons@princeton.edu> parents: 0 diff changeset	175 <output name="othercounts" file="htseq-test_othercounts.tsv" />
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	176 <output name="samoutfile" file="htseq-test_samout.bam" />
3fdeebd7e710 Initial commit lparsons parents: diff changeset	177 </test>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	178 -->
3fdeebd7e710 Initial commit lparsons parents: diff changeset	179 </tests>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	180
3fdeebd7e710 Initial commit lparsons parents: diff changeset	181 <help>
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	182 <![CDATA[
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	183 Overview
3fdeebd7e710 Initial commit lparsons parents: diff changeset	184 --------
3fdeebd7e710 Initial commit lparsons parents: diff changeset	185
3fdeebd7e710 Initial commit lparsons parents: diff changeset	186 This tool takes an alignment file in SAM or BAM format and feature file in GFF format
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	187 and calculates the number of reads mapping to each feature. It uses the htseq-count
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	188 script that is part of the HTSeq python module. See
3fdeebd7e710 Initial commit lparsons parents: diff changeset	189 http://www-huber.embl.de/users/anders/HTSeq/doc/count.html for details.
3fdeebd7e710 Initial commit lparsons parents: diff changeset	190
3fdeebd7e710 Initial commit lparsons parents: diff changeset	191 A feature is an interval (i.e., a range of positions) on a chromosome or a union of
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	192 such intervals. In the case of RNA-Seq, the features are typically genes, where
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	193 each gene is considered here as the union of all its exons. One may also consider
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	194 each exon as a feature, e.g., in order to check for alternative splicing. For
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	195 comparative ChIP-Seq, the features might be binding regions from a pre-determined
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	196 list.
3fdeebd7e710 Initial commit lparsons parents: diff changeset	197
3fdeebd7e710 Initial commit lparsons parents: diff changeset	198
3fdeebd7e710 Initial commit lparsons parents: diff changeset	199 Overlap Modes
3fdeebd7e710 Initial commit lparsons parents: diff changeset	200 -------------
3fdeebd7e710 Initial commit lparsons parents: diff changeset	201
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 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 3fdeebd7e710 Initial commit lparsons parents: diff changeset	203
3fdeebd7e710 Initial commit lparsons parents: diff changeset	204 The htseq-count script allows to choose between three modes: union, intersection-strict, and intersection-nonempty.
3fdeebd7e710 Initial commit lparsons parents: diff changeset	205
3fdeebd7e710 Initial commit lparsons parents: diff changeset	206 The following figure illustrates the effect of these three modes:
3fdeebd7e710 Initial commit lparsons parents: diff changeset	207
16 227f9d3f0e32 Updated HTSeq package to version 0.6.1, fixed input format string, updated dependency definitions lparsons parents: 15 diff changeset	208 .. image:: count_modes.png
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	209
11 f320093f1e8e Removed sorting notice from help lparsons parents: 10 diff changeset	210
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	211 Strandedness
3fdeebd7e710 Initial commit lparsons parents: diff changeset	212 ------------
3fdeebd7e710 Initial commit lparsons parents: diff changeset	213
3fdeebd7e710 Initial commit lparsons 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!
3fdeebd7e710 Initial commit lparsons parents: diff changeset	215
11 f320093f1e8e Removed sorting notice from help lparsons parents: 10 diff changeset	216
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	217 Output
3fdeebd7e710 Initial commit lparsons parents: diff changeset	218 ------
3fdeebd7e710 Initial commit lparsons parents: diff changeset	219
3fdeebd7e710 Initial commit lparsons 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
3fdeebd7e710 Initial commit lparsons parents: diff changeset	221
3fdeebd7e710 Initial commit lparsons parents: diff changeset	222 - no_feature: reads which could not be assigned to any feature (set S as described above was empty).
3fdeebd7e710 Initial commit lparsons parents: diff changeset	223
3fdeebd7e710 Initial commit lparsons 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).
3fdeebd7e710 Initial commit lparsons parents: diff changeset	225
3fdeebd7e710 Initial commit lparsons parents: diff changeset	226 - too_low_aQual: reads which were not counted due to the -a option, see below
3fdeebd7e710 Initial commit lparsons parents: diff changeset	227
3fdeebd7e710 Initial commit lparsons parents: diff changeset	228 - not_aligned: reads in the SAM file without alignment
3fdeebd7e710 Initial commit lparsons parents: diff changeset	229
3fdeebd7e710 Initial commit lparsons 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.)
3fdeebd7e710 Initial commit lparsons parents: diff changeset	231
3fdeebd7e710 Initial commit lparsons parents: diff changeset	232
3fdeebd7e710 Initial commit lparsons parents: diff changeset	233 Options Summary
3fdeebd7e710 Initial commit lparsons parents: diff changeset	234 ---------------
3fdeebd7e710 Initial commit lparsons parents: diff changeset	235
3fdeebd7e710 Initial commit lparsons parents: diff changeset	236 Usage: htseq-count [options] sam_file gff_file
3fdeebd7e710 Initial commit lparsons parents: diff changeset	237
3fdeebd7e710 Initial commit lparsons parents: diff changeset	238 This script takes an alignment file in SAM format and a feature file in GFF
3fdeebd7e710 Initial commit lparsons parents: diff changeset	239 format and calculates for each feature the number of reads mapping to it. See
3fdeebd7e710 Initial commit lparsons parents: diff changeset	240 http://www-huber.embl.de/users/anders/HTSeq/doc/count.html for details.
3fdeebd7e710 Initial commit lparsons parents: diff changeset	241
3fdeebd7e710 Initial commit lparsons parents: diff changeset	242 Options:
3fdeebd7e710 Initial commit lparsons parents: diff changeset	243 -h, --help show this help message and exit
3fdeebd7e710 Initial commit lparsons parents: diff changeset	244 -m MODE, --mode=MODE mode to handle reads overlapping more than one
3fdeebd7e710 Initial commit lparsons parents: diff changeset	245 feature(choices: union, intersection-strict,
3fdeebd7e710 Initial commit lparsons parents: diff changeset	246 intersection-nonempty; default: union)
3fdeebd7e710 Initial commit lparsons parents: diff changeset	247 -s STRANDED, --stranded=STRANDED
3fdeebd7e710 Initial commit lparsons parents: diff changeset	248 whether the data is from a strand-specific assay.
3fdeebd7e710 Initial commit lparsons parents: diff changeset	249 Specify 'yes', 'no', or 'reverse' (default: yes).
3fdeebd7e710 Initial commit lparsons parents: diff changeset	250 'reverse' means 'yes' with reversed strand
3fdeebd7e710 Initial commit lparsons parents: diff changeset	251 interpretation
3fdeebd7e710 Initial commit lparsons parents: diff changeset	252 -a MINAQUAL, --minaqual=MINAQUAL
3fdeebd7e710 Initial commit lparsons parents: diff changeset	253 skip all reads with alignment quality lower than the
3fdeebd7e710 Initial commit lparsons parents: diff changeset	254 given minimum value (default: 0)
3fdeebd7e710 Initial commit lparsons parents: diff changeset	255 -t FEATURETYPE, --type=FEATURETYPE
3fdeebd7e710 Initial commit lparsons parents: diff changeset	256 feature type (3rd column in GFF file) to be used, all
3fdeebd7e710 Initial commit lparsons parents: diff changeset	257 features of other type are ignored (default, suitable
3fdeebd7e710 Initial commit lparsons parents: diff changeset	258 for Ensembl GTF files: exon)
3fdeebd7e710 Initial commit lparsons parents: diff changeset	259 -i IDATTR, --idattr=IDATTR
3fdeebd7e710 Initial commit lparsons parents: diff changeset	260 GFF attribute to be used as feature ID (default,
3fdeebd7e710 Initial commit lparsons parents: diff changeset	261 suitable for Ensembl GTF files: gene_id)
3fdeebd7e710 Initial commit lparsons parents: diff changeset	262 -o SAMOUT, --samout=SAMOUT
3fdeebd7e710 Initial commit lparsons parents: diff changeset	263 write out all SAM alignment records into an output SAM
3fdeebd7e710 Initial commit lparsons parents: diff changeset	264 file called SAMOUT, annotating each line with its
3fdeebd7e710 Initial commit lparsons parents: diff changeset	265 feature assignment (as an optional field with tag
3fdeebd7e710 Initial commit lparsons parents: diff changeset	266 'XF')
3fdeebd7e710 Initial commit lparsons parents: diff changeset	267 -q, --quiet suppress progress report and warnings
3fdeebd7e710 Initial commit lparsons parents: diff changeset	268
3fdeebd7e710 Initial commit lparsons parents: diff changeset	269 Written by Simon Anders (sanders@fs.tum.de), European Molecular Biology
3fdeebd7e710 Initial commit lparsons parents: diff changeset	270 Laboratory (EMBL). (c) 2010. Released under the terms of the GNU General
3fdeebd7e710 Initial commit lparsons parents: diff changeset	271 Public License v3. Part of the 'HTSeq' framework.
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	272 ]]>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	273 </help>
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	274
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	275 <citations>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	276 <citation type="bibtex">
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	277 @article{anders_htseqpython_2015,
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	278 title = {{HTSeq}—a {Python} framework to work with high-throughput sequencing data},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	279 volume = {31},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	280 issn = {1367-4803, 1460-2059},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	281 url = {http://bioinformatics.oxfordjournals.org/content/31/2/166},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	282 doi = {10.1093/bioinformatics/btu638},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 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.
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 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.
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 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.
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	286 Contact: sanders\{at\}fs.tum.de},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	287 language = {en},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	288 number = {2},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	289 urldate = {2015-04-21},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	290 journal = {Bioinformatics},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	291 author = {Anders, Simon and Pyl, Paul Theodor and Huber, Wolfgang},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	292 month = jan,
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	293 year = {2015},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	294 pmid = {25260700},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	295 pages = {166--169},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 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}
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	297 }
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	298 </citation>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	299 </citations>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	300 </tool>

Mercurial > repos > lparsons > htseq_count

annotate htseq-count.xml @ 20:3b3601a2a7c7 draft