htseq_count: htseq-count.xml annotate

annotate htseq-count.xml @ 24:620d5603d1a8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty

author	iuc
date	Fri, 20 Jan 2017 15:46:13 -0500
parents	6e5c95760ab1
children	f1368427a79c

rev	line source
24 620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty iuc parents: 23 diff changeset	1 <tool id="htseq_count" name="htseq-count" version="0.6.1galaxy3" profile="16.04">
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>
22 55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	4 <requirement type="package" version="0.6.1.post1">htseq</requirement>
24 620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty iuc parents: 23 diff changeset	5 <requirement type="package" version="1.3.1">samtools</requirement>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	6 </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	7
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	8 <stdio>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	9 <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	10 <regex match="htseq-count: (command ){0,1}not found" source="stderr" level="fatal" description="The HTSeq python package is not properly installed, contact Galaxy administrators" />
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="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	12 <regex match="Error: Feature (.+) does not contain a '(.+)' attribute" source="both" level="fatal" description="Error parsing the GFF file, at least one feature of the specified 'Feature type' does not have a value for the specified 'ID Attribute'" />
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 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	14 <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	15 <regex match="Warning: Read (.+) claims to have an aligned mate which could not be found. $Is the SAM file properly sorted\?$" source="stderr" level="warning" description="PAIRED DATA MISSING OR NOT PROPERLY SORTED. Try reruning and selecting the option to 'Force sorting of SAM/BAM file by NAME'. See stderr output of this dataset for more information." />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	16 </stdio>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	17
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	18 <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	19
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	20 <command><![CDATA[
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	21 ##set up input files
3fdeebd7e710 Initial commit lparsons parents: diff changeset	22 #set $reference_fasta_filename = "localref.fa"
22 55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	23 #if $samout_conditional.samout == "Yes":
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	24 #if str( $samout_conditional.reference_source.reference_source_selector ) == "history":
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	25 ln -s "${samout_conditional.reference_source.ref_file}" "${reference_fasta_filename}" &&
24 620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty iuc parents: 23 diff changeset	26 samtools faidx '${reference_fasta_filename}' 2>&1 \|\| echo "Error running samtools faidx for htseq-count" >&2 &&
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	27 #else:
3fdeebd7e710 Initial commit lparsons parents: diff changeset	28 #set $reference_fasta_filename = str( $samout_conditional.reference_source.ref_file.fields.path )
3fdeebd7e710 Initial commit lparsons parents: diff changeset	29 #end if
3fdeebd7e710 Initial commit lparsons parents: diff changeset	30 #end if
24 620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty iuc parents: 23 diff changeset	31
22 55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	32 #if $force_sort == "True":
20 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 $samfile.extension == 'bam':
24 620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty iuc parents: 23 diff changeset	34 samtools sort -n -o 'name_sorted_alignment.bam' '$samfile' &&
20 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
24 620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty iuc parents: 23 diff changeset	36 samtools view -Su -t '${reference_fasta_filename}.fai' '$samfile' \| samtools sort -n -o 'name_sorted_alignment.bam' - &&
20 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
24 620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty iuc parents: 23 diff changeset	39
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	40 htseq-count
23 6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790 iuc parents: 22 diff changeset	41 --mode=$mode
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790 iuc parents: 22 diff changeset	42 --stranded=$stranded
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790 iuc parents: 22 diff changeset	43 --minaqual=$minaqual
24 620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty iuc parents: 23 diff changeset	44 --type='$featuretype'
620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty iuc parents: 23 diff changeset	45 --idattr='$idattr'
22 55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	46 #if $samout_conditional.samout == "Yes":
23 6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790 iuc parents: 22 diff changeset	47 --samout='$__new_file_path__/${samoutfile.id}_tmp'
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	48 #end if
22 55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	49 #if $force_sort == "True":
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	50 --order=name
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	51 --format=bam
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	52 name_sorted_alignment.bam
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	53 #else
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	54 --order=pos
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	55 --format=$samfile.extension
23 6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790 iuc parents: 22 diff changeset	56 '$samfile'
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	57 #end if
24 620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty iuc parents: 23 diff changeset	58
23 6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790 iuc parents: 22 diff changeset	59 "$gfffile" \| awk '{if ($1 ~ "no_feature\|ambiguous\|too_low_aQual\|not_aligned\|alignment_not_unique") print $0 \| "cat 1>&2"; else print $0}'
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790 iuc parents: 22 diff changeset	60 > '$counts'
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790 iuc parents: 22 diff changeset	61 2> '$othercounts'
24 620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty iuc parents: 23 diff changeset	62
22 55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	63 #if $samout_conditional.samout == "Yes":
23 6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790 iuc parents: 22 diff changeset	64 && samtools view -Su
24 620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty iuc parents: 23 diff changeset	65 -t '${reference_fasta_filename}.fai'
620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty iuc parents: 23 diff changeset	66 '$__new_file_path__/${samoutfile.id}_tmp'
620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty iuc parents: 23 diff changeset	67 \| samtools sort -o '$samoutfile' -
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 #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	69 ]]>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	70 </command>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	71
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	72 <inputs>
16 227f9d3f0e32 Updated HTSeq package to version 0.6.1, fixed input format string, updated dependency definitions lparsons parents: 15 diff changeset	73 <param format="sam,bam" name="samfile" type="data" label="Aligned SAM/BAM File"/>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	74 <param format="gff" name="gfffile" type="data" label="GFF File"/>
22 55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	75 <param name="mode" type="select" label="Mode" argument="(--mode)">
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	76 <help>Mode to handle reads overlapping more than one feature.</help>
22 55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	77 <option value="union" selected="True">Union</option>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	78 <option value="intersection-strict">Intersection (strict)</option>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	79 <option value="intersection-nonempty">Intersection (nonempty)</option>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	80 </param>
22 55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	81 <param name="stranded" type="select" label="Stranded" argument="(--stranded)">
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	82 <help>Specify whether the data is from a strand-specific assay. 'Reverse' means yes with reversed strand interpretation.</help>
22 55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	83 <option value="yes" selected="True">Yes</option>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	84 <option value="no">No</option>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	85 <option value="reverse">Reverse</option>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	86 </param>
22 55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	87 <param name="minaqual" type="integer" value="10" label="Minimum alignment quality" argument="--minaqual">
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	88 <help>Skip all reads with alignment quality lower than the given minimum value.</help>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	89 </param>
22 55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	90 <param name="featuretype" type="text" value="exon" label="Feature type" argument="--type">
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	91 <help>Feature type (3rd column in GFF file) to be used. All features of other types are ignored. The default, suitable for RNA-Seq and Ensembl GTF files, is exon.</help>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	92 </param>
22 55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	93 <param name="idattr" type="text" value="gene_id" label="ID Attribute" argument="--idattr">
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	94 <help>GFF attribute to be used as feature ID. Several GFF lines with the same feature ID will be considered as parts of the same feature. The feature ID is used to identity the counts in the output table. All features of the specified type MUST have a value for this attribute. The default, suitable for RNA-Seq and Ensembl GTF files, is gene_id.</help>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	95 </param>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	96 <conditional name="samout_conditional">
22 55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	97 <param name="samout" type="select" label="Additional BAM Output">
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	98 <help>Write out all SAM alignment records into an output BAM file, annotating each line with its assignment to a feature or a special counter (as an optional field with tag ‘XF’).</help>
22 55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	99 <option value="No" selected="True">Do not output additional BAM file</option>
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	100 <option value="Yes">Output additional BAM file</option>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	101 </param>
22 55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	102 <when value="Yes">
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	103 <conditional name="reference_source">
3fdeebd7e710 Initial commit lparsons parents: diff changeset	104 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
3fdeebd7e710 Initial commit lparsons parents: diff changeset	105 <option value="cached">Locally cached</option>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	106 <option value="history">History</option>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	107 </param>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	108 <when value="cached">
3fdeebd7e710 Initial commit lparsons parents: diff changeset	109 <param name="ref_file" type="select" label="Using reference genome">
3fdeebd7e710 Initial commit lparsons parents: diff changeset	110 <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	111 <filter type="data_meta" key="dbkey" ref="samfile" column="1"/>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	112 </options>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	113 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	114 </param>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	115 </when>
23 6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790 iuc parents: 22 diff changeset	116 <when value="history">
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	117 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
3fdeebd7e710 Initial commit lparsons parents: diff changeset	118 </when>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	119 </conditional>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	120 </when>
22 55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	121 <when value="No">
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	122 <!-- Do nothing -->
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	123 </when>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	124 </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	125 <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	126 <help>This option can be used for for paired-end data that has many unmapped mates. Use this if you get the warning about paired end data missing or not being properly sorted.</help>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	127 </param>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	128 </inputs>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	129
3fdeebd7e710 Initial commit lparsons parents: diff changeset	130 <outputs>
23 6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790 iuc parents: 22 diff changeset	131 <data format="tabular" name="counts" metadata_source="samfile" label="${tool.name} on ${on_string}">
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790 iuc parents: 22 diff changeset	132 <actions>
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790 iuc parents: 22 diff changeset	133 <action name="column_names" type="metadata" default="Geneid,${samfile.name}" />
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790 iuc parents: 22 diff changeset	134 </actions>
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790 iuc parents: 22 diff changeset	135 </data>
10 5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools) lparsons parents: 9 diff changeset	136 <data format="tabular" name="othercounts" metadata_source="samfile" label="${tool.name} on ${on_string} (no feature)"/>
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools) lparsons parents: 9 diff changeset	137 <data format="bam" name="samoutfile" metadata_source="samfile" label="${tool.name} on ${on_string} (BAM)">
22 55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	138 <filter>samout_conditional['samout'] == "Yes"</filter>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	139 </data>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	140 </outputs>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	141
3fdeebd7e710 Initial commit lparsons parents: diff changeset	142 <tests>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	143 <test>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	144 <param name="samfile" value="htseq-test.sam" />
3fdeebd7e710 Initial commit lparsons parents: diff changeset	145 <param name="gfffile" value="htseq-test.gff" />
22 55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	146 <param name="samout" value="No" />
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	147 <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	148 <output name="othercounts" file="htseq-test_othercounts.tsv" />
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	149 </test>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	150 <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	151 <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	152 <param name="gfffile" value="htseq-test.gff" />
22 55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	153 <param name="samout" value="No" />
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	154 <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	155 <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	156 <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	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 <test>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	159 <param name="samfile" value="htseq-test.bam" />
3fdeebd7e710 Initial commit lparsons parents: diff changeset	160 <param name="gfffile" value="htseq-test.gff" />
22 55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	161 <param name="samout" value="No" />
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	162 <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	163 <output name="othercounts" file="htseq-test_othercounts.tsv" />
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	164 </test>
10 5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools) lparsons parents: 9 diff changeset	165 <test>
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools) lparsons parents: 9 diff changeset	166 <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	167 <param name="singlepaired" value="paired" />
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools) lparsons parents: 9 diff changeset	168 <param name="gfffile" value="htseq-test.gff" />
22 55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	169 <param name="samout" value="No" />
10 5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools) lparsons parents: 9 diff changeset	170 <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	171 <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	172 </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	173 <test>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	174 <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	175 <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	176 <param name="gfffile" value="htseq-test.gff" />
22 55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	177 <param name="samout" value="No" />
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	178 <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	179 <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	180 <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	181 </test>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	182 <test>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	183 <param name="samfile" value="htseq-test.sam" />
3fdeebd7e710 Initial commit lparsons parents: diff changeset	184 <param name="gfffile" value="htseq-test.gff" />
23 6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790 iuc parents: 22 diff changeset	185 <param name="samout" value="Yes" />
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	186 <param name="reference_source_selector" value="history" />
3fdeebd7e710 Initial commit lparsons parents: diff changeset	187 <param name="ref_file" value="htseq-test_reference.fasta" />
3fdeebd7e710 Initial commit lparsons parents: diff changeset	188 <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	189 <output name="othercounts" file="htseq-test_othercounts.tsv" />
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	190 <output name="samoutfile" file="htseq-test_samout.bam" />
3fdeebd7e710 Initial commit lparsons parents: diff changeset	191 </test>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	192 </tests>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	193
3fdeebd7e710 Initial commit lparsons parents: diff changeset	194 <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	195 <![CDATA[
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	196 Overview
3fdeebd7e710 Initial commit lparsons parents: diff changeset	197 --------
3fdeebd7e710 Initial commit lparsons parents: diff changeset	198
3fdeebd7e710 Initial commit lparsons parents: diff changeset	199 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	200 and calculates the number of reads mapping to each feature. It uses the htseq-count
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	201 script that is part of the HTSeq python module. See
3fdeebd7e710 Initial commit lparsons parents: diff changeset	202 http://www-huber.embl.de/users/anders/HTSeq/doc/count.html for details.
3fdeebd7e710 Initial commit lparsons parents: diff changeset	203
3fdeebd7e710 Initial commit lparsons parents: diff changeset	204 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	205 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	206 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	207 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	208 comparative ChIP-Seq, the features might be binding regions from a pre-determined
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	209 list.
3fdeebd7e710 Initial commit lparsons parents: diff changeset	210
3fdeebd7e710 Initial commit lparsons parents: diff changeset	211
3fdeebd7e710 Initial commit lparsons parents: diff changeset	212 Overlap Modes
3fdeebd7e710 Initial commit lparsons parents: diff changeset	213 -------------
3fdeebd7e710 Initial commit lparsons parents: diff changeset	214
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	215 Special care must be taken to decide how to deal with reads that overlap more than one feature.
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	216
3fdeebd7e710 Initial commit lparsons parents: diff changeset	217 The htseq-count script allows to choose between three modes: union, intersection-strict, and intersection-nonempty.
3fdeebd7e710 Initial commit lparsons parents: diff changeset	218
3fdeebd7e710 Initial commit lparsons parents: diff changeset	219 The following figure illustrates the effect of these three modes:
3fdeebd7e710 Initial commit lparsons parents: diff changeset	220
16 227f9d3f0e32 Updated HTSeq package to version 0.6.1, fixed input format string, updated dependency definitions lparsons parents: 15 diff changeset	221 .. image:: count_modes.png
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	222
11 f320093f1e8e Removed sorting notice from help lparsons parents: 10 diff changeset	223
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	224 Strandedness
3fdeebd7e710 Initial commit lparsons parents: diff changeset	225 ------------
3fdeebd7e710 Initial commit lparsons parents: diff changeset	226
3fdeebd7e710 Initial commit lparsons parents: diff changeset	227 Important: The default for strandedness is yes. If your RNA-Seq data has not been made with a strand-specific protocol, this causes half of the reads to be lost. Hence, make sure to set the option Stranded to 'No' unless you have strand-specific data!
3fdeebd7e710 Initial commit lparsons parents: diff changeset	228
11 f320093f1e8e Removed sorting notice from help lparsons parents: 10 diff changeset	229
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	230 Output
3fdeebd7e710 Initial commit lparsons parents: diff changeset	231 ------
3fdeebd7e710 Initial commit lparsons parents: diff changeset	232
3fdeebd7e710 Initial commit lparsons parents: diff changeset	233 The script outputs a table with counts for each feature, followed by the special counters, which count reads that were not counted for any feature for various reasons, namely
3fdeebd7e710 Initial commit lparsons parents: diff changeset	234
3fdeebd7e710 Initial commit lparsons parents: diff changeset	235 - 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	236
3fdeebd7e710 Initial commit lparsons parents: diff changeset	237 - ambiguous: reads which could have been assigned to more than one feature and hence were not counted for any of these (set S had mroe than one element).
3fdeebd7e710 Initial commit lparsons parents: diff changeset	238
3fdeebd7e710 Initial commit lparsons parents: diff changeset	239 - too_low_aQual: reads which were not counted due to the -a option, see below
3fdeebd7e710 Initial commit lparsons parents: diff changeset	240
3fdeebd7e710 Initial commit lparsons parents: diff changeset	241 - not_aligned: reads in the SAM file without alignment
3fdeebd7e710 Initial commit lparsons parents: diff changeset	242
3fdeebd7e710 Initial commit lparsons parents: diff changeset	243 - alignment_not_unique: reads with more than one reported alignment. These reads are recognized from the NH optional SAM field tag. (If the aligner does not set this field, multiply aligned reads will be counted multiple times.)
3fdeebd7e710 Initial commit lparsons parents: diff changeset	244
3fdeebd7e710 Initial commit lparsons parents: diff changeset	245
3fdeebd7e710 Initial commit lparsons parents: diff changeset	246 Options Summary
3fdeebd7e710 Initial commit lparsons parents: diff changeset	247 ---------------
3fdeebd7e710 Initial commit lparsons parents: diff changeset	248
3fdeebd7e710 Initial commit lparsons parents: diff changeset	249 Usage: htseq-count [options] sam_file gff_file
3fdeebd7e710 Initial commit lparsons parents: diff changeset	250
3fdeebd7e710 Initial commit lparsons parents: diff changeset	251 This script takes an alignment file in SAM format and a feature file in GFF
3fdeebd7e710 Initial commit lparsons parents: diff changeset	252 format and calculates for each feature the number of reads mapping to it. See
3fdeebd7e710 Initial commit lparsons parents: diff changeset	253 http://www-huber.embl.de/users/anders/HTSeq/doc/count.html for details.
3fdeebd7e710 Initial commit lparsons parents: diff changeset	254
3fdeebd7e710 Initial commit lparsons parents: diff changeset	255 Options:
3fdeebd7e710 Initial commit lparsons parents: diff changeset	256 -h, --help show this help message and exit
3fdeebd7e710 Initial commit lparsons parents: diff changeset	257 -m MODE, --mode=MODE mode to handle reads overlapping more than one
3fdeebd7e710 Initial commit lparsons parents: diff changeset	258 feature(choices: union, intersection-strict,
3fdeebd7e710 Initial commit lparsons parents: diff changeset	259 intersection-nonempty; default: union)
3fdeebd7e710 Initial commit lparsons parents: diff changeset	260 -s STRANDED, --stranded=STRANDED
3fdeebd7e710 Initial commit lparsons parents: diff changeset	261 whether the data is from a strand-specific assay.
3fdeebd7e710 Initial commit lparsons parents: diff changeset	262 Specify 'yes', 'no', or 'reverse' (default: yes).
3fdeebd7e710 Initial commit lparsons parents: diff changeset	263 'reverse' means 'yes' with reversed strand
3fdeebd7e710 Initial commit lparsons parents: diff changeset	264 interpretation
3fdeebd7e710 Initial commit lparsons parents: diff changeset	265 -a MINAQUAL, --minaqual=MINAQUAL
3fdeebd7e710 Initial commit lparsons parents: diff changeset	266 skip all reads with alignment quality lower than the
3fdeebd7e710 Initial commit lparsons parents: diff changeset	267 given minimum value (default: 0)
3fdeebd7e710 Initial commit lparsons parents: diff changeset	268 -t FEATURETYPE, --type=FEATURETYPE
3fdeebd7e710 Initial commit lparsons parents: diff changeset	269 feature type (3rd column in GFF file) to be used, all
3fdeebd7e710 Initial commit lparsons parents: diff changeset	270 features of other type are ignored (default, suitable
3fdeebd7e710 Initial commit lparsons parents: diff changeset	271 for Ensembl GTF files: exon)
3fdeebd7e710 Initial commit lparsons parents: diff changeset	272 -i IDATTR, --idattr=IDATTR
3fdeebd7e710 Initial commit lparsons parents: diff changeset	273 GFF attribute to be used as feature ID (default,
3fdeebd7e710 Initial commit lparsons parents: diff changeset	274 suitable for Ensembl GTF files: gene_id)
3fdeebd7e710 Initial commit lparsons parents: diff changeset	275 -o SAMOUT, --samout=SAMOUT
3fdeebd7e710 Initial commit lparsons parents: diff changeset	276 write out all SAM alignment records into an output SAM
3fdeebd7e710 Initial commit lparsons parents: diff changeset	277 file called SAMOUT, annotating each line with its
3fdeebd7e710 Initial commit lparsons parents: diff changeset	278 feature assignment (as an optional field with tag
3fdeebd7e710 Initial commit lparsons parents: diff changeset	279 'XF')
3fdeebd7e710 Initial commit lparsons parents: diff changeset	280 -q, --quiet suppress progress report and warnings
3fdeebd7e710 Initial commit lparsons parents: diff changeset	281
3fdeebd7e710 Initial commit lparsons parents: diff changeset	282 Written by Simon Anders (sanders@fs.tum.de), European Molecular Biology
3fdeebd7e710 Initial commit lparsons parents: diff changeset	283 Laboratory (EMBL). (c) 2010. Released under the terms of the GNU General
3fdeebd7e710 Initial commit lparsons parents: diff changeset	284 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	285 ]]>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	286 </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	287 <citations>
23 6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790 iuc parents: 22 diff changeset	288 <citation type="doi">10.1093/bioinformatics/btu638</citation>
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	289 </citations>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	290 </tool>

Mercurial > repos > lparsons > htseq_count

annotate htseq-count.xml @ 24:620d5603d1a8 draft