htseq_count: htseq-count.xml annotate

annotate htseq-count.xml @ 28:bc4ada69b61f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 95fe80d08fb14c4c344da4979290e72261e31ae5"

author	iuc
date	Thu, 10 Oct 2019 04:05:45 -0400
parents	4dd515072667
children	44c91703f6a5

rev	line source
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	1 <tool id="htseq_count" name="htseq-count" version="0.9.1" profile="16.04">
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	2 <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	3 <requirements>
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	4 <requirement type="package" version="0.9.1">htseq</requirement>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	5 <requirement type="package" version="1.7">samtools</requirement>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	6 </requirements>
18 737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	7
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	8 <stdio>
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	9 <exit_code range="1:" level="fatal" description="Unknown error occurred" />
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	10 <regex match="htseq-count: (command ){0,1}not found" source="stderr" level="fatal" description="The HTSeq python package is not properly installed, contact Galaxy administrators" />
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	11 <regex match="samtools: (command ){0,1}not found" source="stderr" level="fatal" description="The samtools package is not properly installed, contact Galaxy administrators" />
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	12 <regex match="Error: Feature (.+) does not contain a '(.+)' attribute" source="both" level="fatal" description="Error parsing the GFF file, at least one feature of the specified 'Feature type' does not have a value for the specified 'ID Attribute'" />
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	13 <regex match="Error occured in line (\d+) of file" source="stderr" level="fatal" description="Unknown error parsing the GFF file" />
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	14 <regex match="Error" source="stderr" level="fatal" description="Unknown error occured" />
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	15 </stdio>
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	16
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	17 <version_command>htseq-count -h \| grep version \| sed 's/^$.$$version .*$\./\2/'</version_command>
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	18
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	19 <command><![CDATA[
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	20 ##set up input files
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	21 #set $reference_fasta_filename = "localref.fa"
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	22 #set $name_sorted_alignment_filename = "name_sorted_alignment.sam"
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	23 #if str( $advanced_options.advanced_options_selector ) == "advanced":
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	24 #if str( $advanced_options.samout_conditional.samout ) == "Yes":
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	25 #if str( $advanced_options.samout_conditional.reference_source.reference_source_selector ) == "history":
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	26 ln -s "${advanced_options.samout_conditional.reference_source.ref_file}" "${reference_fasta_filename}" &&
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	27 samtools faidx '${reference_fasta_filename}' 2>&1 \|\| echo "Error running samtools faidx for htseq-count" >&2 &&
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	28 #else:
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	29 #set $reference_fasta_filename = str( $advanced_options.samout_conditional.reference_source.ref_file.fields.path )
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	30 #end if
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	31 #end if
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	32 #end if
25 88cea300225a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit da411ad3afa5b8fb7d28fdb1b13a777854e87212 iuc parents: 24 diff changeset	33
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	34 #if $samfile.extension == 'bam':
28 bc4ada69b61f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 95fe80d08fb14c4c344da4979290e72261e31ae5" iuc parents: 27 diff changeset	35 samtools sort -n -T "\${TMPDIR:-.}" --output-fmt=SAM -o '$name_sorted_alignment_filename' '$samfile' &&
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	36 #else
28 bc4ada69b61f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 95fe80d08fb14c4c344da4979290e72261e31ae5" iuc parents: 27 diff changeset	37 samtools view -Su -t '${reference_fasta_filename}.fai' '$samfile' \| samtools sort -n -T "\${TMPDIR:-.}" --output-fmt=SAM -o '$name_sorted_alignment_filename' - &&
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	38 #end if
25 88cea300225a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit da411ad3afa5b8fb7d28fdb1b13a777854e87212 iuc parents: 24 diff changeset	39
18 737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	40 htseq-count
24 0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	41 --mode=$mode
0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	42 --stranded=$stranded
0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	43 --minaqual=$minaqual
25 88cea300225a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit da411ad3afa5b8fb7d28fdb1b13a777854e87212 iuc parents: 24 diff changeset	44 --type='$featuretype'
88cea300225a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit da411ad3afa5b8fb7d28fdb1b13a777854e87212 iuc parents: 24 diff changeset	45 --idattr='$idattr'
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	46
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	47 #if str( $advanced_options.advanced_options_selector ) == "advanced":
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	48 --nonunique=$advanced_options.nonunique
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	49 --secondary-alignments=${advanced_options.secondary_alignments}
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	50 --supplementary-alignments=${advanced_options.supplementary_alignments}
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	51 #if $advanced_options.samout_conditional.samout == "Yes":
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	52 --samout='$__new_file_path__/${samoutfile.id}_tmp.sam'
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	53 #end if
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	54 #end if
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	55
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	56 --order=name
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	57 --format=sam
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	58 '$name_sorted_alignment_filename'
25 88cea300225a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit da411ad3afa5b8fb7d28fdb1b13a777854e87212 iuc parents: 24 diff changeset	59
24 0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	60 "$gfffile" \| awk '{if ($1 ~ "no_feature\|ambiguous\|too_low_aQual\|not_aligned\|alignment_not_unique") print $0 \| "cat 1>&2"; else print $0}'
0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	61 > '$counts'
0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	62 2> '$othercounts'
25 88cea300225a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit da411ad3afa5b8fb7d28fdb1b13a777854e87212 iuc parents: 24 diff changeset	63
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	64 #if str( $advanced_options.advanced_options_selector ) == "advanced":
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	65 #if $advanced_options.samout_conditional.samout == "Yes":
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	66 && samtools view -Su
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	67 -t '${reference_fasta_filename}.fai'
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	68 '$__new_file_path__/${samoutfile.id}_tmp.sam'
28 bc4ada69b61f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 95fe80d08fb14c4c344da4979290e72261e31ae5" iuc parents: 27 diff changeset	69 \| samtools sort -T "\${TMPDIR:-.}" -o '$samoutfile' -
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	70 #end if
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	71 #end if
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	72 ]]>
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	73 </command>
18 737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	74
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	75 <inputs>
13 256d3114ce31 Fix input format string and change dependency owners to devteam lparsons parents: 12 diff changeset	76 <param format="sam,bam" name="samfile" type="data" label="Aligned SAM/BAM File"/>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	77 <param format="gff" name="gfffile" type="data" label="GFF File"/>
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	78 <param name="mode" type="select" label="Mode" argument="--mode">
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	79 <help>Mode to handle reads overlapping more than one feature.</help>
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	80 <option value="union" selected="True">Union</option>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	81 <option value="intersection-strict">Intersection (strict)</option>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	82 <option value="intersection-nonempty">Intersection (nonempty)</option>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	83 </param>
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	84 <param name="stranded" type="select" label="Stranded" argument="--stranded">
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	85 <help>Specify whether the data is from a strand-specific assay.
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	86 Be sure to choose the correct value (see help for more
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	87 information).</help>
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	88 <option value="yes" selected="True">Yes</option>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	89 <option value="no">No</option>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	90 <option value="reverse">Reverse</option>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	91 </param>
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	92 <param name="minaqual" type="integer" value="10" label="Minimum alignment quality" argument="--minaqual">
b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	93 <help>Skip all reads with alignment quality lower than the given minimum value.</help>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	94 </param>
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	95 <param name="featuretype" type="text" value="exon" label="Feature type" argument="--type">
b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	96 <help>Feature type (3rd column in GFF file) to be used. All features of other types are ignored. The default, suitable for RNA-Seq and Ensembl GTF files, is exon.</help>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	97 </param>
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	98 <param name="idattr" type="text" value="gene_id" label="ID Attribute" argument="--idattr">
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	99 <help>GFF attribute to be used as feature ID. Several GFF lines with the same feature ID will be considered as parts of the same feature. The feature ID is used to identity the counts in the output table. All features of the specified type MUST have a value for this attribute. The default, suitable for RNA-Seq and Ensembl GTF files, is gene_id.</help>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	100 </param>
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	101
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	102 <conditional name="advanced_options">
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	103 <param name="advanced_options_selector" type="select" label="Set advanced options">
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	104 <option value="simple" selected="true">Default settings</option>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	105 <option value="advanced">Set advanced options</option>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	106 </param>
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	107 <when value="simple">
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	108 </when>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	109 <when value="advanced">
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	110 <param argument="--nonunique" type="select" label="How to count nonunique or ambiguous mapping reads">
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	111 <option value="none" selected="true">None - do not count nonuniquely or ambiguously mapped reads for any features</option>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	112 <option value="all">All - count nonuniquely or ambiguously mapped reads in BOTH in the nonunique or ambiguous category AND for any features they overlap</option>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	113 </param>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	114 <param argument="--secondary-alignments" name="secondary_alignments" type="boolean" truevalue="ignore" falsevalue="score" checked="false" label="Ignore seconday alignments (0x100 flag)" />
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	115 <param argument="--supplementary-alignments" name="supplementary_alignments" type="boolean" truevalue="ignore" falsevalue="score" checked="false" label="Ignore supplementary alignments (0x800 flag)" />
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	116 <conditional name="samout_conditional">
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	117 <param name="samout" type="select" label="Additional BAM Output">
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	118 <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>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	119 <option value="No" selected="True">Do not output additional BAM file</option>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	120 <option value="Yes">Output additional BAM file</option>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	121 </param>
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	122 <when value="Yes">
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	123 <conditional name="reference_source">
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	124 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	125 <option value="cached">Locally cached</option>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	126 <option value="history">History</option>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	127 </param>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	128 <when value="cached">
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	129 <param name="ref_file" type="select" label="Using reference genome">
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	130 <options from_data_table="sam_fa_indexes">
28 bc4ada69b61f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 95fe80d08fb14c4c344da4979290e72261e31ae5" iuc parents: 27 diff changeset	131 <filter type="data_meta" key="dbkey" ref="samfile" column="value"/>
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	132 </options>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	133 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	134 </param>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	135 </when>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	136 <when value="history">
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	137 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	138 </when>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	139 </conditional>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	140 </when>
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	141 <when value="No">
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	142 <!-- Do nothing -->
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	143 </when>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	144 </conditional>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	145 </when>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	146 </conditional>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	147 </inputs>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	148
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	149 <outputs>
24 0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	150 <data format="tabular" name="counts" metadata_source="samfile" label="${tool.name} on ${on_string}">
0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	151 <actions>
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	152 <action name="column_names" type="metadata" default="Geneid,${samfile.element_identifier}" />
24 0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	153 </actions>
0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	154 </data>
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	155 <data format="tabular" name="othercounts" metadata_source="samfile" label="${tool.name} on ${on_string} (no feature)">
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	156 <actions>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	157 <action name="column_names" type="metadata" default="Category,${samfile.element_identifier}" />
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	158 </actions>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	159 </data>
5 0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	160 <data format="bam" name="samoutfile" metadata_source="samfile" label="${tool.name} on ${on_string} (BAM)">
27 4dd515072667 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 3e7db651397e9a42de15c5d6f60cec780f4b32df iuc parents: 26 diff changeset	161 <filter>advanced_options['advanced_options_selector'] == 'advanced' and advanced_options['samout_conditional']['samout'] == "Yes"</filter>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	162 </data>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	163 </outputs>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	164
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	165 <tests>
27 4dd515072667 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 3e7db651397e9a42de15c5d6f60cec780f4b32df iuc parents: 26 diff changeset	166 <test expect_num_outputs="2">
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	167 <param name="samfile" value="htseq-test.sam" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	168 <param name="gfffile" value="htseq-test.gff" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	169 <output name="counts" file="htseq-test_counts.tsv" />
5 0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	170 <output name="othercounts" file="htseq-test_othercounts.tsv" />
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	171 </test>
27 4dd515072667 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 3e7db651397e9a42de15c5d6f60cec780f4b32df iuc parents: 26 diff changeset	172 <test expect_num_outputs="2">
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	173 <param name="samfile" value="htseq-test.sam" />
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	174 <param name="gfffile" value="htseq-test.gff" />
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	175 <output name="counts" file="htseq-test_counts.tsv" />
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	176 <output name="othercounts" file="htseq-test_othercounts.tsv" />
8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	177 </test>
27 4dd515072667 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 3e7db651397e9a42de15c5d6f60cec780f4b32df iuc parents: 26 diff changeset	178 <test expect_num_outputs="2">
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	179 <param name="samfile" value="htseq-test.bam" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	180 <param name="gfffile" value="htseq-test.gff" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	181 <output name="counts" file="htseq-test_counts.tsv" />
5 0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	182 <output name="othercounts" file="htseq-test_othercounts.tsv" />
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	183 </test>
27 4dd515072667 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 3e7db651397e9a42de15c5d6f60cec780f4b32df iuc parents: 26 diff changeset	184 <test expect_num_outputs="2">
5 0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	185 <param name="samfile" value="htseq-test-paired.bam" />
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	186 <param name="gfffile" value="htseq-test.gff" />
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	187 <output name="counts" file="htseq-test-paired_counts.tsv" />
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	188 <output name="othercounts" file="htseq-test-paired_othercounts.tsv" />
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	189 </test>
27 4dd515072667 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 3e7db651397e9a42de15c5d6f60cec780f4b32df iuc parents: 26 diff changeset	190 <test expect_num_outputs="2">
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	191 <param name="samfile" value="htseq-test-paired.bam" />
5 0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	192 <param name="gfffile" value="htseq-test.gff" />
23 b638ba24d9fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 22 diff changeset	193 <param name="samout" value="No" />
5 0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	194 <output name="counts" file="htseq-test-paired_counts.tsv" />
0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	195 <output name="othercounts" file="htseq-test-paired_othercounts.tsv" />
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	196 </test>
27 4dd515072667 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 3e7db651397e9a42de15c5d6f60cec780f4b32df iuc parents: 26 diff changeset	197 <test expect_num_outputs="3">
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	198 <param name="samfile" value="htseq-test.sam" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	199 <param name="gfffile" value="htseq-test.gff" />
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	200 <param name="advanced_options_selector" value="advanced" />
24 0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	201 <param name="samout" value="Yes" />
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	202 <param name="reference_source_selector" value="history" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	203 <param name="ref_file" value="htseq-test_reference.fasta" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	204 <output name="counts" file="htseq-test_counts.tsv" />
5 0a835934d792 Version 0.3 lparsons parents: 4 diff changeset	205 <output name="othercounts" file="htseq-test_othercounts.tsv" />
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	206 <output name="samoutfile" file="htseq-test_samout.bam" />
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	207 </test>
27 4dd515072667 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 3e7db651397e9a42de15c5d6f60cec780f4b32df iuc parents: 26 diff changeset	208 <test expect_num_outputs="2">
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	209 <param name="samfile" value="htseq-test.sam" />
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	210 <param name="gfffile" value="htseq-test.gff" />
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	211 <param name="advanced_options_selector" value="advanced" />
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	212 <param name="nonunique" value="all" />
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	213 <param name="secondary_alignments" value="ignore" />
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	214 <param name="supplementary_alignments" value="ignore" />
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	215 <output name="counts" file="htseq-test_counts_nonunique.tsv" />
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	216 <output name="othercounts" file="htseq-test_othercounts.tsv" />
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	217 </test>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	218 </tests>
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	219
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	220 <help>
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	221 <![CDATA[
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	222 Overview
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	223 --------
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	224
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	225 This tool takes an alignment file in SAM or BAM format and feature file in GFF format
18 737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	226 and calculates the number of reads mapping to each feature. It uses the htseq-count
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	227 script that is part of the HTSeq python module. See
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	228 http://www-huber.embl.de/users/anders/HTSeq/doc/count.html for details.
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	229
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	230 A feature is an interval (i.e., a range of positions) on a chromosome or a union of
18 737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	231 such intervals. In the case of RNA-Seq, the features are typically genes, where
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	232 each gene is considered here as the union of all its exons. One may also consider
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	233 each exon as a feature, e.g., in order to check for alternative splicing. For
737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	234 comparative ChIP-Seq, the features might be binding regions from a pre-determined
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	235 list.
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	236
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	237
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	238 Overlap Modes
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	239 -------------
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	240
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	241 Special care must be taken to decide how to deal with reads that align to or
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	242 overlap with more than one feature. The ``htseq-count`` script allows to choose
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	243 between three modes. See also the FAQ_, if the following explanation seems too
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	244 technical.
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	245
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	246 The three overlap resolution modes of `htseq-count` work as follows. For each
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	247 position i in the read, a set S(i) is defined as the set of all features
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	248 overlapping position i. Then, consider the set S, which is (with i
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	249 running through all position within the read or a read pair)
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	250
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	251 - the union of all the sets S(i) for mode ``union``. This mode is
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	252 recommended for most use cases.
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	253 - the intersection of all the sets S(i) for mode ``intersection-strict``.
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	254 - the intersection of all non-empty sets S(i) for mode
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	255 ``intersection-nonempty``.
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	256
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	257 If S contains precisely one feature, the read (or read pair) is counted for
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	258 this feature. If S is empty, the read (or read pair) is counted as
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	259 ``no_feature``. If S contains more than one feature, ``htseq-count`` behaves
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	260 differently based on the ``--nonunique`` option:
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	261
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	262 - ``--nonunique none`` (default): the read (or read pair) is counted as
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	263 ``ambiguous`` and not counted for any features. Also, if the read (or read
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	264 pair) aligns to more than one location in the reference, it is scored as
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	265 ``alignment_not_unique``.
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	266 - ``--nonunique all``: the read (or read pair) is counted as ``ambiguous`` and
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	267 is also counted in all features to which it was assigned. Also, if the read
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	268 (or read pair) aligns to more than one location in the reference, it is
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	269 scored as ``alignment_not_unique`` and also separately for each location.
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	270
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	271 Notice that when using ``--nonunique all`` the sum of all counts will not be
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	272 equal to the number of reads (or read pairs), because those with multiple
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	273 alignments or overlaps get scored multiple times.
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	274
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	275 The following figure illustrates the effect of these three modes and the
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	276 ``--nonunique`` option:
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	277
14 c1db55359a86 Fix image path and size lparsons parents: 13 diff changeset	278 .. image:: count_modes.png
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	279
6 08a11d1eaec6 Updated HTSEQ package to version 0.5.4p1, attempted to fix galaxy install where lib64 directory does not exist lparsons parents: 5 diff changeset	280
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	281 Strandedness
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	282 ------------
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	283
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	284 Important: The default for strandedness is yes. Be sure to choose the correct value.
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	285
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	286 To check which value is correct, select forward and reverse independently. If
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	287 the overall counts drop at one condition then the opposite condition is
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	288 correct, otherwise your data is not stranded.
6 08a11d1eaec6 Updated HTSEQ package to version 0.5.4p1, attempted to fix galaxy install where lib64 directory does not exist lparsons parents: 5 diff changeset	289
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	290 Output
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	291 ------
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	292
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	293 The script outputs a table with counts for each feature, followed by the special counters, which count reads that were not counted for any feature for various reasons, namely
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	294
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	295 - no_feature: reads which could not be assigned to any feature (set S as described above was empty).
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	296
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	297 - ambiguous: reads which could have been assigned to more than one feature and hence were not counted for any of these (set S had mroe than one element).
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	298
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	299 - too_low_aQual: reads which were not counted due to the -a option, see below
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	300
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	301 - not_aligned: reads in the SAM file without alignment
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	302
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	303 - alignment_not_unique: reads with more than one reported alignment. These reads are recognized from the NH optional SAM field tag. (If the aligner does not set this field, multiply aligned reads will be counted multiple times.)
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	304
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	305
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	306 Options Summary
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	307 ---------------
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	308
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	309 Usage: htseq-count [options] sam_file gff_file
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	310
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	311 This script takes an alignment file in SAM format and a feature file in GFF
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	312 format and calculates for each feature the number of reads mapping to it. See
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	313 https://htseq.readthedocs.io/en/release_0.9.1/count.html for details.
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	314
b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	315 Options:
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	316 -f <format>, --format=<format>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	317
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	318 Format of the input data. Possible values are sam (for text SAM files) and bam (for binary BAM files). Default is sam.
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	319
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	320 -r <order>, --order=<order>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	321
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	322 For paired-end data, the alignment have to be sorted either by read name or by alignment position. If your data is not sorted, use the samtools sort function of samtools to sort it. Use this option, with name or pos for <order> to indicate how the input data has been sorted. The default is name.
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	323
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	324 If name is indicated, htseq-count expects all the alignments for the reads of a given read pair to appear in adjacent records in the input data. For pos, this is not expected; rather, read alignments whose mate alignment have not yet been seen are kept in a buffer in memory until the mate is found. While, strictly speaking, the latter will also work with unsorted data, sorting ensures that most alignment mates appear close to each other in the data and hence the buffer is much less likely to overflow.
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	325
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	326 --max-reads-in-buffer=<number>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	327
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	328 When <alignment_file> is paired end sorted by position, allow only so many reads to stay in memory until the mates are found (raising this number will use more memory). Has no effect for single end or paired end sorted by name. (default: 30000000)
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	329
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	330 -s <yes/no/reverse>, --stranded=<yes/no/reverse>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	331
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	332 whether the data is from a strand-specific assay (default: yes)
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	333
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	334 For stranded=no, a read is considered overlapping with a feature regardless of whether it is mapped to the same or the opposite strand as the feature. For stranded=yes and single-end reads, the read has to be mapped to the same strand as the feature. For paired-end reads, the first read has to be on the same strand and the second read on the opposite strand. For stranded=reverse, these rules are reversed.
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	335
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	336 -a <minaqual>, --a=<minaqual>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	337
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	338 skip all reads with alignment quality lower than the given minimum value (default: 10 — Note: the default used to be 0 until version 0.5.4.)
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	339
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	340 -t <feature type>, --type=<feature type>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	341
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	342 feature type (3rd column in GFF file) to be used, all features of other type are ignored (default, suitable for RNA-Seq analysis using an Ensembl GTF file: exon)
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	343
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	344 -i <id attribute>, --idattr=<id attribute>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	345
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	346 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. The default, suitable for RNA-Seq analysis using an Ensembl GTF file, is gene_id.
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	347
26 d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	348 --additional-attr=<id attributes>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	349
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	350 Additional feature attributes, which will be printed as an additional column after the primary attribute column but before the counts column(s). The default is none, a suitable value to get gene names using an Ensembl GTF file is gene_name.
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	351
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	352 -m <mode>, --mode=<mode>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	353
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	354 Mode to handle reads overlapping more than one feature. Possible values for <mode> are union, intersection-strict and intersection-nonempty (default: union)
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	355
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	356 --nonunique=<nonunique mode>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	357
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	358 Mode to handle reads that align to or are assigned to more than one feature in the overlap <mode> of choice (see -m option). <nonunique mode> are none and all (default: none)
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	359
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	360 --secondary-alignments=<mode>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	361
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	362 Mode to handle secondary alignments (SAM flag 0x100). <mode> can be score and ignore (default: score)
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	363
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	364 --supplementary-alignments=<mode>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	365
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	366 Mode to handle supplementary/chimeric alignments (SAM flag 0x800). <mode> can be score and ignore (default: score)
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	367
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	368 -o <samout>, --samout=<samout>
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	369
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	370 write out all SAM alignment records into an output SAM file called <samout>, annotating each line with its assignment to a feature or a special counter (as an optional field with tag ‘XF’)
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	371
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	372 -q, --quiet
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	373
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	374 suppress progress report and warnings
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	375
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	376 -h, --help
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	377
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	378 Show a usage summary and exit
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	379
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	380 .. _FAQ: https://htseq.readthedocs.io/en/release_0.9.1/count.html#frequenctly-asked-questions
d8c5761a8ba7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 25 diff changeset	381
19 8bc865a85024 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit e53f827acbedaec2da3a44488fb6628c9e922055 lparsons parents: 18 diff changeset	382 ]]>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	383 </help>
18 737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	384 <citations>
24 0c01ed8d0e60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 66df855014c39f31f97345e1249ddca5eb9f6e59 iuc parents: 23 diff changeset	385 <citation type="doi">10.1093/bioinformatics/btu638</citation>
18 737cda668bdd planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502 lparsons parents: 17 diff changeset	386 </citations>
0 b8349d8458fa Initial commit Lance Parsons <lparsons@princeton.edu> parents: diff changeset	387 </tool>

Mercurial > repos > lparsons > htseq_count

annotate htseq-count.xml @ 28:bc4ada69b61f draft