htseq_count: htseq-count.xml annotate

annotate htseq-count.xml @ 29:4418229c501e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece

author	iuc
date	Wed, 31 Jan 2024 12:51:03 +0000
parents	916cb26bd9d3
children

rev	line source
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	1 <tool id="htseq_count" name="htseq-count" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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>
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	3 <macros>
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	4 <token name="@TOOL_VERSION@">2.0.5</token>
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	5 <token name="@VERSION_SUFFIX@">0</token>
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	6 <token name="@PROFILE@">23.0</token>
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	7 </macros>
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	8 <xrefs>
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	9 <xref type="bio.tools">htseq</xref>
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	10 </xrefs>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	11 <requirements>
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	12 <requirement type="package" version="@TOOL_VERSION@">htseq</requirement>
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	13 <requirement type="package" version="1.19.2">samtools</requirement>
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	14 <requirement type="package" version="5.3.0">gawk</requirement>
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	15 <requirement type="package" version="9.4">coreutils</requirement>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	16 </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	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 <stdio>
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	19 <exit_code range="1:" level="fatal" />
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	20 <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	21 <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	22 <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	23 <regex match="Error occured in line (\d+) of file" source="stderr" level="fatal" description="Unknown error parsing the GFF file" />
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	24 <regex match="no SQ lines present" source="stderr" level="fatal" description="Input SAM dataset is missing header or SQ header lines. Please provide a FASTA reference sequence as additional input." />
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 <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	26 </stdio>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	27
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	28 <version_command>htseq-count --version</version_command>
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	29
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	30 <command><![CDATA[
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	31 ##set up input files
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	32 #set $name_sorted_alignment_filename = "name_sorted.bam"
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	33 #set $ref_index = "ref.fai"
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	34 #if $samfile.extension == 'sam':
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	35 #if str($reference_source.reference_source_selector) == "history":
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	36 samtools faidx --fai-idx $ref_index '${reference_source.ref_file}' 2>&1 \|\| echo "Error running samtools faidx for htseq-count" >&2 &&
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	37 #elif str($reference_source.reference_source_selector) == "cached":
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	38 ln -s '${reference_source.ref_file.fields.path}.fai' $ref_index
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	39 #end if
3fdeebd7e710 Initial commit lparsons parents: diff changeset	40 #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	41
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	42 #if $samfile.extension == 'sam' and str($reference_source.reference_source_selector):
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	43 samtools view -u -t $ref_index '$samfile' \| samtools sort -n -T "\${TMPDIR:-.}" -o $name_sorted_alignment_filename - &&
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	44 #else:
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	45 samtools sort -n -T "\${TMPDIR:-.}" -o $name_sorted_alignment_filename '$samfile' &&
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	46 #end if
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	47
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	48 #if $gfffile.is_of_type('gtf'):
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	49 ## htseq-count requires .gtf suffix to recognize GTF-formatted feature files
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	50 ## and to handle textual attributes should surrounded by doublequotes correctly
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	51 #set $genomic_features = 'features.gtf'
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	52 ln -s '$gfffile' $genomic_features &&
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	53 #else:
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	54 #set $genomic_features = $gfffile
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	55 #end if
24 620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty iuc parents: 23 diff changeset	56
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	57 htseq-count
23 6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790 iuc parents: 22 diff changeset	58 --mode=$mode
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790 iuc parents: 22 diff changeset	59 --stranded=$stranded
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790 iuc parents: 22 diff changeset	60 --minaqual=$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	61 --type='$featuretype'
620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty iuc parents: 23 diff changeset	62 --idattr='$idattr'
25 f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	63
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	64 #if str( $advanced_options.advanced_options_selector ) == "advanced":
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	65 --nonunique=$advanced_options.nonunique
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	66 --secondary-alignments=${advanced_options.secondary_alignments}
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	67 --supplementary-alignments=${advanced_options.supplementary_alignments}
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	68 #if $advanced_options.samout:
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	69 -o samout.sam
25 f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	70 #end if
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	71 #end if
25 f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	72
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	73 --order=name
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	74 $name_sorted_alignment_filename
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	75
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	76 '$genomic_features' \| csplit -q - /^__/ &&
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	77
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	78 ## csplit above creates two files,
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	79 ## xx00 with the feature counts and xx01 with category counts.
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	80 ## Now we calculate the sum over all feature counts in xx00 and append that
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	81 ## sum as the __aligned count to xx01.
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	82 echo -e "__aligned\t\$(cut -f2 xx00 \| awk '{s+=$1}END{print s}' -)" >> xx01
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	83
25 f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	84 #if str( $advanced_options.advanced_options_selector ) == "advanced":
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	85 #if $advanced_options.samout:
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	86 && samtools sort -T "\${TMPDIR:-.}" -o out.bam samout.sam
25 f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	87 #end if
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	88 #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	89 ]]>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	90 </command>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	91 <inputs>
16 227f9d3f0e32 Updated HTSeq package to version 0.6.1, fixed input format string, updated dependency definitions lparsons parents: 15 diff changeset	92 <param format="sam,bam" name="samfile" type="data" label="Aligned SAM/BAM File"/>
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	93 <param format="gff" name="gfffile" type="data" label="GFF/GTF File"/>
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	94 <param type="select" label="Mode" argument="--mode">
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	95 <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	96 <option value="union" selected="True">Union</option>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	97 <option value="intersection-strict">Intersection (strict)</option>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	98 <option value="intersection-nonempty">Intersection (nonempty)</option>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	99 </param>
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	100 <param type="select" label="Stranded" argument="--stranded">
25 f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	101 <help>Specify whether the data is from a strand-specific assay.
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	102 Be sure to choose the correct value (see help for more
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	103 information).</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	104 <option value="yes" selected="True">Yes</option>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	105 <option value="no">No</option>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	106 <option value="reverse">Reverse</option>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	107 </param>
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	108 <param type="integer" value="10" label="Minimum alignment quality" argument="--minaqual">
22 55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 iuc parents: 21 diff changeset	109 <help>Skip all reads with alignment quality lower than the given minimum value.</help>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	110 </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	111 <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	112 <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	113 </param>
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	114 <param 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	115 <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	116 </param>
25 f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	117
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	118 <conditional name="advanced_options">
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	119 <param name="advanced_options_selector" type="select" label="Set advanced options">
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	120 <option value="simple" selected="true">Default settings</option>
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	121 <option value="advanced">Set advanced options</option>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	122 </param>
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	123 <when value="simple" />
25 f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	124 <when value="advanced">
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	125 <param argument="--nonunique" type="select" label="How to count nonunique or ambiguous mapping reads">
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	126 <option value="none" selected="true">None - do not count nonuniquely or ambiguously mapped reads for any features</option>
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	127 <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>
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	128 </param>
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	129 <param argument="--secondary-alignments" type="boolean" truevalue="ignore" falsevalue="score" checked="false" label="Ignore seconday alignments (0x100 flag)" />
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	130 <param argument="--supplementary-alignments" type="boolean" truevalue="ignore" falsevalue="score" checked="false" label="Ignore supplementary alignments (0x800 flag)" />
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	131 <param argument="--samout" type="boolean" label="Additional BAM Output" 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’)." />
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	132 </when>
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	133 </conditional>
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	134 <conditional name="reference_source">
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	135 <param name="reference_source_selector" type="select" label="Provide a reference sequence?" help="Required for SAM input without @SQ headers, not necessary otherwise and ignored for BAM input.">
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	136 <option value="">No</option>
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	137 <option value="cached">Locally cached</option>
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	138 <option value="history">History</option>
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	139 </param>
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	140 <when value="" />
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	141 <when value="cached">
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	142 <param name="ref_file" type="select" label="Using reference genome">
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	143 <options from_data_table="sam_fa_indexes">
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	144 <filter type="data_meta" key="dbkey" ref="samfile" column="value"/>
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	145 </options>
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	146 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	147 </param>
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	148 </when>
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	149 <when value="history">
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	150 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	151 </when>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	152 </conditional>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	153 </inputs>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	154
3fdeebd7e710 Initial commit lparsons parents: diff changeset	155 <outputs>
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	156 <data name="counts" format="tabular" metadata_source="samfile" from_work_dir="xx00" label="${tool.name} on ${on_string}">
23 6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790 iuc parents: 22 diff changeset	157 <actions>
25 f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	158 <action name="column_names" type="metadata" default="Geneid,${samfile.element_identifier}" />
23 6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790 iuc parents: 22 diff changeset	159 </actions>
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790 iuc parents: 22 diff changeset	160 </data>
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	161 <data name="allcounts" format="tabular" metadata_source="samfile" from_work_dir="xx01" label="${tool.name} on ${on_string}: summary">
25 f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	162 <actions>
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	163 <action name="column_names" type="metadata" default="Category,${samfile.element_identifier}" />
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	164 </actions>
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	165 </data>
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	166 <data name="samoutfile" format="bam" metadata_source="samfile" from_work_dir="out.bam" label="${tool.name} on ${on_string} (BAM)">
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	167 <filter>advanced_options['advanced_options_selector'] == 'advanced' and advanced_options['samout']</filter>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	168 </data>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	169 </outputs>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	170
3fdeebd7e710 Initial commit lparsons parents: diff changeset	171 <tests>
26 7f5a8d427b39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 3e7db651397e9a42de15c5d6f60cec780f4b32df iuc parents: 25 diff changeset	172 <test expect_num_outputs="2">
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	173 <param name="samfile" value="htseq-test.sam" />
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	174 <param name="gfffile" value="htseq-test.gtf" />
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	175 <output name="counts" file="htseq-test_counts.tsv" />
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	176 <output name="allcounts" file="htseq-test_allcounts.tsv" />
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	177 </test>
26 7f5a8d427b39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 3e7db651397e9a42de15c5d6f60cec780f4b32df iuc parents: 25 diff changeset	178 <test expect_num_outputs="2">
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	179 <!-- same as before, but with gff3 input instead of gtf -->
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	180 <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	181 <param name="gfffile" value="htseq-test.gff" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	182 <output name="counts" file="htseq-test_counts.tsv" />
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	183 <output name="allcounts" file="htseq-test_allcounts.tsv" />
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	184 </test>
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	185 <test expect_num_outputs="2">
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	186 <!-- test SAM with no SQ lines and FASTA reference -->
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	187 <param name="samfile" value="htseq-test_nosq.sam" />
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	188 <param name="gfffile" value="htseq-test.gff" />
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	189 <param name="reference_source_selector" value="history" />
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	190 <param name="ref_file" value="htseq-test_reference.fasta" />
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	191 <output name="counts" file="htseq-test_counts.tsv" />
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	192 <output name="allcounts" file="htseq-test_allcounts.tsv" />
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	193 </test>
26 7f5a8d427b39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 3e7db651397e9a42de15c5d6f60cec780f4b32df iuc parents: 25 diff changeset	194 <test expect_num_outputs="2">
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	195 <param name="samfile" value="htseq-test.bam" />
3fdeebd7e710 Initial commit lparsons parents: diff changeset	196 <param name="gfffile" value="htseq-test.gff" />
3fdeebd7e710 Initial commit lparsons parents: diff changeset	197 <output name="counts" file="htseq-test_counts.tsv" />
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	198 <output name="allcounts" file="htseq-test_allcounts.tsv" />
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	199 </test>
26 7f5a8d427b39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 3e7db651397e9a42de15c5d6f60cec780f4b32df iuc parents: 25 diff changeset	200 <test expect_num_outputs="2">
10 5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools) lparsons parents: 9 diff changeset	201 <param name="samfile" value="htseq-test-paired.bam" />
25 f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	202 <param name="gfffile" value="htseq-test.gff" />
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	203 <output name="counts" file="htseq-test-paired_counts.tsv" />
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	204 <output name="allcounts" file="htseq-test-paired_allcounts.tsv" />
25 f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	205 </test>
26 7f5a8d427b39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 3e7db651397e9a42de15c5d6f60cec780f4b32df iuc parents: 25 diff changeset	206 <test expect_num_outputs="2">
25 f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	207 <param name="samfile" value="htseq-test-paired.bam" />
10 5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools) lparsons parents: 9 diff changeset	208 <param name="gfffile" value="htseq-test.gff" />
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	209 <param name="samout" value="true" />
10 5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools) lparsons parents: 9 diff changeset	210 <output name="counts" file="htseq-test-paired_counts.tsv" />
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	211 <output name="allcounts" file="htseq-test-paired_allcounts.tsv" />
10 5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools) lparsons parents: 9 diff changeset	212 </test>
26 7f5a8d427b39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 3e7db651397e9a42de15c5d6f60cec780f4b32df iuc parents: 25 diff changeset	213 <test expect_num_outputs="3">
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	214 <param name="samfile" value="htseq-test.sam" />
3fdeebd7e710 Initial commit lparsons parents: diff changeset	215 <param name="gfffile" value="htseq-test.gff" />
25 f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	216 <param name="advanced_options_selector" value="advanced" />
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	217 <param name="samout" value="true" />
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	218 <output name="counts" file="htseq-test_counts.tsv" />
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	219 <output name="allcounts" file="htseq-test_allcounts.tsv" />
4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	220 <output name="samoutfile" file="htseq-test_samout.bam" ftype="bam" compare="diff" lines_diff="4" />
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	221 </test>
26 7f5a8d427b39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 3e7db651397e9a42de15c5d6f60cec780f4b32df iuc parents: 25 diff changeset	222 <test expect_num_outputs="2">
25 f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	223 <param name="samfile" value="htseq-test.sam" />
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	224 <param name="gfffile" value="htseq-test.gff" />
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	225 <param name="advanced_options_selector" value="advanced" />
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	226 <param name="nonunique" value="all" />
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	227 <param name="secondary_alignments" value="ignore" />
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	228 <param name="supplementary_alignments" value="ignore" />
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	229 <output name="counts" file="htseq-test_counts_nonunique.tsv" />
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	230 <output name="allcounts" file="htseq-test_allcounts.tsv" />
25 f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	231 </test>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	232 </tests>
3fdeebd7e710 Initial commit lparsons parents: diff changeset	233
3fdeebd7e710 Initial commit lparsons parents: diff changeset	234 <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	235 <![CDATA[
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	236 Overview
3fdeebd7e710 Initial commit lparsons parents: diff changeset	237 --------
3fdeebd7e710 Initial commit lparsons parents: diff changeset	238
3fdeebd7e710 Initial commit lparsons parents: diff changeset	239 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	240 and calculates the number of reads mapping to each feature. It uses the htseq-count
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	241 script that is part of the HTSeq python module. See
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	242 https://htseq.readthedocs.io/en/latest/ for details.
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	243
3fdeebd7e710 Initial commit lparsons parents: diff changeset	244 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	245 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	246 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	247 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	248 comparative ChIP-Seq, the features might be binding regions from a pre-determined
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	249 list.
3fdeebd7e710 Initial commit lparsons parents: diff changeset	250
3fdeebd7e710 Initial commit lparsons parents: diff changeset	251
3fdeebd7e710 Initial commit lparsons parents: diff changeset	252 Overlap Modes
3fdeebd7e710 Initial commit lparsons parents: diff changeset	253 -------------
3fdeebd7e710 Initial commit lparsons parents: diff changeset	254
25 f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	255 Special care must be taken to decide how to deal with reads that align to or
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	256 overlap with more than one feature. The ``htseq-count`` script allows to choose
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	257 between three modes. See also the FAQ_, if the following explanation seems too
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	258 technical.
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	259
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	260 The three overlap resolution modes of `htseq-count` work as follows. For each
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	261 position i in the read, a set S(i) is defined as the set of all features
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	262 overlapping position i. Then, consider the set S, which is (with i
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	263 running through all position within the read or a read pair)
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	264
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	265 - the union of all the sets S(i) for mode ``union``. This mode is
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	266 recommended for most use cases.
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	267 - the intersection of all the sets S(i) for mode ``intersection-strict``.
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	268 - the intersection of all non-empty sets S(i) for mode
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	269 ``intersection-nonempty``.
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	270
25 f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	271 If S contains precisely one feature, the read (or read pair) is counted for
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	272 this feature. If S is empty, the read (or read pair) is counted as
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	273 ``no_feature``. If S contains more than one feature, ``htseq-count`` behaves
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	274 differently based on the ``--nonunique`` option:
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	275
25 f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	276 - ``--nonunique none`` (default): the read (or read pair) is counted as
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	277 ``ambiguous`` and not counted for any features. Also, if the read (or read
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	278 pair) aligns to more than one location in the reference, it is scored as
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	279 ``alignment_not_unique``.
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	280 - ``--nonunique all``: the read (or read pair) is counted as ``ambiguous`` and
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	281 is also counted in all features to which it was assigned. Also, if the read
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	282 (or read pair) aligns to more than one location in the reference, it is
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	283 scored as ``alignment_not_unique`` and also separately for each location.
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	284
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	285 Notice that when using ``--nonunique all`` the sum of all counts will not be
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	286 equal to the number of reads (or read pairs), because those with multiple
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	287 alignments or overlaps get scored multiple times.
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	288
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	289 The following figure illustrates the effect of these three modes and the
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	290 ``--nonunique`` option:
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	291
16 227f9d3f0e32 Updated HTSeq package to version 0.6.1, fixed input format string, updated dependency definitions lparsons parents: 15 diff changeset	292 .. image:: count_modes.png
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	293
11 f320093f1e8e Removed sorting notice from help lparsons parents: 10 diff changeset	294
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	295 Strandedness
3fdeebd7e710 Initial commit lparsons parents: diff changeset	296 ------------
3fdeebd7e710 Initial commit lparsons parents: diff changeset	297
25 f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	298 Important: The default for strandedness is yes. Be sure to choose the correct value.
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	299
25 f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	300 To check which value is correct, select forward and reverse independently. If
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	301 the overall counts drop at one condition then the opposite condition is
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	302 correct, otherwise your data is not stranded.
11 f320093f1e8e Removed sorting notice from help lparsons parents: 10 diff changeset	303
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	304 Output
3fdeebd7e710 Initial commit lparsons parents: diff changeset	305 ------
3fdeebd7e710 Initial commit lparsons parents: diff changeset	306
3fdeebd7e710 Initial commit lparsons parents: diff changeset	307 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	308
3fdeebd7e710 Initial commit lparsons parents: diff changeset	309 - 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	310
3fdeebd7e710 Initial commit lparsons parents: diff changeset	311 - 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	312
3fdeebd7e710 Initial commit lparsons parents: diff changeset	313 - too_low_aQual: reads which were not counted due to the -a option, see below
3fdeebd7e710 Initial commit lparsons parents: diff changeset	314
3fdeebd7e710 Initial commit lparsons parents: diff changeset	315 - not_aligned: reads in the SAM file without alignment
3fdeebd7e710 Initial commit lparsons parents: diff changeset	316
3fdeebd7e710 Initial commit lparsons parents: diff changeset	317 - 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	318
3fdeebd7e710 Initial commit lparsons parents: diff changeset	319
3fdeebd7e710 Initial commit lparsons parents: diff changeset	320 Options Summary
3fdeebd7e710 Initial commit lparsons parents: diff changeset	321 ---------------
3fdeebd7e710 Initial commit lparsons parents: diff changeset	322
3fdeebd7e710 Initial commit lparsons parents: diff changeset	323 Usage: htseq-count [options] sam_file gff_file
3fdeebd7e710 Initial commit lparsons parents: diff changeset	324
3fdeebd7e710 Initial commit lparsons parents: diff changeset	325 This script takes an alignment file in SAM format and a feature file in GFF
3fdeebd7e710 Initial commit lparsons parents: diff changeset	326 format and calculates for each feature the number of reads mapping to it. See
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	327 https://htseq.readthedocs.io/en/latest/ for details.
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	328
3fdeebd7e710 Initial commit lparsons parents: diff changeset	329 Options:
25 f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	330 -f <format>, --format=<format>
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	331
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	332 Format of the input data. Possible values are sam (for text SAM files) and bam (for binary BAM files). Default is sam.
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	333
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	334 -r <order>, --order=<order>
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	335
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	336 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.
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	337
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	338 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.
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	339
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	340 --max-reads-in-buffer=<number>
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	341
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	342 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)
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	343
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	344 -s <yes/no/reverse>, --stranded=<yes/no/reverse>
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	345
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	346 whether the data is from a strand-specific assay (default: yes)
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	347
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	348 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.
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	349
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	350 -a <minaqual>, --a=<minaqual>
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	351
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	352 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.)
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	353
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	354 -t <feature type>, --type=<feature type>
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	355
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	356 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)
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	357
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	358 -i <id attribute>, --idattr=<id attribute>
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	359
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	360 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 3fdeebd7e710 Initial commit lparsons parents: diff changeset	361
25 f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	362 --additional-attr=<id attributes>
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	363
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	364 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.
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	365
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	366 -m <mode>, --mode=<mode>
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	367
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	368 Mode to handle reads overlapping more than one feature. Possible values for <mode> are union, intersection-strict and intersection-nonempty (default: union)
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	369
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	370 --nonunique=<nonunique mode>
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	371
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	372 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)
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	373
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	374 --secondary-alignments=<mode>
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	375
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	376 Mode to handle secondary alignments (SAM flag 0x100). <mode> can be score and ignore (default: score)
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	377
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	378 --supplementary-alignments=<mode>
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	379
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	380 Mode to handle supplementary/chimeric alignments (SAM flag 0x800). <mode> can be score and ignore (default: score)
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	381
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	382 -o <samout>, --samout=<samout>
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	383
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	384 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’)
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	385
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	386 -q, --quiet
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	387
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	388 suppress progress report and warnings
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	389
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	390 -h, --help
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	391
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	392 Show a usage summary and exit
f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	393
29 4418229c501e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece iuc parents: 28 diff changeset	394 .. _FAQ: https://htseq.readthedocs.io/en/master/index.html
25 f1368427a79c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 76065f751b678abf87e6c723be680fecaa8cb589 iuc parents: 24 diff changeset	395
20 3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23 lparsons parents: 17 diff changeset	396 ]]>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	397 </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	398 <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	399 <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	400 </citations>
0 3fdeebd7e710 Initial commit lparsons parents: diff changeset	401 </tool>

Mercurial > repos > lparsons > htseq_count

annotate htseq-count.xml @ 29:4418229c501e draft default tip