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

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty
author iuc
date Fri, 20 Jan 2017 15:46:13 -0500
parents 6e5c95760ab1
children f1368427a79c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
24
620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty
iuc
parents: 23
diff changeset
1 <tool id="htseq_count" name="htseq-count" version="0.6.1galaxy3" profile="16.04">
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
2 <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
3 <requirements>
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
4 <requirement type="package" version="0.6.1.post1">htseq</requirement>
24
620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty
iuc
parents: 23
diff changeset
5 <requirement type="package" version="1.3.1">samtools</requirement>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
6 </requirements>
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
7
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
8 <stdio>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
9 <exit_code range="1:" level="fatal" description="Unknown error occurred" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
10 <regex match="htseq-count: (command ){0,1}not found" source="stderr" level="fatal" description="The HTSeq python package is not properly installed, contact Galaxy administrators" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
11 <regex match="samtools: (command ){0,1}not found" source="stderr" level="fatal" description="The samtools package is not properly installed, contact Galaxy administrators" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
12 <regex match="Error: Feature (.+) does not contain a '(.+)' attribute" source="both" level="fatal" description="Error parsing the GFF file, at least one feature of the specified 'Feature type' does not have a value for the specified 'ID Attribute'" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
13 <regex match="Error occured in line (\d+) of file" source="stderr" level="fatal" description="Unknown error parsing the GFF file" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
14 <regex match="Error" source="stderr" level="fatal" description="Unknown error occured" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
15 <regex match="Warning: Read (.+) claims to have an aligned mate which could not be found. \(Is the SAM file properly sorted\?\)" source="stderr" level="warning" description="PAIRED DATA MISSING OR NOT PROPERLY SORTED. Try reruning and selecting the option to 'Force sorting of SAM/BAM file by NAME'. See stderr output of this dataset for more information." />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
16 </stdio>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
17
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
18 <version_command>htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/'</version_command>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
19
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
20 <command><![CDATA[
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
21 ##set up input files
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
22 #set $reference_fasta_filename = "localref.fa"
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
23 #if $samout_conditional.samout == "Yes":
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
24 #if str( $samout_conditional.reference_source.reference_source_selector ) == "history":
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
25 ln -s "${samout_conditional.reference_source.ref_file}" "${reference_fasta_filename}" &&
24
620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty
iuc
parents: 23
diff changeset
26 samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for htseq-count" >&2 &&
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
27 #else:
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
28 #set $reference_fasta_filename = str( $samout_conditional.reference_source.ref_file.fields.path )
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
29 #end if
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
30 #end if
24
620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty
iuc
parents: 23
diff changeset
31
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
32 #if $force_sort == "True":
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
33 #if $samfile.extension == 'bam':
24
620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty
iuc
parents: 23
diff changeset
34 samtools sort -n -o 'name_sorted_alignment.bam' '$samfile' &&
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
35 #else
24
620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty
iuc
parents: 23
diff changeset
36 samtools view -Su -t '${reference_fasta_filename}.fai' '$samfile' | samtools sort -n -o 'name_sorted_alignment.bam' - &&
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
37 #end if
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
38 #end if
24
620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty
iuc
parents: 23
diff changeset
39
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
40 htseq-count
23
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790
iuc
parents: 22
diff changeset
41 --mode=$mode
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790
iuc
parents: 22
diff changeset
42 --stranded=$stranded
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790
iuc
parents: 22
diff changeset
43 --minaqual=$minaqual
24
620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty
iuc
parents: 23
diff changeset
44 --type='$featuretype'
620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty
iuc
parents: 23
diff changeset
45 --idattr='$idattr'
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
46 #if $samout_conditional.samout == "Yes":
23
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790
iuc
parents: 22
diff changeset
47 --samout='$__new_file_path__/${samoutfile.id}_tmp'
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
48 #end if
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
49 #if $force_sort == "True":
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
50 --order=name
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
51 --format=bam
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
52 name_sorted_alignment.bam
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
53 #else
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
54 --order=pos
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
55 --format=$samfile.extension
23
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790
iuc
parents: 22
diff changeset
56 '$samfile'
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
57 #end if
24
620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty
iuc
parents: 23
diff changeset
58
23
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790
iuc
parents: 22
diff changeset
59 "$gfffile" | awk '{if ($1 ~ "no_feature|ambiguous|too_low_aQual|not_aligned|alignment_not_unique") print $0 | "cat 1>&2"; else print $0}'
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790
iuc
parents: 22
diff changeset
60 > '$counts'
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790
iuc
parents: 22
diff changeset
61 2> '$othercounts'
24
620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty
iuc
parents: 23
diff changeset
62
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
63 #if $samout_conditional.samout == "Yes":
23
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790
iuc
parents: 22
diff changeset
64 && samtools view -Su
24
620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty
iuc
parents: 23
diff changeset
65 -t '${reference_fasta_filename}.fai'
620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty
iuc
parents: 23
diff changeset
66 '$__new_file_path__/${samoutfile.id}_tmp'
620d5603d1a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f-dirty
iuc
parents: 23
diff changeset
67 | samtools sort -o '$samoutfile' -
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
68 #end if
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
69 ]]>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
70 </command>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
71
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
72 <inputs>
16
227f9d3f0e32 Updated HTSeq package to version 0.6.1, fixed input format string, updated dependency definitions
lparsons
parents: 15
diff changeset
73 <param format="sam,bam" name="samfile" type="data" label="Aligned SAM/BAM File"/>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
74 <param format="gff" name="gfffile" type="data" label="GFF File"/>
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
75 <param name="mode" type="select" label="Mode" argument="(--mode)">
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
76 <help>Mode to handle reads overlapping more than one feature.</help>
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
77 <option value="union" selected="True">Union</option>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
78 <option value="intersection-strict">Intersection (strict)</option>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
79 <option value="intersection-nonempty">Intersection (nonempty)</option>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
80 </param>
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
81 <param name="stranded" type="select" label="Stranded" argument="(--stranded)">
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
82 <help>Specify whether the data is from a strand-specific assay. 'Reverse' means yes with reversed strand interpretation.</help>
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
83 <option value="yes" selected="True">Yes</option>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
84 <option value="no">No</option>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
85 <option value="reverse">Reverse</option>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
86 </param>
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
87 <param name="minaqual" type="integer" value="10" label="Minimum alignment quality" argument="--minaqual">
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
88 <help>Skip all reads with alignment quality lower than the given minimum value.</help>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
89 </param>
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
90 <param name="featuretype" type="text" value="exon" label="Feature type" argument="--type">
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
91 <help>Feature type (3rd column in GFF file) to be used. All features of other types are ignored. The default, suitable for RNA-Seq and Ensembl GTF files, is exon.</help>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
92 </param>
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
93 <param name="idattr" type="text" value="gene_id" label="ID Attribute" argument="--idattr">
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
94 <help>GFF attribute to be used as feature ID. Several GFF lines with the same feature ID will be considered as parts of the same feature. The feature ID is used to identity the counts in the output table. All features of the specified type MUST have a value for this attribute. The default, suitable for RNA-Seq and Ensembl GTF files, is gene_id.</help>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
95 </param>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
96 <conditional name="samout_conditional">
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
97 <param name="samout" type="select" label="Additional BAM Output">
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
98 <help>Write out all SAM alignment records into an output BAM file, annotating each line with its assignment to a feature or a special counter (as an optional field with tag ‘XF’).</help>
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
99 <option value="No" selected="True">Do not output additional BAM file</option>
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
100 <option value="Yes">Output additional BAM file</option>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
101 </param>
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
102 <when value="Yes">
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
103 <conditional name="reference_source">
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
104 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
105 <option value="cached">Locally cached</option>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
106 <option value="history">History</option>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
107 </param>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
108 <when value="cached">
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
109 <param name="ref_file" type="select" label="Using reference genome">
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
110 <options from_data_table="sam_fa_indexes">
9
971e20519fb8 Fix for dbkey column check when output additional bam is selected
lparsons
parents: 8
diff changeset
111 <filter type="data_meta" key="dbkey" ref="samfile" column="1"/>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
112 </options>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
113 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
114 </param>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
115 </when>
23
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790
iuc
parents: 22
diff changeset
116 <when value="history">
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
117 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
118 </when>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
119 </conditional>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
120 </when>
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
121 <when value="No">
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
122 <!-- Do nothing -->
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
123 </when>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
124 </conditional>
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
125 <param name="force_sort" type="boolean" value="False" truevalue="True" falsevalue="False" label="Force sorting of SAM/BAM file by NAME">
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
126 <help>This option can be used for for paired-end data that has many unmapped mates. Use this if you get the warning about paired end data missing or not being properly sorted.</help>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
127 </param>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
128 </inputs>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
129
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
130 <outputs>
23
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790
iuc
parents: 22
diff changeset
131 <data format="tabular" name="counts" metadata_source="samfile" label="${tool.name} on ${on_string}">
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790
iuc
parents: 22
diff changeset
132 <actions>
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790
iuc
parents: 22
diff changeset
133 <action name="column_names" type="metadata" default="Geneid,${samfile.name}" />
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790
iuc
parents: 22
diff changeset
134 </actions>
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790
iuc
parents: 22
diff changeset
135 </data>
10
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
136 <data format="tabular" name="othercounts" metadata_source="samfile" label="${tool.name} on ${on_string} (no feature)"/>
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
137 <data format="bam" name="samoutfile" metadata_source="samfile" label="${tool.name} on ${on_string} (BAM)">
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
138 <filter>samout_conditional['samout'] == "Yes"</filter>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
139 </data>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
140 </outputs>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
141
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
142 <tests>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
143 <test>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
144 <param name="samfile" value="htseq-test.sam" />
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
145 <param name="gfffile" value="htseq-test.gff" />
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
146 <param name="samout" value="No" />
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
147 <output name="counts" file="htseq-test_counts.tsv" />
3
f7a5b54a8d4f Split feature and non-feature counts, removed tool_dependencies.xml (for now)
Lance Parsons <lparsons@princeton.edu>
parents: 0
diff changeset
148 <output name="othercounts" file="htseq-test_othercounts.tsv" />
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
149 </test>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
150 <test>
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
151 <param name="samfile" value="htseq-test.sam" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
152 <param name="gfffile" value="htseq-test.gff" />
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
153 <param name="samout" value="No" />
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
154 <param name="force_sort" value="True" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
155 <output name="counts" file="htseq-test_counts.tsv" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
156 <output name="othercounts" file="htseq-test_othercounts.tsv" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
157 </test>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
158 <test>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
159 <param name="samfile" value="htseq-test.bam" />
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
160 <param name="gfffile" value="htseq-test.gff" />
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
161 <param name="samout" value="No" />
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
162 <output name="counts" file="htseq-test_counts.tsv" />
3
f7a5b54a8d4f Split feature and non-feature counts, removed tool_dependencies.xml (for now)
Lance Parsons <lparsons@princeton.edu>
parents: 0
diff changeset
163 <output name="othercounts" file="htseq-test_othercounts.tsv" />
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
164 </test>
10
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
165 <test>
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
166 <param name="samfile" value="htseq-test-paired.bam" />
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
167 <param name="singlepaired" value="paired" />
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
168 <param name="gfffile" value="htseq-test.gff" />
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
169 <param name="samout" value="No" />
10
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
170 <output name="counts" file="htseq-test-paired_counts.tsv" />
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
171 <output name="othercounts" file="htseq-test-paired_othercounts.tsv" />
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
172 </test>
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
173 <test>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
174 <param name="samfile" value="htseq-test-paired.bam" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
175 <param name="singlepaired" value="paired" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
176 <param name="gfffile" value="htseq-test.gff" />
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
177 <param name="samout" value="No" />
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
178 <param name="force_sort" value="True" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
179 <output name="counts" file="htseq-test-paired_counts.tsv" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
180 <output name="othercounts" file="htseq-test-paired_othercounts.tsv" />
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
181 </test>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
182 <test>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
183 <param name="samfile" value="htseq-test.sam" />
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
184 <param name="gfffile" value="htseq-test.gff" />
23
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790
iuc
parents: 22
diff changeset
185 <param name="samout" value="Yes" />
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
186 <param name="reference_source_selector" value="history" />
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
187 <param name="ref_file" value="htseq-test_reference.fasta" />
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
188 <output name="counts" file="htseq-test_counts.tsv" />
3
f7a5b54a8d4f Split feature and non-feature counts, removed tool_dependencies.xml (for now)
Lance Parsons <lparsons@princeton.edu>
parents: 0
diff changeset
189 <output name="othercounts" file="htseq-test_othercounts.tsv" />
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
190 <output name="samoutfile" file="htseq-test_samout.bam" />
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
191 </test>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
192 </tests>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
193
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
194 <help>
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
195 <![CDATA[
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
196 Overview
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
197 --------
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
198
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
199 This tool takes an alignment file in SAM or BAM format and feature file in GFF format
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
200 and calculates the number of reads mapping to each feature. It uses the *htseq-count*
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
201 script that is part of the HTSeq python module. See
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
202 http://www-huber.embl.de/users/anders/HTSeq/doc/count.html for details.
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
203
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
204 A feature is an interval (i.e., a range of positions) on a chromosome or a union of
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
205 such intervals. In the case of RNA-Seq, the features are typically genes, where
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
206 each gene is considered here as the union of all its exons. One may also consider
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
207 each exon as a feature, e.g., in order to check for alternative splicing. For
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
208 comparative ChIP-Seq, the features might be binding regions from a pre-determined
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
209 list.
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
210
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
211
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
212 Overlap Modes
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
213 -------------
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
214
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
215 Special care must be taken to decide how to deal with reads that overlap more than one feature.
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
216
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
217 The htseq-count script allows to choose between three modes: *union*, *intersection-strict*, and *intersection-nonempty*.
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
218
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
219 The following figure illustrates the effect of these three modes:
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
220
16
227f9d3f0e32 Updated HTSeq package to version 0.6.1, fixed input format string, updated dependency definitions
lparsons
parents: 15
diff changeset
221 .. image:: count_modes.png
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
222
11
f320093f1e8e Removed sorting notice from help
lparsons
parents: 10
diff changeset
223
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
224 Strandedness
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
225 ------------
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
226
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
227 **Important**: The default for strandedness is yes. If your RNA-Seq data has not been made with a strand-specific protocol, this causes half of the reads to be lost. Hence, make sure to set the option Stranded to 'No' unless you have strand-specific data!
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
228
11
f320093f1e8e Removed sorting notice from help
lparsons
parents: 10
diff changeset
229
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
230 Output
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
231 ------
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
232
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
233 The script outputs a table with counts for each feature, followed by the special counters, which count reads that were not counted for any feature for various reasons, namely
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
234
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
235 - *no_feature*: reads which could not be assigned to any feature (set S as described above was empty).
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
236
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
237 - *ambiguous*: reads which could have been assigned to more than one feature and hence were not counted for any of these (set S had mroe than one element).
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
238
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
239 - *too_low_aQual*: reads which were not counted due to the -a option, see below
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
240
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
241 - *not_aligned*: reads in the SAM file without alignment
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
242
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
243 - *alignment_not_unique*: reads with more than one reported alignment. These reads are recognized from the NH optional SAM field tag. (If the aligner does not set this field, multiply aligned reads will be counted multiple times.)
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
244
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
245
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
246 Options Summary
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
247 ---------------
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
248
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
249 Usage: htseq-count [options] sam_file gff_file
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
250
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
251 This script takes an alignment file in SAM format and a feature file in GFF
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
252 format and calculates for each feature the number of reads mapping to it. See
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
253 http://www-huber.embl.de/users/anders/HTSeq/doc/count.html for details.
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
254
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
255 Options:
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
256 -h, --help show this help message and exit
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
257 -m MODE, --mode=MODE mode to handle reads overlapping more than one
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
258 feature(choices: union, intersection-strict,
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
259 intersection-nonempty; default: union)
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
260 -s STRANDED, --stranded=STRANDED
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
261 whether the data is from a strand-specific assay.
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
262 Specify 'yes', 'no', or 'reverse' (default: yes).
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
263 'reverse' means 'yes' with reversed strand
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
264 interpretation
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
265 -a MINAQUAL, --minaqual=MINAQUAL
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
266 skip all reads with alignment quality lower than the
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
267 given minimum value (default: 0)
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
268 -t FEATURETYPE, --type=FEATURETYPE
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
269 feature type (3rd column in GFF file) to be used, all
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
270 features of other type are ignored (default, suitable
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
271 for Ensembl GTF files: exon)
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
272 -i IDATTR, --idattr=IDATTR
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
273 GFF attribute to be used as feature ID (default,
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
274 suitable for Ensembl GTF files: gene_id)
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
275 -o SAMOUT, --samout=SAMOUT
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
276 write out all SAM alignment records into an output SAM
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
277 file called SAMOUT, annotating each line with its
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
278 feature assignment (as an optional field with tag
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
279 'XF')
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
280 -q, --quiet suppress progress report and warnings
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
281
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
282 Written by Simon Anders (sanders@fs.tum.de), European Molecular Biology
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
283 Laboratory (EMBL). (c) 2010. Released under the terms of the GNU General
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
284 Public License v3. Part of the 'HTSeq' framework.
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
285 ]]>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
286 </help>
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
287 <citations>
23
6e5c95760ab1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790
iuc
parents: 22
diff changeset
288 <citation type="doi">10.1093/bioinformatics/btu638</citation>
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
289 </citations>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
290 </tool>