annotate htseq-count.xml @ 22:55ed198f2c1c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
author iuc
date Tue, 20 Sep 2016 17:51:06 -0400
parents a6dcb86af112
children 6e5c95760ab1
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
1 <tool id="htseq_count" name="htseq-count" version="0.6.1galaxy2">
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>
13
30bb8acb77a4 Updated to v0.5.4p5, use repository dependencies.
lparsons
parents: 12
diff changeset
5 <requirement type="package" version="0.1.19">samtools</requirement>
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}" "${reference_fasta_filename}" &&
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
26 samtools faidx "${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
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
31 #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
32 #if $samfile.extension == 'bam':
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
33 samtools sort -n "$samfile" "name_sorted_alignment" &&
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
34 #else
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
35 samtools view -Su -t "${reference_fasta_filename}.fai" "$samfile" | samtools sort -n - "name_sorted_alignment" &&
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
36 #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
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 htseq-count
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
39 --mode=$mode
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
40 --stranded=$stranded
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
41 --minaqual=$minaqual
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
42 --type="$featuretype"
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
43 --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
44 #if $samout_conditional.samout == "Yes":
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
45 --samout=$__new_file_path__/${samoutfile.id}_tmp
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
46 #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
47 #if $force_sort == "True":
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
48 --order=name
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
49 --format=bam
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
50 name_sorted_alignment.bam
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
51 #else
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
52 --order=pos
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
53 --format=$samfile.extension
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
54 $samfile
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
55 #end if
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
56 "$gfffile"
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
57 | awk '{if ($1 ~ "no_feature|ambiguous|too_low_aQual|not_aligned|alignment_not_unique") print $0 | "cat 1>&2"; else print $0}' > $counts 2>$othercounts
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
58 #if $samout_conditional.samout == "Yes":
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
59 && samtools view -Su -t "${reference_fasta_filename}.fai" "$__new_file_path__/${samoutfile.id}_tmp" | samtools sort -o - sorted > "$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
60 #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
61 ]]>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
62 </command>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
63
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
64 <inputs>
16
227f9d3f0e32 Updated HTSeq package to version 0.6.1, fixed input format string, updated dependency definitions
lparsons
parents: 15
diff changeset
65 <param format="sam,bam" name="samfile" type="data" label="Aligned SAM/BAM File"/>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
66 <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
67 <param name="mode" type="select" label="Mode" argument="(--mode)">
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
68 <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
69 <option value="union" selected="True">Union</option>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
70 <option value="intersection-strict">Intersection (strict)</option>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
71 <option value="intersection-nonempty">Intersection (nonempty)</option>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
72 </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
73 <param name="stranded" type="select" label="Stranded" argument="(--stranded)">
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
74 <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
75 <option value="yes" selected="True">Yes</option>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
76 <option value="no">No</option>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
77 <option value="reverse">Reverse</option>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
78 </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
79 <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
80 <help>Skip all reads with alignment quality lower than the given minimum value.</help>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
81 </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
82 <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
83 <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
84 </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
85 <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
86 <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
87 </param>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
88 <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
89 <param name="samout" type="select" label="Additional BAM Output">
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
90 <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
91 <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
92 <option value="Yes">Output additional BAM file</option>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
93 </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
94 <when value="Yes">
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
95 <conditional name="reference_source">
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
96 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
97 <option value="cached">Locally cached</option>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
98 <option value="history">History</option>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
99 </param>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
100 <when value="cached">
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
101 <param name="ref_file" type="select" label="Using reference genome">
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
102 <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
103 <filter type="data_meta" key="dbkey" ref="samfile" column="1"/>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
104 </options>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
105 <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
106 </param>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
107 </when>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
108 <when value="history"> <!-- FIX ME!!!! -->
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
109 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
110 </when>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
111 </conditional>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
112 </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
113 <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
114 <!-- 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
115 </when>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
116 </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
117 <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
118 <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
119 </param>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
120 </inputs>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
121
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
122 <outputs>
10
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
123 <data format="tabular" name="counts" metadata_source="samfile" label="${tool.name} on ${on_string}"/>
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
124 <data format="tabular" name="othercounts" metadata_source="samfile" label="${tool.name} on ${on_string} (no feature)"/>
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
125 <data format="bam" name="samoutfile" metadata_source="samfile" label="${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
126 <filter>samout_conditional['samout'] == "Yes"</filter>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
127 </data>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
128 </outputs>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
129
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
130 <tests>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
131 <test>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
132 <param name="samfile" value="htseq-test.sam" />
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
133 <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
134 <param name="samout" value="No" />
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
135 <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
136 <output name="othercounts" file="htseq-test_othercounts.tsv" />
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
137 </test>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
138 <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
139 <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
140 <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
141 <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
142 <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
143 <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
144 <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
145 </test>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
146 <test>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
147 <param name="samfile" value="htseq-test.bam" />
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
148 <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
149 <param name="samout" value="No" />
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
150 <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
151 <output name="othercounts" file="htseq-test_othercounts.tsv" />
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
152 </test>
10
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
153 <test>
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
154 <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
155 <param name="singlepaired" value="paired" />
5d969cb56112 Version 0.3 - paried-end sorting is now built-in (uses Picard tools)
lparsons
parents: 9
diff changeset
156 <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
157 <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
158 <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
159 <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
160 </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
161 <test>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
162 <param name="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
163 <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
164 <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
165 <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
166 <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
167 <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
168 <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
169 </test>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
170
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
171 <!-- Seems to be an issue setting the $reference_fasta_filename variable during test
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
172 <test>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
173 <param name="samfile" value="htseq-test.sam" />
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
174 <param name="gfffile" value="htseq-test.gff" />
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
175 <param name="samout" value="True" />
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
176 <param name="reference_source_selector" value="history" />
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
177 <param name="ref_file" value="htseq-test_reference.fasta" />
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
178 <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
179 <output name="othercounts" file="htseq-test_othercounts.tsv" />
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
180 <output name="samoutfile" file="htseq-test_samout.bam" />
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
181 </test>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
182 -->
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
183 </tests>
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
184
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
185 <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
186 <![CDATA[
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
187 Overview
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
188 --------
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
189
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
190 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
191 and calculates the number of reads mapping to each feature. It uses the *htseq-count*
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
192 script that is part of the HTSeq python module. See
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
193 http://www-huber.embl.de/users/anders/HTSeq/doc/count.html for details.
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
194
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
195 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
196 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
197 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
198 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
199 comparative ChIP-Seq, the features might be binding regions from a pre-determined
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
200 list.
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
201
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
202
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
203 Overlap Modes
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
204 -------------
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
205
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
206 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
207
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
208 The htseq-count script allows to choose between three modes: *union*, *intersection-strict*, and *intersection-nonempty*.
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
209
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
210 The following figure illustrates the effect of these three modes:
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
211
16
227f9d3f0e32 Updated HTSeq package to version 0.6.1, fixed input format string, updated dependency definitions
lparsons
parents: 15
diff changeset
212 .. image:: count_modes.png
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
213
11
f320093f1e8e Removed sorting notice from help
lparsons
parents: 10
diff changeset
214
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
215 Strandedness
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
216 ------------
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
217
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
218 **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
219
11
f320093f1e8e Removed sorting notice from help
lparsons
parents: 10
diff changeset
220
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
221 Output
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
222 ------
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
223
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
224 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
225
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
226 - *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
227
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
228 - *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
229
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
230 - *too_low_aQual*: reads which were not counted due to the -a option, see below
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
231
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
232 - *not_aligned*: reads in the SAM file without alignment
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
233
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
234 - *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
235
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
236
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
237 Options Summary
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
238 ---------------
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
239
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
240 Usage: htseq-count [options] sam_file gff_file
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
241
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
242 This script takes an alignment file in SAM format and a feature file in GFF
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
243 format and calculates for each feature the number of reads mapping to it. See
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
244 http://www-huber.embl.de/users/anders/HTSeq/doc/count.html for details.
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
245
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
246 Options:
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
247 -h, --help show this help message and exit
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
248 -m MODE, --mode=MODE mode to handle reads overlapping more than one
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
249 feature(choices: union, intersection-strict,
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
250 intersection-nonempty; default: union)
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
251 -s STRANDED, --stranded=STRANDED
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
252 whether the data is from a strand-specific assay.
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
253 Specify 'yes', 'no', or 'reverse' (default: yes).
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
254 'reverse' means 'yes' with reversed strand
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
255 interpretation
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
256 -a MINAQUAL, --minaqual=MINAQUAL
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
257 skip all reads with alignment quality lower than the
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
258 given minimum value (default: 0)
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
259 -t FEATURETYPE, --type=FEATURETYPE
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
260 feature type (3rd column in GFF file) to be used, all
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
261 features of other type are ignored (default, suitable
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
262 for Ensembl GTF files: exon)
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
263 -i IDATTR, --idattr=IDATTR
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
264 GFF attribute to be used as feature ID (default,
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
265 suitable for Ensembl GTF files: gene_id)
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
266 -o SAMOUT, --samout=SAMOUT
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
267 write out all SAM alignment records into an output SAM
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
268 file called SAMOUT, annotating each line with its
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
269 feature assignment (as an optional field with tag
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
270 'XF')
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
271 -q, --quiet suppress progress report and warnings
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
272
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
273 Written by Simon Anders (sanders@fs.tum.de), European Molecular Biology
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
274 Laboratory (EMBL). (c) 2010. Released under the terms of the GNU General
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
275 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
276 ]]>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
277 </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
278
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
279 <citations>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
280 <citation type="bibtex">
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
281 @article{anders_htseqpython_2015,
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
282 title = {{HTSeq}—a {Python} framework to work with high-throughput sequencing data},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
283 volume = {31},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
284 issn = {1367-4803, 1460-2059},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
285 url = {http://bioinformatics.oxfordjournals.org/content/31/2/166},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
286 doi = {10.1093/bioinformatics/btu638},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
287 abstract = {Motivation: A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard workflows, custom scripts are needed.
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
288 Results: We present HTSeq, a Python library to facilitate the rapid development of such scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data, such as genomic coordinates, sequences, sequencing reads, alignments, gene model information and variant calls, and provides data structures that allow for querying via genomic coordinates. We also present htseq-count, a tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes.
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
289 Availability and implementation: HTSeq is released as an open-source software under the GNU General Public Licence and available from http://www-huber.embl.de/HTSeq or from the Python Package Index at https://pypi.python.org/pypi/HTSeq.
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
290 Contact: sanders\{at\}fs.tum.de},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
291 language = {en},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
292 number = {2},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
293 urldate = {2015-04-21},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
294 journal = {Bioinformatics},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
295 author = {Anders, Simon and Pyl, Paul Theodor and Huber, Wolfgang},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
296 month = jan,
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
297 year = {2015},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
298 pmid = {25260700},
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
299 pages = {166--169},
22
55ed198f2c1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents: 21
diff changeset
300 }
20
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
301 }
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
302 </citation>
3b3601a2a7c7 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
lparsons
parents: 17
diff changeset
303 </citations>
0
3fdeebd7e710 Initial commit
lparsons
parents:
diff changeset
304 </tool>