Mercurial > repos > lparsons > htseq_count
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 |
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date | Tue, 20 Sep 2016 17:51:06 -0400 |
parents | a6dcb86af112 |
children | 6e5c95760ab1 |
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55ed198f2c1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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1 <tool id="htseq_count" name="htseq-count" version="0.6.1galaxy2"> |
0 | 2 <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description> |
3 <requirements> | |
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55ed198f2c1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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4 <requirement type="package" version="0.6.1.post1">htseq</requirement> |
13 | 5 <requirement type="package" version="0.1.19">samtools</requirement> |
0 | 6 </requirements> |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
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7 |
3b3601a2a7c7
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
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8 <stdio> |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
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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
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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
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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
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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
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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
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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
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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
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16 </stdio> |
3b3601a2a7c7
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
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17 |
3b3601a2a7c7
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
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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
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19 |
3b3601a2a7c7
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
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20 <command><![CDATA[ |
0 | 21 ##set up input files |
22 #set $reference_fasta_filename = "localref.fa" | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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23 #if $samout_conditional.samout == "Yes": |
0 | 24 #if str( $samout_conditional.reference_source.reference_source_selector ) == "history": |
20
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
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25 ln -s "${samout_conditional.reference_source.ref_file}" "${reference_fasta_filename}" && |
3b3601a2a7c7
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
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26 samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for htseq-count" >&2 && |
0 | 27 #else: |
28 #set $reference_fasta_filename = str( $samout_conditional.reference_source.ref_file.fields.path ) | |
29 #end if | |
30 #end if | |
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55ed198f2c1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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31 #if $force_sort == "True": |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
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32 #if $samfile.extension == 'bam': |
3b3601a2a7c7
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
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33 samtools sort -n "$samfile" "name_sorted_alignment" && |
3b3601a2a7c7
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
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34 #else |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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35 samtools view -Su -t "${reference_fasta_filename}.fai" "$samfile" | samtools sort -n - "name_sorted_alignment" && |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
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36 #end if |
3b3601a2a7c7
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
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37 #end if |
3b3601a2a7c7
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
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38 htseq-count |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
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39 --mode=$mode |
3b3601a2a7c7
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
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40 --stranded=$stranded |
3b3601a2a7c7
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
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41 --minaqual=$minaqual |
3b3601a2a7c7
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
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42 --type="$featuretype" |
3b3601a2a7c7
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
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43 --idattr="$idattr" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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44 #if $samout_conditional.samout == "Yes": |
0 | 45 --samout=$__new_file_path__/${samoutfile.id}_tmp |
46 #end if | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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47 #if $force_sort == "True": |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
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48 --order=name |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
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49 --format=bam |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
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50 name_sorted_alignment.bam |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
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51 #else |
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52 --order=pos |
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53 --format=$samfile.extension |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23
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54 $samfile |
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55 #end if |
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56 "$gfffile" |
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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 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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58 #if $samout_conditional.samout == "Yes": |
55ed198f2c1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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59 && samtools view -Su -t "${reference_fasta_filename}.fai" "$__new_file_path__/${samoutfile.id}_tmp" | samtools sort -o - sorted > "$samoutfile" |
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60 #end if |
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61 ]]> |
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62 </command> |
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63 |
0 | 64 <inputs> |
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65 <param format="sam,bam" name="samfile" type="data" label="Aligned SAM/BAM File"/> |
0 | 66 <param format="gff" name="gfffile" type="data" label="GFF File"/> |
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67 <param name="mode" type="select" label="Mode" argument="(--mode)"> |
0 | 68 <help>Mode to handle reads overlapping more than one feature.</help> |
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69 <option value="union" selected="True">Union</option> |
0 | 70 <option value="intersection-strict">Intersection (strict)</option> |
71 <option value="intersection-nonempty">Intersection (nonempty)</option> | |
72 </param> | |
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73 <param name="stranded" type="select" label="Stranded" argument="(--stranded)"> |
0 | 74 <help>Specify whether the data is from a strand-specific assay. 'Reverse' means yes with reversed strand interpretation.</help> |
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75 <option value="yes" selected="True">Yes</option> |
0 | 76 <option value="no">No</option> |
77 <option value="reverse">Reverse</option> | |
78 </param> | |
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79 <param name="minaqual" type="integer" value="10" label="Minimum alignment quality" argument="--minaqual"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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80 <help>Skip all reads with alignment quality lower than the given minimum value.</help> |
0 | 81 </param> |
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82 <param name="featuretype" type="text" value="exon" label="Feature type" argument="--type"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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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 | 84 </param> |
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85 <param name="idattr" type="text" value="gene_id" label="ID Attribute" argument="--idattr"> |
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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 | 87 </param> |
88 <conditional name="samout_conditional"> | |
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89 <param name="samout" type="select" label="Additional BAM Output"> |
0 | 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> |
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91 <option value="No" selected="True">Do not output additional BAM file</option> |
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92 <option value="Yes">Output additional BAM file</option> |
0 | 93 </param> |
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94 <when value="Yes"> |
0 | 95 <conditional name="reference_source"> |
96 <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> | |
97 <option value="cached">Locally cached</option> | |
98 <option value="history">History</option> | |
99 </param> | |
100 <when value="cached"> | |
101 <param name="ref_file" type="select" label="Using reference genome"> | |
102 <options from_data_table="sam_fa_indexes"> | |
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Fix for dbkey column check when output additional bam is selected
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103 <filter type="data_meta" key="dbkey" ref="samfile" column="1"/> |
0 | 104 </options> |
105 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
106 </param> | |
107 </when> | |
108 <when value="history"> <!-- FIX ME!!!! --> | |
109 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> | |
110 </when> | |
111 </conditional> | |
112 </when> | |
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113 <when value="No"> |
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114 <!-- Do nothing --> |
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115 </when> |
0 | 116 </conditional> |
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117 <param name="force_sort" type="boolean" value="False" truevalue="True" falsevalue="False" label="Force sorting of SAM/BAM file by NAME"> |
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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> |
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119 </param> |
0 | 120 </inputs> |
121 | |
122 <outputs> | |
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123 <data format="tabular" name="counts" metadata_source="samfile" label="${tool.name} on ${on_string}"/> |
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124 <data format="tabular" name="othercounts" metadata_source="samfile" label="${tool.name} on ${on_string} (no feature)"/> |
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125 <data format="bam" name="samoutfile" metadata_source="samfile" label="${tool.name} on ${on_string} (BAM)"> |
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126 <filter>samout_conditional['samout'] == "Yes"</filter> |
0 | 127 </data> |
128 </outputs> | |
129 | |
130 <tests> | |
131 <test> | |
132 <param name="samfile" value="htseq-test.sam" /> | |
133 <param name="gfffile" value="htseq-test.gff" /> | |
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134 <param name="samout" value="No" /> |
0 | 135 <output name="counts" file="htseq-test_counts.tsv" /> |
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136 <output name="othercounts" file="htseq-test_othercounts.tsv" /> |
0 | 137 </test> |
138 <test> | |
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139 <param name="samfile" value="htseq-test.sam" /> |
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140 <param name="gfffile" value="htseq-test.gff" /> |
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141 <param name="samout" value="No" /> |
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142 <param name="force_sort" value="True" /> |
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143 <output name="counts" file="htseq-test_counts.tsv" /> |
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144 <output name="othercounts" file="htseq-test_othercounts.tsv" /> |
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145 </test> |
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146 <test> |
0 | 147 <param name="samfile" value="htseq-test.bam" /> |
148 <param name="gfffile" value="htseq-test.gff" /> | |
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149 <param name="samout" value="No" /> |
0 | 150 <output name="counts" file="htseq-test_counts.tsv" /> |
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151 <output name="othercounts" file="htseq-test_othercounts.tsv" /> |
0 | 152 </test> |
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153 <test> |
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154 <param name="samfile" value="htseq-test-paired.bam" /> |
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155 <param name="singlepaired" value="paired" /> |
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156 <param name="gfffile" value="htseq-test.gff" /> |
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157 <param name="samout" value="No" /> |
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158 <output name="counts" file="htseq-test-paired_counts.tsv" /> |
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159 <output name="othercounts" file="htseq-test-paired_othercounts.tsv" /> |
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160 </test> |
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161 <test> |
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162 <param name="samfile" value="htseq-test-paired.bam" /> |
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163 <param name="singlepaired" value="paired" /> |
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164 <param name="gfffile" value="htseq-test.gff" /> |
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165 <param name="samout" value="No" /> |
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166 <param name="force_sort" value="True" /> |
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167 <output name="counts" file="htseq-test-paired_counts.tsv" /> |
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168 <output name="othercounts" file="htseq-test-paired_othercounts.tsv" /> |
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169 </test> |
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170 |
0 | 171 <!-- Seems to be an issue setting the $reference_fasta_filename variable during test |
172 <test> | |
173 <param name="samfile" value="htseq-test.sam" /> | |
174 <param name="gfffile" value="htseq-test.gff" /> | |
175 <param name="samout" value="True" /> | |
176 <param name="reference_source_selector" value="history" /> | |
177 <param name="ref_file" value="htseq-test_reference.fasta" /> | |
178 <output name="counts" file="htseq-test_counts.tsv" /> | |
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179 <output name="othercounts" file="htseq-test_othercounts.tsv" /> |
0 | 180 <output name="samoutfile" file="htseq-test_samout.bam" /> |
181 </test> | |
182 --> | |
183 </tests> | |
184 | |
185 <help> | |
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186 <![CDATA[ |
0 | 187 Overview |
188 -------- | |
189 | |
190 This tool takes an alignment file in SAM or BAM format and feature file in GFF format | |
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191 and calculates the number of reads mapping to each feature. It uses the *htseq-count* |
0 | 192 script that is part of the HTSeq python module. See |
193 http://www-huber.embl.de/users/anders/HTSeq/doc/count.html for details. | |
194 | |
195 A feature is an interval (i.e., a range of positions) on a chromosome or a union of | |
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196 such intervals. In the case of RNA-Seq, the features are typically genes, where |
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197 each gene is considered here as the union of all its exons. One may also consider |
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198 each exon as a feature, e.g., in order to check for alternative splicing. For |
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199 comparative ChIP-Seq, the features might be binding regions from a pre-determined |
0 | 200 list. |
201 | |
202 | |
203 Overlap Modes | |
204 ------------- | |
205 | |
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206 Special care must be taken to decide how to deal with reads that overlap more than one feature. |
0 | 207 |
208 The htseq-count script allows to choose between three modes: *union*, *intersection-strict*, and *intersection-nonempty*. | |
209 | |
210 The following figure illustrates the effect of these three modes: | |
211 | |
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212 .. image:: count_modes.png |
0 | 213 |
11 | 214 |
0 | 215 Strandedness |
216 ------------ | |
217 | |
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! | |
219 | |
11 | 220 |
0 | 221 Output |
222 ------ | |
223 | |
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 | |
225 | |
226 - *no_feature*: reads which could not be assigned to any feature (set S as described above was empty). | |
227 | |
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). | |
229 | |
230 - *too_low_aQual*: reads which were not counted due to the -a option, see below | |
231 | |
232 - *not_aligned*: reads in the SAM file without alignment | |
233 | |
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.) | |
235 | |
236 | |
237 Options Summary | |
238 --------------- | |
239 | |
240 Usage: htseq-count [options] sam_file gff_file | |
241 | |
242 This script takes an alignment file in SAM format and a feature file in GFF | |
243 format and calculates for each feature the number of reads mapping to it. See | |
244 http://www-huber.embl.de/users/anders/HTSeq/doc/count.html for details. | |
245 | |
246 Options: | |
247 -h, --help show this help message and exit | |
248 -m MODE, --mode=MODE mode to handle reads overlapping more than one | |
249 feature(choices: union, intersection-strict, | |
250 intersection-nonempty; default: union) | |
251 -s STRANDED, --stranded=STRANDED | |
252 whether the data is from a strand-specific assay. | |
253 Specify 'yes', 'no', or 'reverse' (default: yes). | |
254 'reverse' means 'yes' with reversed strand | |
255 interpretation | |
256 -a MINAQUAL, --minaqual=MINAQUAL | |
257 skip all reads with alignment quality lower than the | |
258 given minimum value (default: 0) | |
259 -t FEATURETYPE, --type=FEATURETYPE | |
260 feature type (3rd column in GFF file) to be used, all | |
261 features of other type are ignored (default, suitable | |
262 for Ensembl GTF files: exon) | |
263 -i IDATTR, --idattr=IDATTR | |
264 GFF attribute to be used as feature ID (default, | |
265 suitable for Ensembl GTF files: gene_id) | |
266 -o SAMOUT, --samout=SAMOUT | |
267 write out all SAM alignment records into an output SAM | |
268 file called SAMOUT, annotating each line with its | |
269 feature assignment (as an optional field with tag | |
270 'XF') | |
271 -q, --quiet suppress progress report and warnings | |
272 | |
273 Written by Simon Anders (sanders@fs.tum.de), European Molecular Biology | |
274 Laboratory (EMBL). (c) 2010. Released under the terms of the GNU General | |
275 Public License v3. Part of the 'HTSeq' framework. | |
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276 ]]> |
0 | 277 </help> |
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278 |
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279 <citations> |
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280 <citation type="bibtex"> |
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281 @article{anders_htseqpython_2015, |
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282 title = {{HTSeq}—a {Python} framework to work with high-throughput sequencing data}, |
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283 volume = {31}, |
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284 issn = {1367-4803, 1460-2059}, |
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285 url = {http://bioinformatics.oxfordjournals.org/content/31/2/166}, |
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286 doi = {10.1093/bioinformatics/btu638}, |
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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. |
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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. |
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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. |
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290 Contact: sanders\{at\}fs.tum.de}, |
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291 language = {en}, |
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292 number = {2}, |
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293 urldate = {2015-04-21}, |
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294 journal = {Bioinformatics}, |
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295 author = {Anders, Simon and Pyl, Paul Theodor and Huber, Wolfgang}, |
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296 month = jan, |
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297 year = {2015}, |
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298 pmid = {25260700}, |
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299 pages = {166--169}, |
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300 } |
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301 } |
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302 </citation> |
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303 </citations> |
0 | 304 </tool> |