Mercurial > repos > iuc > featurecounts
annotate featurecounts.xml @ 24:a37612abf7f9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 809715c88721d082b304cf4e4a37b52d30162f08"
author | iuc |
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date | Fri, 06 Sep 2019 11:08:21 -0400 |
parents | 9301937c9037 |
children | 90d16db017d7 |
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24
a37612abf7f9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 809715c88721d082b304cf4e4a37b52d30162f08"
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1 <tool id="featurecounts" name="featureCounts" version="1.6.4+galaxy1" profile="16.04"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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2 <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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3 <requirements> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 8c751ba49b1465ad147574fcede7ad4a27f8805d
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4 <requirement type="package" version="1.6.4">subread</requirement> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a956e32b176d645db54db3c86586cc0bfa2fbd3c
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5 <requirement type="package" version="1.9">samtools</requirement> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 8c751ba49b1465ad147574fcede7ad4a27f8805d
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6 <requirement type="package" version="8.31">coreutils</requirement> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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7 </requirements> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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8 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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9 <version_command>featureCounts -v 2>&1 | grep .</version_command> |
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10 <command detect_errors="exit_code"><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
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11 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
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12 ## Export fc path for its built-in annotation |
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13 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
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14 export FC_PATH=\$(command -v featureCounts | sed 's@/bin/featureCounts$@@') && |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
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15 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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16 ## Check whether all alignments are from the same type (bam || sam) |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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17 featureCounts |
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18 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
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19 #if $anno.anno_select=="history": |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
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20 -a '$anno.reference_gene_sets' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
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21 -F "GTF" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
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22 #elif $anno.anno_select=="cached": |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
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23 -a '$anno.reference_gene_sets_builtin.fields.path' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
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24 -F "GTF" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
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25 #elif $anno.anno_select=="builtin": |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
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26 -a \${FC_PATH}/annotation/${anno.bgenome}_RefSeq_exon.txt |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
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27 -F "SAF" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f
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28 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f
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29 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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30 -o "output" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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31 -T \${GALAXY_SLOTS:-2} |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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32 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca
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33 -s $strand_specificity |
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34 -t '$extended_parameters.gff_feature_type' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
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35 -g '$extended_parameters.gff_feature_attribute' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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36 $extended_parameters.summarization_level |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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37 $extended_parameters.contribute_to_multiple_features |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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38 $extended_parameters.multimapping_enabled.multimapping_counts |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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39 |
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40 #if str($extended_parameters.multimapping_enabled.multimapping_counts) == " -M": |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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41 $extended_parameters.multimapping_enabled.fraction |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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42 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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43 |
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44 $extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads |
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45 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J": |
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46 #if $extended_parameters.exon_exon_junction_read_counting_enabled.genome: |
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47 -G '$extended_parameters.exon_exon_junction_read_counting_enabled.genome' |
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48 #end if |
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49 #end if |
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50 |
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51 $extended_parameters.long_reads |
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52 |
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53 $extended_parameters.by_read_group |
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54 |
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55 -Q $extended_parameters.mapping_quality |
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56 $extended_parameters.largest_overlap |
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57 --minOverlap $extended_parameters.min_overlap |
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58 --fracOverlap $extended_parameters.frac_overlap |
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59 --fracOverlapFeature $extended_parameters.frac_overlap_feature |
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60 $extended_parameters.read_reduction |
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61 $extended_parameters.primary |
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62 $extended_parameters.ignore_dup |
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63 #if $extended_parameters.R: |
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64 $extended_parameters.R |
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65 #end if |
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66 #if str($extended_parameters.read_extension_5p) != "0": |
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67 --readExtension5 $extended_parameters.read_extension_5p |
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68 #end if |
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69 |
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70 #if str($extended_parameters.read_extension_3p) != "0": |
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71 --readExtension3 $extended_parameters.read_extension_3p |
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72 #end if |
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73 |
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74 $pe_parameters.fragment_counting_enabled.fragment_counting |
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75 #if str($pe_parameters.fragment_counting_enabled.fragment_counting) == " -p": |
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76 $pe_parameters.fragment_counting_enabled.check_distance_enabled.check_distance |
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77 #if str($pe_parameters.fragment_counting_enabled.check_distance_enabled.check_distance) == " -P": |
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78 -d $pe_parameters.fragment_counting_enabled.check_distance_enabled.minimum_fragment_length |
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79 -D $pe_parameters.fragment_counting_enabled.check_distance_enabled.maximum_fragment_length |
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80 #end if |
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81 #end if |
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82 |
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83 $pe_parameters.only_both_ends |
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84 $pe_parameters.exclude_chimerics |
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85 |
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86 '${alignment}' |
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87 |
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88 ## Remove comment and add sample name to header |
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89 && grep -v "^#" "output" |
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90 | sed -e 's|${alignment}|${alignment.element_identifier}|g' |
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91 > body.txt |
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92 ## Set the right columns for the tabular formats |
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93 #if $format.value == "tabdel_medium": |
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94 && cut -f 1,7 body.txt > expression_matrix.txt |
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95 |
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96 ## Paste doesn't allow a non ordered list of columns: -f 1,7,8,6 will only return columns 1,7 and 8 |
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97 ## Thus the gene length column (last column) has to be added separately |
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98 && cut -f 6 body.txt > gene_lengths.txt |
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99 && paste expression_matrix.txt gene_lengths.txt > expression_matrix.txt.bak |
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100 && mv -f expression_matrix.txt.bak '${output_medium}' |
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101 #elif $format.value == "tabdel_short": |
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102 && cut -f 1,7 body.txt > '${output_short}' |
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103 #else: |
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104 && cp body.txt '${output_full}' |
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105 #end if |
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106 |
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107 #if str($include_feature_length_file) == "true": |
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108 && cut -f 1,6 body.txt > '${output_feature_lengths}' |
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109 #end if |
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110 |
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111 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J": |
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112 && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.jcounts' > '${output_jcounts}' |
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113 #end if |
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114 |
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115 #if $extended_parameters.R: |
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116 && samtools sort -o '$output_bam' -@ \${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" *.featureCounts.bam |
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117 #end if |
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118 && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.summary' > '${output_summary}' |
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119 ]]></command> |
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120 <inputs> |
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121 <param name="alignment" |
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122 type="data" |
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123 multiple="false" |
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124 format="bam,sam" |
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125 label="Alignment file" |
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126 help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files must be in the same format. Unless you are using a Gene annotation file from the History, these files must have the database/genome attribute already specified e.g. hg38, not the default: ?" > |
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127 </param> |
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128 |
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129 <param name="strand_specificity" |
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130 type="select" |
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131 label="Specify strand information" |
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132 argument="-s" |
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133 help="Indicate if the data is stranded and if strand-specific read counting should be performed. Strand setting must be the same as the strand settings used to produce the mapped BAM input(s)"> |
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134 <option value="0" selected="true">Unstranded</option> |
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135 <option value="1">Stranded (Forward)</option> |
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136 <option value="2">Stranded (Reverse)</option> |
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137 </param> |
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138 |
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139 <conditional name="anno"> |
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140 <param name="anno_select" type="select" label="Gene annotation file"> |
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141 <option value="builtin">featureCounts built-in</option> |
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142 <option value="cached" selected="True">locally cached</option> |
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143 <option value="history">in your history</option> |
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144 </param> |
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145 <when value="builtin"> |
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146 <param name="bgenome" type="select" label="Select built-in genome" help="Built-in gene annotations for genomes hg38, hg19, mm10 and mm9 are included in featureCounts"> |
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147 <options from_data_table="featurecounts_anno"> |
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148 <filter type="data_meta" key="dbkey" ref="alignment" column="dbkey"/> |
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149 </options> |
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150 </param> |
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151 </when> |
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152 <when value="cached"> |
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153 <param name="reference_gene_sets_builtin" type="select" label="Using locally cached annotation" help="If the annotation file you require is not listed here, please contact the Galaxy administrator"> |
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154 <options from_data_table="gene_sets"> |
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155 <filter type="data_meta" key="dbkey" ref="alignment" column="dbkey"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 809715c88721d082b304cf4e4a37b52d30162f08"
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156 <filter type="sort_by" column="2" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
157 </options> |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
158 <validator type="no_options" message="An annotation file is not available for the build associated with the selected input file"/> |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
159 </param> |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
160 </when> |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
161 <when value="history"> |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
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162 <param name="reference_gene_sets" |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
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163 format="gff,gtf,gff3" |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
164 type="data" |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
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165 label="Gene annotation file" |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
166 help="The program assumes that the provided annotation file is in GTF format. Make sure that the gene annotation file corresponds to the same reference genome as used for the alignment"> |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
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167 </param> |
3
dae123c03a74
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f
iuc
parents:
2
diff
changeset
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168 </when> |
dae123c03a74
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f
iuc
parents:
2
diff
changeset
|
169 </conditional> |
8
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
|
170 |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
171 <param name="format" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
172 type="select" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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173 label="Output format" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff
changeset
|
174 help="The output format will be tabular, select the preferred columns here"> |
13
386220cf6877
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4
iuc
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diff
changeset
|
175 <option value="tabdel_short">Gene-ID "\t" read-count (MultiQC/DESeq2/edgeR/limma-voom compatible)</option> |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
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changeset
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176 <option value="tabdel_medium">Gene-ID "\t" read-count "\t" gene-length</option> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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changeset
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177 <option value="tabdel_full">featureCounts 1.4.0+ default (includes regions provided by the GTF file)</option> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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178 </param> |
8
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
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changeset
|
179 |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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180 <param name="include_feature_length_file" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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181 type="boolean" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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182 truevalue="true" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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183 falsevalue="false" |
2
a80f96e55958
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 9a92d439f147a5cf2370e0686854911107de1144
iuc
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1
diff
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184 checked="false" |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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185 label="Create gene-length file" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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changeset
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186 help="Creates a tabular file that contains the effective (nucleotides used for counting reads) length of the feature; might be useful for estimating FPKM/RPKM" /> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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187 |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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188 |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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changeset
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189 <section name="pe_parameters" title="Options for paired-end reads"> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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190 <conditional name="fragment_counting_enabled"> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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changeset
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191 |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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192 <param name="fragment_counting" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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193 type="select" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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194 argument="-p" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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195 checked="true" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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196 label="Count fragments instead of reads" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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197 help="If specified, fragments (or templates) will be counted instead of reads."> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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198 <option value="" selected="true">Disabled; all reads/mates will be counted individually</option> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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199 <option value=" -p">Enabled; fragments (or templates) will be counted instead of reads</option> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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200 </param> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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201 |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
202 <when value=" -p"> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff
changeset
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203 <conditional name="check_distance_enabled"> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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204 <param name="check_distance" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
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changeset
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205 type="boolean" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
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changeset
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206 truevalue=" -P" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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207 falsevalue="" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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208 argument="-P" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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209 label="Check paired-end distance" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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210 help="If specified, paired-end distance will be checked when assigning fragments to meta-features or features. This option is only applicable when -p (Count fragments instead of reads) is specified. The distance thresholds should be specified using -d and -D (minimum and maximum fragment/template length) options." /> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
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211 <when value=" -P"> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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212 <param name="minimum_fragment_length" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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213 type="integer" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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214 value="50" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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215 argument="-d" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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216 label="Minimum fragment/template length." /> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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217 <param name="maximum_fragment_length" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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218 type="integer" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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219 value="600" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
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changeset
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220 argument="-D" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
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changeset
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221 label="Maximum fragment/template length." /> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
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changeset
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222 </when> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
223 <when value="" /> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
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changeset
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224 </conditional> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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changeset
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225 </when> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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226 <when value="" /> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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227 </conditional> |
8
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
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228 |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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229 <param name="only_both_ends" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
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230 type="boolean" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
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changeset
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231 truevalue=" -B" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
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232 falsevalue="" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
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changeset
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233 argument="-B" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
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changeset
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234 label="Only allow fragments with both reads aligned" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
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235 help="If specified, only fragments that have both ends successfully aligned will be considered for summarization. This option is only applicable for paired-end reads." /> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
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changeset
|
236 |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
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changeset
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237 <param name="exclude_chimerics" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
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238 type="boolean" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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239 truevalue=" -C" |
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240 falsevalue="" |
9e7a369eec58
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241 argument="-C" |
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242 checked="true" |
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243 label="Exclude chimeric fragments" |
9e7a369eec58
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244 help="If specified, the chimeric fragments (those fragments that have their two ends aligned to different chromosomes) will NOT be included for summarization. This option is only applicable for paired-end read data." /> |
9e7a369eec58
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245 </section> |
8
2a8bb8223a45
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246 |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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247 <section name="extended_parameters" title="Advanced options"> |
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248 <param name="gff_feature_type" |
9e7a369eec58
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249 type="text" |
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250 value="exon" |
9e7a369eec58
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251 argument="-t" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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252 label="GFF feature type filter" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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253 help="Specify the feature type. Only rows which have the matched matched feature type in the provided GTF annotation file will be included for read counting. `exon' by default." /> |
9e7a369eec58
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254 |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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255 <param name="gff_feature_attribute" |
9e7a369eec58
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256 type="text" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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257 value="gene_id" |
9e7a369eec58
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258 argument="-g" |
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259 label="GFF gene identifier" |
9e7a369eec58
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260 help="Specify the attribute type used to group features (eg. exons) into meta-features (eg. genes), when GTF annotation is provided. `gene_id' by default. This attribute type is usually the gene identifier. This argument is useful for the meta-feature level summarization." /> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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261 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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262 <param name="summarization_level" |
9e7a369eec58
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263 type="boolean" |
9e7a369eec58
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264 truevalue=" -f" |
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265 falsevalue="" |
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266 argument="-f" |
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267 label="On feature level" |
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268 help="If specified, read summarization will be performed at the feature level. By default (-f is not specified), the read summarization is performed at the meta-feature level." /> |
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269 |
11
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
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270 <param name="contribute_to_multiple_features" |
0
9e7a369eec58
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271 type="boolean" |
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272 truevalue=" -O" |
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273 falsevalue="" |
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274 argument="-O" |
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275 label="Allow read to contribute to multiple features" |
3
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f
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276 help="If specified, reads (or fragments if -p is specified) will be allowed to be assigned to more than one matched meta-feature (or matched feature if -f is specified)" /> |
0
9e7a369eec58
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277 |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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278 <conditional name="multimapping_enabled"> |
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279 <param name="multimapping_counts" |
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280 type="select" |
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281 argument="-M" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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282 label="Count multi-mapping reads/fragments" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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283 help="If specified, multi-mapping reads/fragments will be counted (ie. a multi-mapping read will be counted up to N times if it has N reported mapping locations). The program uses the `NH' tag to find multi-mapping reads."> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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284 <option value="" selected="true">Disabled; multi-mapping reads are excluded (default)</option> |
9e7a369eec58
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285 <option value=" -M">Enabled; multi-mapping reads are included</option> |
9e7a369eec58
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286 </param> |
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287 <when value=" -M"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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288 <param name="fraction" |
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289 type="boolean" |
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290 truevalue="--fraction" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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291 falsevalue="" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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292 argument="--fraction" |
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293 label="Assign fractions to multimapping reads" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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294 help="If specified, a fractional count 1/n will be generated for each multi-mapping read, where n is the number of alignments (indica- ted by 'NH' tag) reported for the read. This option must be used together with the '-M' option." /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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295 </when> |
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296 <when value="" /> |
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297 </conditional> |
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298 |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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299 <param name="mapping_quality" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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300 type="integer" |
23
9301937c9037
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 8c751ba49b1465ad147574fcede7ad4a27f8805d
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diff
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301 value="0" |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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302 argument="-Q" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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303 label="Minimum mapping quality per read" |
23
9301937c9037
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 8c751ba49b1465ad147574fcede7ad4a27f8805d
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diff
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304 help="The minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria. 0 by default." /> |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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305 |
6
9d60a36b5c6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
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306 <conditional name="exon_exon_junction_read_counting_enabled"> |
9d60a36b5c6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
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307 <param name="count_exon_exon_junction_reads" argument="-J" type="boolean" truevalue="-J" falsevalue="" |
9d60a36b5c6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
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308 label="Exon-exon junctions" |
9d60a36b5c6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
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309 help="If specified, reads supporting each exon-exon junction will be counted" /> |
9d60a36b5c6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
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310 <when value="-J"> |
7
3ce1c701b0df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17
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311 <param name="genome" argument="-G" type="data" format="fasta" optional="true" |
3ce1c701b0df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17
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312 label="Reference sequence file" |
6
9d60a36b5c6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
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313 help="The FASTA-format file that contains the reference sequences used in read mapping can be used to improve read counting for junctions" /> |
9d60a36b5c6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
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314 </when> |
9d60a36b5c6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
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315 <when value="" /> |
9d60a36b5c6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
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316 </conditional> |
9d60a36b5c6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
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317 |
9d60a36b5c6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
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318 <param name="long_reads" argument="-L" type="boolean" truevalue="-L" falsevalue="" |
9d60a36b5c6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
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319 label="Long reads" |
9d60a36b5c6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
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changeset
|
320 help="If specified, long reads such as Nanopore and PacBio reads will be counted. Long read counting can only run in one thread and only reads (not read-pairs) can be counted." /> |
9d60a36b5c6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents:
4
diff
changeset
|
321 |
10
46cccc52be5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents:
9
diff
changeset
|
322 <param name="by_read_group" argument="--byReadGroup" type="boolean" truevalue="--byReadGroup" falsevalue="" |
8
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
|
323 label="Count reads by read group" |
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
|
324 help="If specified, reads are counted for each read group separately. The 'RG' tag must be present in the input BAM/SAM alignment files." /> |
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
|
325 |
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
|
326 |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
327 <param name="largest_overlap" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
328 type="boolean" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
329 truevalue=" --largestOverlap" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
330 falsevalue="" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
331 argument="--largestOverlap" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
332 label="Largest overlap" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
333 help="If specified, reads (or fragments) will be assigned to the target that has the largest number of overlapping bases" /> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
334 |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
335 <param name="min_overlap" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
336 type="integer" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
337 value="1" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
338 argument="--minOverlap" |
8
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
|
339 label="Minimum bases of overlap" |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
340 help="Specify the minimum required number of overlapping bases between a read (or a fragment) and a feature. 1 by default. If a negative value is provided, the read will be extended from both ends." /> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
341 |
10
46cccc52be5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents:
9
diff
changeset
|
342 <param name="frac_overlap" |
8
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
|
343 type="integer" |
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
|
344 value="0" |
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
|
345 min="0" |
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
|
346 max="1" |
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
|
347 argument="--fracOverlap" |
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
|
348 label="Minimum fraction (of read) overlapping a feature" |
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
|
349 help="Specify the minimum required fraction of overlapping bases between a read (or a fragment) and a feature. Value should be within range [0,1]. 0 by default. Number of overlapping bases is counted from both reads if paired end. Both this option and '--minOverlap' need to be satisfied for read assignment." /> |
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
|
350 |
10
46cccc52be5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents:
9
diff
changeset
|
351 <param name="frac_overlap_feature" |
8
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
|
352 type="integer" |
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
|
353 value="0" |
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
|
354 min="0" |
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
|
355 max="1" |
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
|
356 argument="--fracOverlapFeature" |
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
|
357 label="Minimum fraction (of feature) overlapping a read" |
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
|
358 help="Specify the minimum required fraction of bases included in a feature overlapping bases between a read (or a read-pair). Value should be within range [0,1]. 0 by default." /> |
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
|
359 |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
360 <param name="read_extension_5p" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
361 type="integer" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
362 value="0" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
363 argument="--readExtension5" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
364 label="Read 5' extension" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
365 help="Reads are extended upstream by ... bases from their 5' end" /> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
366 |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
367 <param name="read_extension_3p" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
368 type="integer" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
369 value="0" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
370 argument="--readExtension3" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
371 label="Read 3' extension" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
372 help="Reads are extended upstream by ... bases from their 3' end" /> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
373 |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
374 <param name="read_reduction" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
375 type="select" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
376 label="Reduce read to single position" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
377 argument="--read2pos" |
3
dae123c03a74
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f
iuc
parents:
2
diff
changeset
|
378 help="The read is reduced to its 5' most base or 3'most base. Read summarization is then performed based on the single base the the read is reduced to."> |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
379 <option value="" selected="true">Leave the read as it is</option> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
380 <option value="--read2pos 5">Reduce it to the 5' end</option> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
381 <option value="--read2pos 3">Reduce it to the 3' end</option> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
382 </param> |
8
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
|
383 |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
384 <param name="primary" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
385 type="boolean" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
386 truevalue=" --primary" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
387 falsevalue="" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
388 argument="--primary" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
389 label="Only count primary alignments" |
3
dae123c03a74
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f
iuc
parents:
2
diff
changeset
|
390 help="If specified, only primary alignments will be counted. Primary and secondary alignments are identified using bit 0x100 in theFlag field of SAM/BAM files. All primary alignments in a dataset will be counted regardless of whether they are from multi-mapping reads or not ('-M' is ignored)." /> |
8
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
|
391 |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
392 <param name="ignore_dup" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
393 type="boolean" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
394 truevalue=" --ignoreDup" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
395 falsevalue="" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
396 argument="--ignoreDup" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
397 label="Ignore reads marked as duplicate" |
3
dae123c03a74
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f
iuc
parents:
2
diff
changeset
|
398 help="If specified, reads that were marked as duplicates will be ignored. Bit Ox400 in the FLAG field of a SAM/BAM file is used for identifying duplicate reads. In paired end data, the entire read pair will be ignored if at least one end is found to be a duplicate read." /> |
8
2a8bb8223a45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents:
7
diff
changeset
|
399 |
17
8ce1e2c7ee72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents:
15
diff
changeset
|
400 <param type="boolean" |
8ce1e2c7ee72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents:
15
diff
changeset
|
401 truevalue="-R BAM" |
8ce1e2c7ee72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents:
15
diff
changeset
|
402 falsevalue="" |
8ce1e2c7ee72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents:
15
diff
changeset
|
403 argument="-R" |
8ce1e2c7ee72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents:
15
diff
changeset
|
404 label="Annotates the alignment file with 'XS:Z:'-tags to described per read or read-pair the corresponding assigned feature(s)." |
8ce1e2c7ee72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents:
15
diff
changeset
|
405 help="" /> |
8ce1e2c7ee72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents:
15
diff
changeset
|
406 |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
407 <param name="count_split_alignments_only" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
408 type="boolean" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
409 truevalue=" --countSplitAlignmentsOnly" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
410 falsevalue="" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
411 argument="--countSplitAlignmentsOnly" |
3
dae123c03a74
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f
iuc
parents:
2
diff
changeset
|
412 label="Ignore unspliced alignments" |
dae123c03a74
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f
iuc
parents:
2
diff
changeset
|
413 help="If specified, only split alignments (CIGAR strings containing the letter `N') will be counted. All the other alignments will be ignored. An example of split alignments are exon-spanning reads in RNA-seq data." /> |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
414 </section> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
415 </inputs> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
416 <outputs> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
417 <data format="tabular" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
418 name="output_medium" |
20
1759d845181e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5
iuc
parents:
19
diff
changeset
|
419 label="${tool.name} on ${on_string}: Counts (with length)"> |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
420 <filter>format == "tabdel_medium"</filter> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
421 <actions> |
9
e6a2a912677a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4fb528145289ad4db04e4589c02e9ddaa1194138
iuc
parents:
8
diff
changeset
|
422 <action name="column_names" type="metadata" default="Geneid,${alignment.element_identifier},Length" /> |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
423 </actions> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
424 </data> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
425 |
17
8ce1e2c7ee72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents:
15
diff
changeset
|
426 <data format="bam" |
8ce1e2c7ee72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents:
15
diff
changeset
|
427 name="output_bam" |
8ce1e2c7ee72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents:
15
diff
changeset
|
428 label="${tool.name} on ${on_string}: Alignment file"> |
8ce1e2c7ee72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents:
15
diff
changeset
|
429 <filter>extended_parameters['R']</filter> |
8ce1e2c7ee72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents:
15
diff
changeset
|
430 </data> |
8ce1e2c7ee72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents:
15
diff
changeset
|
431 |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
432 <data format="tabular" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
433 name="output_short" |
20
1759d845181e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5
iuc
parents:
19
diff
changeset
|
434 label="${tool.name} on ${on_string}: Counts"> |
13
386220cf6877
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4
iuc
parents:
12
diff
changeset
|
435 <filter>format == "tabdel_short"</filter> |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
436 <actions> |
9
e6a2a912677a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4fb528145289ad4db04e4589c02e9ddaa1194138
iuc
parents:
8
diff
changeset
|
437 <action name="column_names" type="metadata" default="Geneid,${alignment.element_identifier}" /> |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
438 </actions> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
439 </data> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
440 |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
441 <data format="tabular" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
442 name="output_full" |
20
1759d845181e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5
iuc
parents:
19
diff
changeset
|
443 label="${tool.name} on ${on_string}: Counts (with location)"> |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
444 <filter>format == "tabdel_full"</filter> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
445 <actions> |
9
e6a2a912677a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4fb528145289ad4db04e4589c02e9ddaa1194138
iuc
parents:
8
diff
changeset
|
446 <action name="column_names" type="metadata" default="Geneid,Chr,Start,End,Strand,Length,${alignment.element_identifier}" /> |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
447 </actions> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
448 </data> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
449 |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
450 <data format="tabular" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
451 name="output_summary" |
20
1759d845181e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5
iuc
parents:
19
diff
changeset
|
452 label="${tool.name} on ${on_string}: Summary"> |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
453 <actions> |
9
e6a2a912677a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4fb528145289ad4db04e4589c02e9ddaa1194138
iuc
parents:
8
diff
changeset
|
454 <action name="column_names" type="metadata" default="Status,${alignment.element_identifier}" /> |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
455 </actions> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
456 </data> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
457 |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
458 <data format="tabular" |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
459 name="output_feature_lengths" |
20
1759d845181e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5
iuc
parents:
19
diff
changeset
|
460 label="${tool.name} on ${on_string}: Feature lengths"> |
6
9d60a36b5c6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents:
4
diff
changeset
|
461 <filter>include_feature_length_file</filter> |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
462 <actions> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
463 <action name="column_names" type="metadata" default="Feature,Length" /> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
464 </actions> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
465 </data> |
6
9d60a36b5c6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents:
4
diff
changeset
|
466 |
9d60a36b5c6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents:
4
diff
changeset
|
467 <data name="output_jcounts" format="tabular" |
20
1759d845181e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5
iuc
parents:
19
diff
changeset
|
468 label="${tool.name} on ${on_string}: Junction counts"> |
7
3ce1c701b0df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17
iuc
parents:
6
diff
changeset
|
469 <filter>extended_parameters['exon_exon_junction_read_counting_enabled']['count_exon_exon_junction_reads']</filter> |
6
9d60a36b5c6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents:
4
diff
changeset
|
470 <actions> |
10
46cccc52be5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents:
9
diff
changeset
|
471 <action name="column_names" type="metadata" |
46cccc52be5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents:
9
diff
changeset
|
472 default="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,${alignment.element_identifier}" /> |
6
9d60a36b5c6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents:
4
diff
changeset
|
473 </actions> |
9d60a36b5c6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents:
4
diff
changeset
|
474 </data> |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
475 </outputs> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
476 <tests> |
7
3ce1c701b0df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17
iuc
parents:
6
diff
changeset
|
477 <test expect_num_outputs="3"> |
11
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
478 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38" /> |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
479 <param name="anno_select" value="history"/> |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
480 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38" /> |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
481 <param name="format" value="tabdel_medium" /> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
482 <param name="include_feature_length_file" value="true"/> |
4
d417fb66494e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents:
3
diff
changeset
|
483 <output name="output_medium" file="output_1_medium.tab"> |
d417fb66494e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents:
3
diff
changeset
|
484 <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/> |
d417fb66494e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents:
3
diff
changeset
|
485 </output> |
d417fb66494e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents:
3
diff
changeset
|
486 <output name="output_summary" file="output_1_summary.tab"> |
d417fb66494e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents:
3
diff
changeset
|
487 <metadata name="column_names" value="Status,featureCounts_input1.bam"/> |
d417fb66494e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents:
3
diff
changeset
|
488 </output> |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
489 </test> |
7
3ce1c701b0df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17
iuc
parents:
6
diff
changeset
|
490 <test expect_num_outputs="3"> |
11
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
491 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38" /> |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
492 <param name="anno_select" value="history"/> |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
493 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38" /> |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
494 <param name="format" value="tabdel_full" /> |
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
495 <param name="include_feature_length_file" value="true"/> |
4
d417fb66494e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents:
3
diff
changeset
|
496 <output name="output_full" file="output_1_full.tab"> |
d417fb66494e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents:
3
diff
changeset
|
497 <metadata name="column_names" value="Geneid,Chr,Start,End,Strand,Length,featureCounts_input1.bam"/> |
d417fb66494e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents:
3
diff
changeset
|
498 </output> |
d417fb66494e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents:
3
diff
changeset
|
499 <output name="output_summary" file="output_1_summary.tab"> |
d417fb66494e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents:
3
diff
changeset
|
500 <metadata name="column_names" value="Status,featureCounts_input1.bam"/> |
d417fb66494e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents:
3
diff
changeset
|
501 </output> |
d417fb66494e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents:
3
diff
changeset
|
502 <output name="output_feature_lengths" file="output_feature_lengths.tab"> |
d417fb66494e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents:
3
diff
changeset
|
503 <metadata name="column_names" value="Feature,Length"/> |
d417fb66494e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents:
3
diff
changeset
|
504 </output> |
0
9e7a369eec58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff
changeset
|
505 </test> |
10
46cccc52be5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents:
9
diff
changeset
|
506 <test expect_num_outputs="4"> |
11
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
507 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38" /> |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
508 <param name="anno_select" value="history"/> |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
509 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38" /> |
10
46cccc52be5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents:
9
diff
changeset
|
510 <param name="format" value="tabdel_short" /> |
46cccc52be5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents:
9
diff
changeset
|
511 <param name="include_feature_length_file" value="true"/> |
46cccc52be5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents:
9
diff
changeset
|
512 <param name="count_exon_exon_junction_reads" value="-J"/> |
13
386220cf6877
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4
iuc
parents:
12
diff
changeset
|
513 <output name="output_short" file="output_1_short.tab"> |
10
46cccc52be5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents:
9
diff
changeset
|
514 <metadata name="column_names" value="Geneid,featureCounts_input1.bam"/> |
46cccc52be5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents:
9
diff
changeset
|
515 </output> |
13
386220cf6877
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4
iuc
parents:
12
diff
changeset
|
516 <output name="output_summary" file="output_1_summary.tab"> |
10
46cccc52be5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents:
9
diff
changeset
|
517 <metadata name="column_names" value="Status,featureCounts_input1.bam"/> |
46cccc52be5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents:
9
diff
changeset
|
518 </output> |
13
386220cf6877
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4
iuc
parents:
12
diff
changeset
|
519 <output name="output_jcounts" file="output_1_jcounts.tab"> |
10
46cccc52be5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents:
9
diff
changeset
|
520 <metadata name="column_names" value="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,featureCounts_input1.bam"/> |
46cccc52be5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents:
9
diff
changeset
|
521 </output> |
46cccc52be5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents:
9
diff
changeset
|
522 </test> |
11
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
523 <!-- Ensure featureCounts built-in annotation works --> |
17
8ce1e2c7ee72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents:
15
diff
changeset
|
524 <test expect_num_outputs="3"> |
11
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
525 <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" dbkey="hg19" /> |
10
46cccc52be5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents:
9
diff
changeset
|
526 <param name="anno_select" value="builtin"/> |
46cccc52be5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents:
9
diff
changeset
|
527 <param name="format" value="tabdel_short" /> |
17
8ce1e2c7ee72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents:
15
diff
changeset
|
528 <section name="extended_parameters"> |
8ce1e2c7ee72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents:
15
diff
changeset
|
529 <param name="R" value="true" /> |
8ce1e2c7ee72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents:
15
diff
changeset
|
530 </section> |
10
46cccc52be5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents:
9
diff
changeset
|
531 <output name="output_short" file="output_builtin_hg19.tab"> |
46cccc52be5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents:
9
diff
changeset
|
532 <metadata name="column_names" value="Geneid,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> |
46cccc52be5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents:
9
diff
changeset
|
533 </output> |
46cccc52be5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents:
9
diff
changeset
|
534 <output name="output_summary" file="output_summary_builtin_hg19.tab"/> |
17
8ce1e2c7ee72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents:
15
diff
changeset
|
535 <output name="output_bam" file="output.bam" ftype="bam"/> |
10
46cccc52be5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents:
9
diff
changeset
|
536 </test> |
11
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
537 <!-- Ensure cached GTFs work --> |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
538 <test expect_num_outputs="3"> |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
539 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38" /> |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
540 <param name="anno_select" value="cached"/> |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
541 <param name="format" value="tabdel_medium" /> |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
542 <param name="include_feature_length_file" value="true"/> |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
543 <output name="output_medium" file="output_1_medium.tab"> |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
544 <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/> |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
545 </output> |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
546 <output name="output_summary" file="output_1_summary.tab"> |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
547 <metadata name="column_names" value="Status,featureCounts_input1.bam"/> |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
548 </output> |
e803ca6407c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents:
10
diff
changeset
|
549 </test> |
18
d60b1c4e0347
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9
iuc
parents:
17
diff
changeset
|
550 <!-- Ensure BAM output works --> |
d60b1c4e0347
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9
iuc
parents:
17
diff
changeset
|
551 <test> |
d60b1c4e0347
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9
iuc
parents:
17
diff
changeset
|
552 <param name="alignment" value="subset.sorted.bam" ftype="bam" /> |
d60b1c4e0347
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9
iuc
parents:
17
diff
changeset
|
553 <param name="anno_select" value="history" /> |
d60b1c4e0347
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9
iuc
parents:
17
diff
changeset
|
554 <param name="reference_gene_sets" value="small.gtf" ftype="gtf" /> |
d60b1c4e0347
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9
iuc
parents:
17
diff
changeset
|
555 <section name="extended_parameters" > |
d60b1c4e0347
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9
iuc
parents:
17
diff
changeset
|
556 <param name="R" value="true" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9
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557 </section> |
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558 <output name="output_bam" value="subset.sorted.featurecounts.bam" compare="sim_size"/> |
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559 </test> |
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560 </tests> |
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561 |
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562 <help><![CDATA[ |
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563 featureCounts |
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564 ############# |
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565 |
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566 Overview |
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567 -------- |
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568 FeatureCounts is a light-weight read counting program written entirely in the C programming language. It can be used to count both gDNA-seq and RNA-seq reads for genomic features in in SAM/BAM files. FeatureCounts is part of the Subread_ package. |
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569 |
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570 Input formats |
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571 ------------- |
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572 Alignments should be provided in either: |
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573 |
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574 - SAM format, http://samtools.sourceforge.net/samtools.shtml#5 |
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575 - BAM format |
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576 |
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577 Annotations for gene regions should be provided in the GFF/GTF format: |
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578 |
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579 - http://genome.ucsc.edu/FAQ/FAQformat.html#format3 |
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580 - http://www.ensembl.org/info/website/upload/gff.html |
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581 |
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582 Alternatively, the featureCounts built-in annotations for genomes hg38, hg19, mm10 and mm9 can be used through selecting the built-in option above. These annotation files are in simplified annotation format (SAF) as shown below. The GeneID column contains Entrez gene identifiers and each entry (row) is taken as a feature (e.g. an exon). |
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583 |
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584 Example - **Built-in annotation format**: |
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585 |
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586 ====== ==== ======= ======= ====== |
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587 GeneID Chr Start End Strand |
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588 ====== ==== ======= ======= ====== |
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589 497097 chr1 3204563 3207049 - |
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590 497097 chr1 3411783 3411982 - |
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591 497097 chr1 3660633 3661579 - |
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592 ====== ==== ======= ======= ====== |
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593 |
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594 These annotation files can be found in the `Subread package`_. You can see the version of Subread used by this wrapper in the tool form above under `Options > Requirements`. To create the files, the annotations were downloaded from NCBI RefSeq database and then adapted by merging overlapping exons from the same gene to form a set of disjoint exons for each gene. Genes with the same Entrez gene identifiers were also merged into one gene. See the `Subread User's Guide`_ for more information. Gene names can be obtained for these Entrez identifiers with the Galaxy **annotateMyIDs** tool. |
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595 |
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596 Output format |
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597 ------------- |
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598 FeatureCounts produces a table containing counted reads, per gene, per row. Optionally the last column can be set to be the effective gene-length. These tables are compatible with the DESeq2, edgeR and limma-voom Galaxy wrappers by IUC. |
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599 |
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600 .. _Subread: http://subread.sourceforge.net/ |
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601 .. _`Subread User's Guide`: http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf |
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602 .. _`Subread package`: https://sourceforge.net/projects/subread/files/ |
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603 ]]></help> |
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604 <citations> |
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605 <citation type="doi">10.1093/bioinformatics/btt656</citation> |
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606 </citations> |
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607 </tool> |