annotate featurecounts.xml @ 8:2a8bb8223a45 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
author iuc
date Wed, 15 Nov 2017 15:53:25 -0500
parents 3ce1c701b0df
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1 <tool id="featurecounts" name="featureCounts" version="1.6.0" profile="16.04">
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2 <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
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3 <requirements>
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4 <requirement type="package" version="1.6.0">subread</requirement>
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5 </requirements>
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7 <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command>
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8 <command><![CDATA[
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9 ## Check whether all alignments are from the same type (bam || sam)
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10 featureCounts
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11 #if $gtf_source.ref_source=="history":
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12 -a '$gtf_source.reference_gene_sets'
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13 #else:
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14 -a '$gtf_source.reference_gene_sets_builtin.fields.path'
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15 #end if
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16
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17 -o "output"
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18 -T \${GALAXY_SLOTS:-2}
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20 -t '$extended_parameters.gff_feature_type'
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21 -g '$extended_parameters.gff_feature_attribute'
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22 $extended_parameters.summarization_level
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23 $extended_parameters.contribute_to_multiple_features
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24 -s $extended_parameters.strand_specificity
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25 $extended_parameters.multimapping_enabled.multimapping_counts
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27 #if str($extended_parameters.multimapping_enabled.multimapping_counts) == " -M"
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28 $extended_parameters.multimapping_enabled.fraction
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29 #end if
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30
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31 $extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads
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32 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J"
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33 #if $extended_parameters.exon_exon_junction_read_counting_enabled.genome
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34 -G '$extended_parameters.exon_exon_junction_read_counting_enabled.genome'
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35 #end if
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36 #end if
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38 $extended_parameters.long_reads
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39
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40 $extended_parameters.by_read_group
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41
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42 -Q $extended_parameters.mapping_quality
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43 $extended_parameters.largest_overlap
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44 --minOverlap $extended_parameters.min_overlap
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45 --fracOverlap $extended_parameters.frac_overlap
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46 --fracOverlapFeature $extended_parameters.frac_overlap_feature
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47 $extended_parameters.read_reduction
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48 $extended_parameters.primary
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49 $extended_parameters.ignore_dup
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50
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51 #if str($extended_parameters.read_extension_5p) != "0"
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52 --readExtension5 $extended_parameters.read_extension_5p
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53 #end if
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54
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55 #if str($extended_parameters.read_extension_3p) != "0"
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56 --readExtension3 $extended_parameters.read_extension_3p
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57 #end if
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58
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59 $pe_parameters.fragment_counting_enabled.fragment_counting
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60 #if str($pe_parameters.fragment_counting_enabled.fragment_counting) == " -p"
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61 $pe_parameters.fragment_counting_enabled.check_distance_enabled.check_distance
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62 #if str($pe_parameters.fragment_counting_enabled.check_distance_enabled.check_distance) == " -P"
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63 -d $pe_parameters.fragment_counting_enabled.check_distance_enabled.minimum_fragment_length
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64 -D $pe_parameters.fragment_counting_enabled.check_distance_enabled.maximum_fragment_length
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65 #end if
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66 #end if
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67
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68 $pe_parameters.only_both_ends
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69 $pe_parameters.exclude_chimerics
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70
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71 '${alignment}'
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72
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73 ## Removal of comment and column-header line
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74 && grep -v "^#" "output" | tail -n+2 > body.txt
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75
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76 ## Set the right columns for the tabular formats
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77 #if $format.value == "tabdel_medium"
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78 && cut -f 1,7 body.txt > expression_matrix.txt
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79
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80 ## Paste doesn't allow a non ordered list of columns: -f 1,7,8,6 will only return columns 1,7 and 8
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81 ## Thus the gene length column (last column) has to be added separately
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82 && cut -f 6 body.txt > gene_lengths.txt
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83 && paste expression_matrix.txt gene_lengths.txt > expression_matrix.txt.bak
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84 && mv -f expression_matrix.txt.bak '${output_medium}'
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85 #elif $format.value == "tabdel_short"
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86 && cut -f 1,7 body.txt > '${output_short}'
0
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87 #else
6
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88 && cp body.txt '${output_full}'
0
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89 #end if
8
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90
0
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91
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92 #if str($include_feature_length_file) == "true"
6
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93 && cut -f 1,6 body.txt > '${output_feature_lengths}'
0
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94 #end if
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95
6
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96 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J"
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97 && tail -n+2 'output.jcounts' > '${output_jcounts}'
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98 #end if
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99
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100 && tail -n+2 'output.summary' > '${output_summary}'
0
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101
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102 ]]></command>
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103 <inputs>
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104 <param name="alignment"
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105 type="data"
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106 multiple="false"
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107 format="bam,sam"
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108 label="Alignment file"
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109 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" />
8
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110
3
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111 <conditional name="gtf_source">
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112 <param name="ref_source" type="select" label="Gene annotation file">
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113 <option value="cached">locally cached</option>
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114 <option value="history">in your history</option>
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115 </param>
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116 <when value="cached">
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117 <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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118 <options from_data_table="gene_sets">
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119 <filter type="sort_by" column="1" />
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120 <validator type="no_options" message="No annotations are available." />
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121 </options>
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122 </param>
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123 </when>
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124 <when value="history">
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125 <param name="reference_gene_sets"
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126 format="gff,gtf,gff3"
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127 type="data"
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128 label="Gene annotation file"
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129 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" />
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130 </when>
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131 </conditional>
8
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132
0
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133 <param name="format"
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134 type="select"
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135 label="Output format"
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136 help="The output format will be tabular, select the preferred columns here">
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137 <option value="tabdel_short" selected="true">Gene-ID "\t" read-count (DESeq2 IUC wrapper compatible)</option>
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138 <option value="tabdel_medium">Gene-ID "\t" read-count "\t" gene-length</option>
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139 <option value="tabdel_full">featureCounts 1.4.0+ default (includes regions provided by the GTF file)</option>
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140 </param>
8
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141
0
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142 <param name="include_feature_length_file"
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143 type="boolean"
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144 truevalue="true"
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145 falsevalue="false"
2
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146 checked="false"
0
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147 label="Create gene-length file"
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148 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" />
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149
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150
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151 <section name="pe_parameters" title="Options for paired-end reads">
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152 <conditional name="fragment_counting_enabled">
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diff changeset
153
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154 <param name="fragment_counting"
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155 type="select"
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156 argument="-p"
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157 checked="true"
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158 label="Count fragments instead of reads"
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159 help="If specified, fragments (or templates) will be counted instead of reads.">
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160 <option value="" selected="true">Disabled; all reads/mates will be counted individually</option>
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161 <option value=" -p">Enabled; fragments (or templates) will be counted instead of reads</option>
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162 </param>
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163
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164 <when value=" -p">
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165 <conditional name="check_distance_enabled">
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166 <param name="check_distance"
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167 type="boolean"
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168 truevalue=" -P"
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diff changeset
169 falsevalue=""
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170 argument="-P"
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171 label="Check paired-end distance"
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172 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." />
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173 <when value=" -P">
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174 <param name="minimum_fragment_length"
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diff changeset
175 type="integer"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
176 value="50"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
177 argument="-d"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
178 label="Minimum fragment/template length." />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
179 <param name="maximum_fragment_length"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
180 type="integer"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
181 value="600"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
182 argument="-D"
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iuc
parents:
diff changeset
183 label="Maximum fragment/template length." />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
184 </when>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
185 <when value="" />
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diff changeset
186 </conditional>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
187 </when>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
188 <when value="" />
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diff changeset
189 </conditional>
8
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parents: 7
diff changeset
190
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
191 <param name="only_both_ends"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
192 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
193 truevalue=" -B"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
194 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
195 argument="-B"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
196 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
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diff changeset
197 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:
diff changeset
198
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
199 <param name="exclude_chimerics"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
200 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
201 truevalue=" -C"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
202 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
203 argument="-C"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
204 checked="true"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
205 label="Exclude chimeric fragments"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
206 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 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
207 </section>
8
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parents: 7
diff changeset
208
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
209 <section name="extended_parameters" title="Advanced options">
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
210 <param name="gff_feature_type"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
211 type="text"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
212 value="exon"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
213 argument="-t"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
214 label="GFF feature type filter"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
215 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 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
216
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
217 <param name="gff_feature_attribute"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
218 type="text"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
219 value="gene_id"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
220 argument="-g"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
221 label="GFF gene identifier"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
222 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
iuc
parents:
diff changeset
223
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
224 <param name="summarization_level"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
225 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
226 truevalue=" -f"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
227 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
228 argument="-f"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
229 label="On feature level"
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diff changeset
230 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." />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
231
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
232 <param name ="contribute_to_multiple_features"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
233 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
234 truevalue=" -O"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
235 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
236 argument="-O"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
237 label="Allow read to contribute to multiple features"
3
dae123c03a74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f
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parents: 2
diff changeset
238 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 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
239
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
240 <param name="strand_specificity"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
241 type="select"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
242 label="Strand specificity of the protocol"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
243 argument="-s"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
244 help="Indicate if strand-specific read counting should be performed.">
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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245 <option value="0" selected="true">Unstranded</option>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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246 <option value="1">Stranded (forwards)</option>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
247 <option value="2">Stranded (reverse)</option>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
248 </param>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
249
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
250 <conditional name="multimapping_enabled">
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
251 <param name="multimapping_counts"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
252 type="select"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
253 argument="-M"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
254 label="Count multi-mapping reads/fragments"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
255 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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parents:
diff changeset
256 <option value="" selected="true">Disabled; multi-mapping reads are excluded (default)</option>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
257 <option value=" -M">Enabled; multi-mapping reads are included</option>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
258 </param>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
259 <when value=" -M">
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
260 <param name="fraction"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
261 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
262 truevalue="--fraction"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
263 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
264 argument="--fraction"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
265 label="Assign fractions to multimapping reads"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
266 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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diff changeset
267 </when>
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268 <when value="" />
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diff changeset
269 </conditional>
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270
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271 <param name="mapping_quality"
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diff changeset
272 type="integer"
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273 value="12"
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diff changeset
274 argument="-Q"
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275 label="Minimum mapping quality per read"
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276 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. 12 by default." />
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277
6
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278 <conditional name="exon_exon_junction_read_counting_enabled">
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279 <param name="count_exon_exon_junction_reads" argument="-J" type="boolean" truevalue="-J" falsevalue=""
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280 label="Exon-exon junctions"
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281 help="If specified, reads supporting each exon-exon junction will be counted" />
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282 <when value="-J">
7
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283 <param name="genome" argument="-G" type="data" format="fasta" optional="true"
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284 label="Reference sequence file"
6
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285 help="The FASTA-format file that contains the reference sequences used in read mapping can be used to improve read counting for junctions" />
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286 </when>
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287 <when value="" />
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288 </conditional>
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289
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290 <param name="long_reads" argument="-L" type="boolean" truevalue="-L" falsevalue=""
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291 label="Long reads"
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292 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." />
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293
8
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294 <param name="by_read_group" argument="--byReadGroup" type="boolean" truevalue="--byReadGroup" falsevalue=""
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295 label="Count reads by read group"
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296 help="If specified, reads are counted for each read group separately. The 'RG' tag must be present in the input BAM/SAM alignment files." />
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297
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298
0
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299 <param name="largest_overlap"
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diff changeset
300 type="boolean"
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diff changeset
301 truevalue=" --largestOverlap"
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diff changeset
302 falsevalue=""
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diff changeset
303 argument="--largestOverlap"
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304 label="Largest overlap"
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305 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
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diff changeset
306
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diff changeset
307 <param name="min_overlap"
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diff changeset
308 type="integer"
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diff changeset
309 value="1"
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diff changeset
310 argument="--minOverlap"
8
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311 label="Minimum bases of overlap"
0
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312 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." />
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diff changeset
313
8
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314 <param name="frac_overlap"
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diff changeset
315 type="integer"
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316 value="0"
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317 min="0"
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318 max="1"
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diff changeset
319 argument="--fracOverlap"
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320 label="Minimum fraction (of read) overlapping a feature"
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321 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
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322
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323 <param name="frac_overlap_feature"
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diff changeset
324 type="integer"
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diff changeset
325 value="0"
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326 min="0"
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327 max="1"
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328 argument="--fracOverlapFeature"
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329 label="Minimum fraction (of feature) overlapping a read"
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330 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." />
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331
0
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332 <param name="read_extension_5p"
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diff changeset
333 type="integer"
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diff changeset
334 value="0"
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335 argument="--readExtension5"
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336 label="Read 5' extension"
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337 help="Reads are extended upstream by ... bases from their 5' end" />
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diff changeset
338
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339 <param name="read_extension_3p"
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diff changeset
340 type="integer"
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diff changeset
341 value="0"
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342 argument="--readExtension3"
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343 label="Read 3' extension"
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diff changeset
344 help="Reads are extended upstream by ... bases from their 3' end" />
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diff changeset
345
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346 <param name="read_reduction"
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diff changeset
347 type="select"
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348 label="Reduce read to single position"
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349 argument="--read2pos"
3
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350 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
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351 <option value="" selected="true">Leave the read as it is</option>
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352 <option value="--read2pos 5">Reduce it to the 5' end</option>
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353 <option value="--read2pos 3">Reduce it to the 3' end</option>
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diff changeset
354 </param>
8
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iuc
parents: 7
diff changeset
355
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
356 <param name="primary"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
357 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
358 truevalue=" --primary"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
359 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
360 argument="--primary"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
361 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
362 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
363
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
364 <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
365 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
366 truevalue=" --ignoreDup"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
367 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
368 argument="--ignoreDup"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
369 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
370 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
371
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
372 <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
373 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
374 truevalue=" --countSplitAlignmentsOnly"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
375 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
376 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
377 label="Ignore unspliced alignments"
dae123c03a74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f
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parents: 2
diff changeset
378 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
379 </section>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
380 </inputs>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
381 <outputs>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
382 <data format="tabular"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
383 name="output_medium"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
384 label="${tool.name} on ${on_string}">
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
385 <filter>format == "tabdel_medium"</filter>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
386 <actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
387 <action name="column_names" type="metadata" default="Geneid,${alignment.name},Length" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
388 </actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
389 </data>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
390
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
391 <data format="tabular"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
392 name="output_short"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
393 label="${tool.name} on ${on_string}">
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
394 <filter>format == "tabdel_short"</filter>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
395 <actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
396 <action name="column_names" type="metadata" default="Geneid,${alignment.name}" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
397 </actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
398 </data>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
399
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
400 <data format="tabular"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
401 name="output_full"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
402 label="${tool.name} on ${on_string}: count table">
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
403 <filter>format == "tabdel_full"</filter>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
404 <actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
405 <action name="column_names" type="metadata" default="Geneid,Chr,Start,End,Strand,Length,${alignment.name}" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
406 </actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
407 </data>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
408
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
409 <data format="tabular"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
410 name="output_summary"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
411 hidden="true"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
412 label="${tool.name} on ${on_string}: summary">
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
413 <actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
414 <action name="column_names" type="metadata" default="Status,${alignment.name}" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
415 </actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
416 </data>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
417
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
418 <data format="tabular"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
419 name="output_feature_lengths"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
420 label="${tool.name} on ${on_string}: feature lengths">
6
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents: 4
diff changeset
421 <filter>include_feature_length_file</filter>
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
422 <actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
423 <action name="column_names" type="metadata" default="Feature,Length" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
424 </actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
425 </data>
6
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
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parents: 4
diff changeset
426
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents: 4
diff changeset
427 <data name="output_jcounts" format="tabular"
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
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parents: 4
diff changeset
428 label="${tool.name} on ${on_string}: junction counts">
7
3ce1c701b0df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17
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parents: 6
diff changeset
429 <filter>extended_parameters['exon_exon_junction_read_counting_enabled']['count_exon_exon_junction_reads']</filter>
6
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents: 4
diff changeset
430 <actions>
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
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parents: 4
diff changeset
431 <action name="column_names" type="metadata" default="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,${alignment.name}" />
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents: 4
diff changeset
432 </actions>
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents: 4
diff changeset
433 </data>
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
434 </outputs>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
435 <tests>
7
3ce1c701b0df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17
iuc
parents: 6
diff changeset
436 <test expect_num_outputs="4">
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
437 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
438 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
439 <param name="format" value="tabdel_short" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
440 <param name="include_feature_length_file" value="true"/>
3
dae123c03a74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f
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parents: 2
diff changeset
441 <param name="ref_source" value="history" />
7
3ce1c701b0df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17
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parents: 6
diff changeset
442 <param name="count_exon_exon_junction_reads" value="-J"/>
4
d417fb66494e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
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parents: 3
diff changeset
443 <output name="output_short" file="output_1_short.tab">
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444 <metadata name="column_names" value="Geneid,featureCounts_input1.bam"/>
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445 </output>
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446 <output name="output_summary" file="output_1_summary.tab">
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447 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
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448 </output>
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449 <output name="output_jcounts" file="output_1_jcounts.tab">
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450 <metadata name="column_names" value="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,featureCounts_input1.bam"/>
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451 </output>
0
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452 </test>
7
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453 <test expect_num_outputs="3">
0
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454 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
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455 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
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456 <param name="format" value="tabdel_medium" />
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457 <param name="include_feature_length_file" value="true"/>
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458 <param name="ref_source" value="history" />
4
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459 <output name="output_medium" file="output_1_medium.tab">
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460 <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/>
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461 </output>
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462 <output name="output_summary" file="output_1_summary.tab">
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463 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
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464 </output>
0
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465 </test>
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466 <test expect_num_outputs="3">
0
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467 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
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468 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
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469 <param name="format" value="tabdel_full" />
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470 <param name="include_feature_length_file" value="true"/>
3
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471 <param name="ref_source" value="history" />
4
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472 <output name="output_full" file="output_1_full.tab">
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473 <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
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474 </output>
d417fb66494e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
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475 <output name="output_summary" file="output_1_summary.tab">
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476 <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
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477 </output>
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478 <output name="output_feature_lengths" file="output_feature_lengths.tab">
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479 <metadata name="column_names" value="Feature,Length"/>
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480 </output>
0
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481 </test>
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482
0
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483 </tests>
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484
0
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485 <help><![CDATA[
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486 featureCounts
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487 #############
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488
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489 Overview
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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490 --------
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491 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.
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492
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493 Input formats
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494 -------------
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495 Alignments should be provided in either:
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496
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497 - SAM format, http://samtools.sourceforge.net/samtools.shtml#5
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498 - BAM format
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499
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500 Gene regions should be provided in the GFF/GTF format:
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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501
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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502 - http://genome.ucsc.edu/FAQ/FAQformat.html#format3
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503 - http://www.ensembl.org/info/website/upload/gff.html
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504
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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505 Output format
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506 -------------
1
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507 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 Galaxy wrapper by IUC. Column names are added as metadata object.
0
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508 ]]></help>
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509 <citations>
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510 <citation type="doi">10.1093/bioinformatics/btt656</citation>
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511 </citations>
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512 </tool>