Mercurial > repos > iuc > featurecounts

annotate featurecounts.xml @ 18:d60b1c4e0347 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9
author iuc
date Wed, 04 Jul 2018 17:32:47 -0400
parents 8ce1e2c7ee72
children f3a5f075498f
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d60b1c4e0347 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9
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1 <tool id="featurecounts" name="featureCounts" version="1.6.1.0" 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="1.6.1">subread</requirement>
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5 <requirement type="package" version="1.7">samtools</requirement>
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6 </requirements>
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8 <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command>
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9 <command detect_errors="exit_code"><![CDATA[
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10
10
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11 ## Export fc path for its built-in annotation
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12
10
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13 export FC_PATH=\$(command -v featureCounts | sed 's@/bin/featureCounts$@@') &&
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14
0
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15 ## Check whether all alignments are from the same type (bam || sam)
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16 featureCounts
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17
11
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18 #if $anno.anno_select=="history":
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19 -a '$anno.reference_gene_sets'
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20 -F "GTF"
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21 #elif $anno.anno_select=="cached":
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22 -a '$anno.reference_gene_sets_builtin.fields.path'
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23 -F "GTF"
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24 #elif $anno.anno_select=="builtin":
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25 -a \${FC_PATH}/annotation/${anno.bgenome}_RefSeq_exon.txt
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26 -F "SAF"
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27 #end if
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28
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29 -o "output"
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30 -T \${GALAXY_SLOTS:-2}
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31
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32 -s $strand_specificity
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33 -t '$extended_parameters.gff_feature_type'
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34 -g '$extended_parameters.gff_feature_attribute'
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35 $extended_parameters.summarization_level
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36 $extended_parameters.contribute_to_multiple_features
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37 $extended_parameters.multimapping_enabled.multimapping_counts
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38
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39 #if str($extended_parameters.multimapping_enabled.multimapping_counts) == " -M":
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40 $extended_parameters.multimapping_enabled.fraction
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41 #end if
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42
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43 $extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads
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44 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J":
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45 #if $extended_parameters.exon_exon_junction_read_counting_enabled.genome:
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46 -G '$extended_parameters.exon_exon_junction_read_counting_enabled.genome'
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47 #end if
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48 #end if
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50 $extended_parameters.long_reads
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51
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52 $extended_parameters.by_read_group
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53
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54 -Q $extended_parameters.mapping_quality
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55 $extended_parameters.largest_overlap
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56 --minOverlap $extended_parameters.min_overlap
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57 --fracOverlap $extended_parameters.frac_overlap
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58 --fracOverlapFeature $extended_parameters.frac_overlap_feature
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59 $extended_parameters.read_reduction
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60 $extended_parameters.primary
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61 $extended_parameters.ignore_dup
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62 #if $extended_parameters.R:
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63 $extended_parameters.R
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64 #end if
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65 #if str($extended_parameters.read_extension_5p) != "0":
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66 --readExtension5 $extended_parameters.read_extension_5p
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67 #end if
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68
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69 #if str($extended_parameters.read_extension_3p) != "0":
0
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70 --readExtension3 $extended_parameters.read_extension_3p
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71 #end if
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73 $pe_parameters.fragment_counting_enabled.fragment_counting
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74 #if str($pe_parameters.fragment_counting_enabled.fragment_counting) == " -p":
0
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75 $pe_parameters.fragment_counting_enabled.check_distance_enabled.check_distance
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76 #if str($pe_parameters.fragment_counting_enabled.check_distance_enabled.check_distance) == " -P":
0
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77 -d $pe_parameters.fragment_counting_enabled.check_distance_enabled.minimum_fragment_length
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78 -D $pe_parameters.fragment_counting_enabled.check_distance_enabled.maximum_fragment_length
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79 #end if
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80 #end if
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81
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82 $pe_parameters.only_both_ends
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83 $pe_parameters.exclude_chimerics
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84
6
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85 '${alignment}'
0
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86
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87 ## Remove comment and add sample name to header
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88 && grep -v "^#" "output"
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89 | sed -e 's|${alignment}|${alignment.element_identifier}|g'
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90 > body.txt
0
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91 ## Set the right columns for the tabular formats
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92 #if $format.value == "tabdel_medium":
0
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93 && cut -f 1,7 body.txt > expression_matrix.txt
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94
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95 ## Paste doesn't allow a non ordered list of columns: -f 1,7,8,6 will only return columns 1,7 and 8
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96 ## Thus the gene length column (last column) has to be added separately
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97 && cut -f 6 body.txt > gene_lengths.txt
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98 && paste expression_matrix.txt gene_lengths.txt > expression_matrix.txt.bak
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99 && mv -f expression_matrix.txt.bak '${output_medium}'
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100 #elif $format.value == "tabdel_short":
6
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101 && cut -f 1,7 body.txt > '${output_short}'
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102 #else:
6
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103 && cp body.txt '${output_full}'
0
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104 #end if
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105
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106 #if str($include_feature_length_file) == "true":
6
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107 && cut -f 1,6 body.txt > '${output_feature_lengths}'
0
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108 #end if
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109
10
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110 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J":
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111 && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.jcounts' > '${output_jcounts}'
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112 #end if
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113
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114 #if $extended_parameters.R:
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115 && samtools sort -o '$output_bam' -@ \${GALAXY_SLOTS:-2} *.featureCounts.bam
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116 #end if
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117 && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.summary' > '${output_summary}'
0
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118 ]]></command>
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119 <inputs>
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120 <param name="alignment"
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121 type="data"
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122 multiple="false"
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123 format="bam,sam"
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124 label="Alignment file"
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125 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: ?" >
11
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126 </param>
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127
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128 <param name="strand_specificity"
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129 type="select"
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130 label="Specify strand information"
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131 argument="-s"
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132 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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133 <option value="0" selected="true">Unstranded</option>
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134 <option value="1">Stranded (Forward)</option>
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135 <option value="2">Stranded (Reverse)</option>
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136 </param>
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137
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138 <conditional name="anno">
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139 <param name="anno_select" type="select" label="Gene annotation file">
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140 <option value="builtin">featureCounts built-in</option>
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141 <option value="cached" selected="True">locally cached</option>
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142 <option value="history">in your history</option>
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143 </param>
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144 <when value="builtin">
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145 <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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146 <options from_data_table="featurecounts_anno">
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147 <filter type="data_meta" key="dbkey" ref="alignment" column="0"/>
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148 </options>
3
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149 </param>
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150 </when>
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151 <when value="cached">
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152 <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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153 <options from_data_table="gene_sets">
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154 <filter type="data_meta" key="dbkey" ref="alignment" column="0"/>
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155 </options>
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156 <validator type="no_options" message="An annotation file is not available for the build associated with the selected input file"/>
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157 </param>
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158 </when>
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159 <when value="history">
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160 <param name="reference_gene_sets"
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161 format="gff,gtf,gff3"
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162 type="data"
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163 label="Gene annotation file"
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164 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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165 </param>
3
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166 </when>
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167 </conditional>
8
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168
0
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169 <param name="format"
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170 type="select"
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171 label="Output format"
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172 help="The output format will be tabular, select the preferred columns here">
13
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173 <option value="tabdel_short">Gene-ID "\t" read-count (MultiQC/DESeq2/edgeR/limma-voom compatible)</option>
0
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174 <option value="tabdel_medium">Gene-ID "\t" read-count "\t" gene-length</option>
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175 <option value="tabdel_full">featureCounts 1.4.0+ default (includes regions provided by the GTF file)</option>
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176 </param>
8
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177
0
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178 <param name="include_feature_length_file"
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179 type="boolean"
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diff changeset
180 truevalue="true"
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181 falsevalue="false"
2
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parents: 1
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182 checked="false"
0
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183 label="Create gene-length file"
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184 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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diff changeset
185
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diff changeset
186
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187 <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
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188 <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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diff changeset
189
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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190 <param name="fragment_counting"
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diff changeset
191 type="select"
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diff changeset
192 argument="-p"
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diff changeset
193 checked="true"
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194 label="Count fragments instead of reads"
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195 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
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196 <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
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197 <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
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diff changeset
198 </param>
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diff changeset
199
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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200 <when value=" -p">
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diff changeset
201 <conditional name="check_distance_enabled">
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
202 <param name="check_distance"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
203 type="boolean"
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iuc
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diff changeset
204 truevalue=" -P"
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diff changeset
205 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
206 argument="-P"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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207 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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208 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
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diff changeset
209 <when value=" -P">
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diff changeset
210 <param name="minimum_fragment_length"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
211 type="integer"
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diff changeset
212 value="50"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
213 argument="-d"
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diff changeset
214 label="Minimum 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
215 <param name="maximum_fragment_length"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
216 type="integer"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
217 value="600"
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diff changeset
218 argument="-D"
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diff changeset
219 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
220 </when>
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diff changeset
221 <when value="" />
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diff changeset
222 </conditional>
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diff changeset
223 </when>
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diff changeset
224 <when value="" />
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225 </conditional>
8
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diff changeset
226
0
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227 <param name="only_both_ends"
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228 type="boolean"
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diff changeset
229 truevalue=" -B"
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diff changeset
230 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
231 argument="-B"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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232 label="Only allow fragments with both reads aligned"
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233 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
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234
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235 <param name="exclude_chimerics"
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236 type="boolean"
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237 truevalue=" -C"
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diff changeset
238 falsevalue=""
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diff changeset
239 argument="-C"
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diff changeset
240 checked="true"
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241 label="Exclude chimeric fragments"
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242 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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243 </section>
8
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244
0
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245 <section name="extended_parameters" title="Advanced options">
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246 <param name="gff_feature_type"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
247 type="text"
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248 value="exon"
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249 argument="-t"
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diff changeset
250 label="GFF feature type filter"
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251 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
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diff changeset
252
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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253 <param name="gff_feature_attribute"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
254 type="text"
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255 value="gene_id"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
256 argument="-g"
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257 label="GFF gene identifier"
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258 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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diff changeset
259
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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260 <param name="summarization_level"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
261 type="boolean"
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262 truevalue=" -f"
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diff changeset
263 falsevalue=""
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264 argument="-f"
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265 label="On feature level"
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266 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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267
11
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268 <param name="contribute_to_multiple_features"
0
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269 type="boolean"
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270 truevalue=" -O"
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diff changeset
271 falsevalue=""
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272 argument="-O"
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273 label="Allow read to contribute to multiple features"
3
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274 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
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275
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276 <conditional name="multimapping_enabled">
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277 <param name="multimapping_counts"
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278 type="select"
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diff changeset
279 argument="-M"
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280 label="Count multi-mapping reads/fragments"
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281 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.">
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282 <option value="" selected="true">Disabled; multi-mapping reads are excluded (default)</option>
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283 <option value=" -M">Enabled; multi-mapping reads are included</option>
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diff changeset
284 </param>
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diff changeset
285 <when value=" -M">
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diff changeset
286 <param name="fraction"
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diff changeset
287 type="boolean"
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diff changeset
288 truevalue="--fraction"
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diff changeset
289 falsevalue=""
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diff changeset
290 argument="--fraction"
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diff changeset
291 label="Assign fractions to multimapping reads"
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diff changeset
292 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
293 </when>
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diff changeset
294 <when value="" />
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diff changeset
295 </conditional>
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diff changeset
296
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297 <param name="mapping_quality"
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diff changeset
298 type="integer"
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diff changeset
299 value="12"
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diff changeset
300 argument="-Q"
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diff changeset
301 label="Minimum mapping quality per read"
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diff changeset
302 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." />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
303
6
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diff changeset
304 <conditional name="exon_exon_junction_read_counting_enabled">
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305 <param name="count_exon_exon_junction_reads" argument="-J" type="boolean" truevalue="-J" falsevalue=""
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306 label="Exon-exon junctions"
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diff changeset
307 help="If specified, reads supporting each exon-exon junction will be counted" />
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diff changeset
308 <when value="-J">
7
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309 <param name="genome" argument="-G" type="data" format="fasta" optional="true"
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310 label="Reference sequence file"
6
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311 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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312 </when>
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diff changeset
313 <when value="" />
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314 </conditional>
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diff changeset
315
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316 <param name="long_reads" argument="-L" type="boolean" truevalue="-L" falsevalue=""
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317 label="Long reads"
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318 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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319
10
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320 <param name="by_read_group" argument="--byReadGroup" type="boolean" truevalue="--byReadGroup" falsevalue=""
8
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321 label="Count reads by read group"
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322 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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diff changeset
323
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324
0
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325 <param name="largest_overlap"
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326 type="boolean"
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327 truevalue=" --largestOverlap"
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328 falsevalue=""
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329 argument="--largestOverlap"
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330 label="Largest overlap"
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331 help="If specified, reads (or fragments) will be assigned to the target that has the largest number of overlapping bases" />
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diff changeset
332
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333 <param name="min_overlap"
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diff changeset
334 type="integer"
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diff changeset
335 value="1"
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336 argument="--minOverlap"
8
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337 label="Minimum bases of overlap"
0
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338 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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339
10
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340 <param name="frac_overlap"
8
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diff changeset
341 type="integer"
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342 value="0"
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343 min="0"
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diff changeset
344 max="1"
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345 argument="--fracOverlap"
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346 label="Minimum fraction (of read) overlapping a feature"
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347 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." />
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348
10
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349 <param name="frac_overlap_feature"
8
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diff changeset
350 type="integer"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
351 value="0"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
352 min="0"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
353 max="1"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
354 argument="--fracOverlapFeature"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
355 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
356 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
357
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
358 <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
359 type="integer"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
360 value="0"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
361 argument="--readExtension5"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
362 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
363 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
364
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
365 <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
366 type="integer"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
367 value="0"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
368 argument="--readExtension3"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
369 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
370 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
371
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
372 <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
373 type="select"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
374 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
375 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
376 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
377 <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
378 <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
379 <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
380 </param>
8
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
381
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
382 <param name="primary"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
383 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
384 truevalue=" --primary"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
385 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
386 argument="--primary"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
387 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
388 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
389
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
390 <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
391 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
392 truevalue=" --ignoreDup"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
393 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
394 argument="--ignoreDup"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
395 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
396 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
397
17
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
398 <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
399 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
400 falsevalue=""
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
401 argument="-R"
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
402 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
403 help="" />
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
404
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
405 <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
406 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
407 truevalue=" --countSplitAlignmentsOnly"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
408 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
409 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
410 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
411 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
412 </section>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
413 </inputs>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
414 <outputs>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
415 <data format="tabular"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
416 name="output_medium"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
417 label="${tool.name} on ${on_string}">
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
418 <filter>format == "tabdel_medium"</filter>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
419 <actions>
9
e6a2a912677a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4fb528145289ad4db04e4589c02e9ddaa1194138
iuc
parents: 8
diff changeset
420 <action name="column_names" type="metadata" default="Geneid,${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
421 </actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
422 </data>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
423
17
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
424 <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
425 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
426 label="${tool.name} on ${on_string}: Alignment file">
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
427 <filter>extended_parameters['R']</filter>
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
428 </data>
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
429
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
430 <data format="tabular"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
431 name="output_short"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
432 label="${tool.name} on ${on_string}">
13
386220cf6877 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4
iuc
parents: 12
diff changeset
433 <filter>format == "tabdel_short"</filter>
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
434 <actions>
9
e6a2a912677a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4fb528145289ad4db04e4589c02e9ddaa1194138
iuc
parents: 8
diff changeset
435 <action name="column_names" type="metadata" default="Geneid,${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
436 </actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
437 </data>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
438
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
439 <data format="tabular"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
440 name="output_full"
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diff changeset
441 label="${tool.name} on ${on_string}: count table">
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
442 <filter>format == "tabdel_full"</filter>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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443 <actions>
9
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parents: 8
diff changeset
444 <action name="column_names" type="metadata" default="Geneid,Chr,Start,End,Strand,Length,${alignment.element_identifier}" />
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
445 </actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
446 </data>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
447
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
448 <data format="tabular"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
449 name="output_summary"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
450 label="${tool.name} on ${on_string}: summary">
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
451 <actions>
9
e6a2a912677a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4fb528145289ad4db04e4589c02e9ddaa1194138
iuc
parents: 8
diff changeset
452 <action name="column_names" type="metadata" default="Status,${alignment.element_identifier}" />
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
453 </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
454 </data>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
455
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
456 <data format="tabular"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
457 name="output_feature_lengths"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
458 label="${tool.name} on ${on_string}: feature lengths">
6
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iuc
parents: 4
diff changeset
459 <filter>include_feature_length_file</filter>
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
460 <actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
461 <action name="column_names" type="metadata" default="Feature,Length" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
462 </actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
463 </data>
6
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
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parents: 4
diff changeset
464
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents: 4
diff changeset
465 <data name="output_jcounts" format="tabular"
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
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parents: 4
diff changeset
466 label="${tool.name} on ${on_string}: junction counts">
7
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iuc
parents: 6
diff changeset
467 <filter>extended_parameters['exon_exon_junction_read_counting_enabled']['count_exon_exon_junction_reads']</filter>
6
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
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parents: 4
diff changeset
468 <actions>
10
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iuc
parents: 9
diff changeset
469 <action name="column_names" type="metadata"
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
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diff changeset
470 default="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,${alignment.element_identifier}" />
6
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
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parents: 4
diff changeset
471 </actions>
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents: 4
diff changeset
472 </data>
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
473 </outputs>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
474 <tests>
7
3ce1c701b0df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17
iuc
parents: 6
diff changeset
475 <test expect_num_outputs="3">
11
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iuc
parents: 10
diff changeset
476 <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
477 <param name="anno_select" value="history"/>
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
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diff changeset
478 <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
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diff changeset
479 <param name="format" value="tabdel_medium" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
480 <param name="include_feature_length_file" value="true"/>
4
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iuc
parents: 3
diff changeset
481 <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
482 <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
483 </output>
d417fb66494e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents: 3
diff changeset
484 <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
485 <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
486 </output>
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
487 </test>
7
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iuc
parents: 6
diff changeset
488 <test expect_num_outputs="3">
11
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iuc
parents: 10
diff changeset
489 <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
490 <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
491 <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
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diff changeset
492 <param name="format" value="tabdel_full" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
493 <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
494 <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
495 <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
496 </output>
d417fb66494e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents: 3
diff changeset
497 <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
498 <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
499 </output>
d417fb66494e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents: 3
diff changeset
500 <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
501 <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
502 </output>
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
503 </test>
10
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parents: 9
diff changeset
504 <test expect_num_outputs="4">
11
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iuc
parents: 10
diff changeset
505 <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
506 <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
507 <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
508 <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
509 <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
510 <param name="count_exon_exon_junction_reads" value="-J"/>
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parents: 12
diff changeset
511 <output name="output_short" file="output_1_short.tab">
10
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iuc
parents: 9
diff changeset
512 <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
513 </output>
13
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iuc
parents: 12
diff changeset
514 <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
515 <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
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diff changeset
516 </output>
13
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iuc
parents: 12
diff changeset
517 <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
518 <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
519 </output>
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents: 9
diff changeset
520 </test>
11
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
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parents: 10
diff changeset
521 <!-- Ensure featureCounts built-in annotation works -->
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8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
522 <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
523 <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
524 <param name="anno_select" value="builtin"/>
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525 <param name="format" value="tabdel_short" />
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526 <section name="extended_parameters">
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527 <param name="R" value="true" />
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528 </section>
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529 <output name="output_short" file="output_builtin_hg19.tab">
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530 <metadata name="column_names" value="Geneid,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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531 </output>
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532 <output name="output_summary" file="output_summary_builtin_hg19.tab"/>
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533 <output name="output_bam" file="output.bam" ftype="bam"/>
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534 </test>
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535 <!-- Ensure cached GTFs work -->
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536 <test expect_num_outputs="3">
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537 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38" />
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538 <param name="anno_select" value="cached"/>
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539 <param name="format" value="tabdel_medium" />
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540 <param name="include_feature_length_file" value="true"/>
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541 <output name="output_medium" file="output_1_medium.tab">
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542 <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/>
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543 </output>
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544 <output name="output_summary" file="output_1_summary.tab">
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545 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
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546 </output>
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547 </test>
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548 <!-- Ensure BAM output works -->
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549 <test>
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550 <param name="alignment" value="subset.sorted.bam" ftype="bam" />
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551 <param name="anno_select" value="history" />
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552 <param name="reference_gene_sets" value="small.gtf" ftype="gtf" />
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553 <section name="extended_parameters" >
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554 <param name="R" value="true" />
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555 </section>
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556 <output name="output_bam" value="subset.sorted.featurecounts.bam" />
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557 </test>
0
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558 </tests>
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559
0
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560 <help><![CDATA[
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561 featureCounts
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562 #############
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563
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564 Overview
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565 --------
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566 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.
0
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567
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568 Input formats
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569 -------------
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570 Alignments should be provided in either:
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571
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572 - SAM format, http://samtools.sourceforge.net/samtools.shtml#5
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573 - BAM format
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574
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575 Annotations for gene regions should be provided in the GFF/GTF format:
0
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576
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577 - http://genome.ucsc.edu/FAQ/FAQformat.html#format3
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578 - http://www.ensembl.org/info/website/upload/gff.html
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579
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580 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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581
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582 Example - **Built-in annotation format**:
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583
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584 ====== ==== ======= ======= ======
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585 GeneID Chr Start End Strand
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586 ====== ==== ======= ======= ======
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587 497097 chr1 3204563 3207049 -
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588 497097 chr1 3411783 3411982 -
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589 497097 chr1 3660633 3661579 -
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590 ====== ==== ======= ======= ======
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591
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592 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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593
0
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594 Output format
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595 -------------
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596 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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597
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598 .. _Subread: http://subread.sourceforge.net/
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599 .. _`Subread User's Guide`: http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf
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600 .. _`Subread package`: https://sourceforge.net/projects/subread/files/
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601 ]]></help>
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602 <citations>
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603 <citation type="doi">10.1093/bioinformatics/btt656</citation>
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604 </citations>
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605 </tool>