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annotate featurecounts.xml @ 26:ea04b737afa0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 34edb37978466203f104fbd6eb394ad9e560f859"
author iuc
date Sat, 21 Nov 2020 10:22:09 +0000
parents 90d16db017d7
children ce44c6f2ba38
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1 <tool id="featurecounts" name="featureCounts" version="2.0.1" 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="2.0.1">subread</requirement>
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5 <requirement type="package" version="1.11">samtools</requirement>
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6 <requirement type="package" version="8.31">coreutils</requirement>
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7 </requirements>
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9 <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command>
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10 <command detect_errors="exit_code"><![CDATA[
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11
10
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12 ## Export fc path for its built-in annotation
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13
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14 export FC_PATH=\$(command -v featureCounts | sed 's@/bin/featureCounts$@@') &&
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15
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16 ## Check whether all alignments are from the same type (bam || sam)
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17 featureCounts
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19 #if $anno.anno_select=="history":
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20 -a '$anno.reference_gene_sets'
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21 -F "GTF"
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22 #elif $anno.anno_select=="cached":
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23 -a '$anno.reference_gene_sets_builtin.fields.path'
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24 -F "GTF"
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25 #elif $anno.anno_select=="builtin":
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26 -a \${FC_PATH}/annotation/${anno.bgenome}_RefSeq_exon.txt
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27 -F "SAF"
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28 #end if
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29
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30 -o "output"
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31 -T \${GALAXY_SLOTS:-2}
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33 -s $strand_specificity
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34 -t '$extended_parameters.gff_feature_type'
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35 -g '$extended_parameters.gff_feature_attribute'
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36 $extended_parameters.summarization_level
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38 $extended_parameters.multifeatures.multifeat
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39 #if $extended_parameters.multifeatures.multifeat != "":
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40 $extended_parameters.multifeatures.fraction
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41 #end if
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42
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43
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44 ## $extended_parameters.contribute_to_multiple_features
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45 ## $extended_parameters.multimapping_enabled.multimapping_counts
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47 ###if str($extended_parameters.multimapping_enabled.multimapping_counts) == " -M":
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48 ## $extended_parameters.multimapping_enabled.fraction
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49 ###end if -->
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51 $extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads
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52 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J":
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53 #if $extended_parameters.exon_exon_junction_read_counting_enabled.genome:
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54 -G '$extended_parameters.exon_exon_junction_read_counting_enabled.genome'
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55 #end if
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56 #end if
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58 $extended_parameters.long_reads
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59
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60 $extended_parameters.by_read_group
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61
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62 -Q $extended_parameters.mapping_quality
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63 $extended_parameters.largest_overlap
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64 --minOverlap $extended_parameters.min_overlap
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65 --fracOverlap $extended_parameters.frac_overlap
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66 --fracOverlapFeature $extended_parameters.frac_overlap_feature
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67 $extended_parameters.read_reduction
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68 $extended_parameters.primary
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69 $extended_parameters.ignore_dup
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70 #if $extended_parameters.R:
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71 $extended_parameters.R
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72 #end if
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73 #if str($extended_parameters.read_extension_5p) != "0":
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74 --readExtension5 $extended_parameters.read_extension_5p
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75 #end if
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76
10
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77 #if str($extended_parameters.read_extension_3p) != "0":
0
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78 --readExtension3 $extended_parameters.read_extension_3p
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79 #end if
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81 $pe_parameters.fragment_counting_enabled.fragment_counting
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82 #if str($pe_parameters.fragment_counting_enabled.fragment_counting) == " -p":
0
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83 $pe_parameters.fragment_counting_enabled.check_distance_enabled.check_distance
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84 #if str($pe_parameters.fragment_counting_enabled.check_distance_enabled.check_distance) == " -P":
0
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85 -d $pe_parameters.fragment_counting_enabled.check_distance_enabled.minimum_fragment_length
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86 -D $pe_parameters.fragment_counting_enabled.check_distance_enabled.maximum_fragment_length
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87 #end if
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88 #end if
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89
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90 $pe_parameters.only_both_ends
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91 $pe_parameters.exclude_chimerics
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92
6
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93 '${alignment}'
0
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94
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95 ## Remove comment and add sample name to header
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96 && grep -v "^#" "output"
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97 | sed -e 's|${alignment}|${alignment.element_identifier}|g'
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98 > body.txt
0
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99 ## Set the right columns for the tabular formats
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100 #if $format.value == "tabdel_medium":
0
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101 && cut -f 1,7 body.txt > expression_matrix.txt
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102
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103 ## Paste doesn't allow a non ordered list of columns: -f 1,7,8,6 will only return columns 1,7 and 8
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104 ## Thus the gene length column (last column) has to be added separately
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105 && cut -f 6 body.txt > gene_lengths.txt
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106 && paste expression_matrix.txt gene_lengths.txt > expression_matrix.txt.bak
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107 && mv -f expression_matrix.txt.bak '${output_medium}'
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108 #elif $format.value == "tabdel_short":
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109 && cut -f 1,7 body.txt > '${output_short}'
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110 #else:
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111 && cp body.txt '${output_full}'
0
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112 #end if
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113
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114 #if str($include_feature_length_file) == "true":
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115 && cut -f 1,6 body.txt > '${output_feature_lengths}'
0
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116 #end if
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117
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118 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J":
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119 && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.jcounts' > '${output_jcounts}'
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120 #end if
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121
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122 #if $extended_parameters.R:
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123 && samtools sort -o '$output_bam' -@ \${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" *.featureCounts.bam
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124 #end if
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125 && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.summary' > '${output_summary}'
0
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126 ]]></command>
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127 <inputs>
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128 <param name="alignment"
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129 type="data"
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130 multiple="false"
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131 format="bam,sam"
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132 label="Alignment file"
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133 help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files must be in the same format. Unless you are using a Gene annotation file from the History, these files must have the database/genome attribute already specified e.g. hg38, not the default: ?" >
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134 </param>
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135
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136 <param name="strand_specificity"
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137 type="select"
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138 label="Specify strand information"
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139 argument="-s"
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140 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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141 <option value="0" selected="true">Unstranded</option>
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142 <option value="1">Stranded (Forward)</option>
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143 <option value="2">Stranded (Reverse)</option>
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144 </param>
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145
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146 <conditional name="anno">
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147 <param name="anno_select" type="select" label="Gene annotation file">
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148 <option value="builtin">featureCounts built-in</option>
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149 <option value="cached" selected="True">locally cached</option>
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150 <option value="history">in your history</option>
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151 </param>
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152 <when value="builtin">
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153 <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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154 <options from_data_table="featurecounts_anno">
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155 <filter type="data_meta" key="dbkey" ref="alignment" column="dbkey"/>
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156 </options>
3
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157 </param>
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158 </when>
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159 <when value="cached">
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160 <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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161 <options from_data_table="gene_sets">
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162 <filter type="data_meta" key="dbkey" ref="alignment" column="dbkey"/>
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163 <filter type="sort_by" column="2" />
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164 </options>
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165 <validator type="no_options" message="An annotation file is not available for the build associated with the selected input file"/>
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166 </param>
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167 </when>
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168 <when value="history">
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169 <param name="reference_gene_sets"
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170 format="gff,gtf,gff3"
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171 type="data"
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172 label="Gene annotation file"
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parents: 10
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173 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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174 </param>
3
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parents: 2
diff changeset
175 </when>
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176 </conditional>
8
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parents: 7
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177
0
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178 <param name="format"
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diff changeset
179 type="select"
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180 label="Output format"
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181 help="The output format will be tabular, select the preferred columns here">
13
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182 <option value="tabdel_short">Gene-ID "\t" read-count (MultiQC/DESeq2/edgeR/limma-voom compatible)</option>
0
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183 <option value="tabdel_medium">Gene-ID "\t" read-count "\t" gene-length</option>
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184 <option value="tabdel_full">featureCounts 1.4.0+ default (includes regions provided by the GTF file)</option>
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185 </param>
8
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parents: 7
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186
0
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187 <param name="include_feature_length_file"
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diff changeset
188 type="boolean"
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diff changeset
189 truevalue="true"
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190 falsevalue="false"
2
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parents: 1
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191 checked="false"
0
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192 label="Create gene-length file"
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193 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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diff changeset
194
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diff changeset
195
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diff changeset
196 <section name="pe_parameters" title="Options for paired-end reads">
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diff changeset
197 <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
198
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diff changeset
199 <param name="fragment_counting"
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diff changeset
200 type="select"
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diff changeset
201 argument="-p"
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diff changeset
202 checked="true"
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203 label="Count fragments instead of reads"
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diff changeset
204 help="If specified, fragments (or templates) will be counted instead of reads.">
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205 <option value="" selected="true">Disabled; all reads/mates will be counted individually</option>
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206 <option value=" -p">Enabled; fragments (or templates) will be counted instead of reads</option>
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diff changeset
207 </param>
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diff changeset
208
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209 <when value=" -p">
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diff changeset
210 <conditional name="check_distance_enabled">
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diff changeset
211 <param name="check_distance"
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diff changeset
212 type="boolean"
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diff changeset
213 truevalue=" -P"
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diff changeset
214 falsevalue=""
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diff changeset
215 argument="-P"
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216 label="Check paired-end distance"
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217 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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218 <when value=" -P">
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219 <param name="minimum_fragment_length"
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diff changeset
220 type="integer"
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diff changeset
221 value="50"
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diff changeset
222 argument="-d"
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diff changeset
223 label="Minimum fragment/template length." />
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224 <param name="maximum_fragment_length"
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diff changeset
225 type="integer"
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diff changeset
226 value="600"
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diff changeset
227 argument="-D"
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diff changeset
228 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
229 </when>
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diff changeset
230 <when value="" />
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231 </conditional>
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diff changeset
232 </when>
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233 <when value="" />
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234 </conditional>
8
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diff changeset
235
0
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236 <param name="only_both_ends"
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237 type="boolean"
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238 truevalue=" -B"
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diff changeset
239 falsevalue=""
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diff changeset
240 argument="-B"
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241 label="Only allow fragments with both reads aligned"
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242 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." />
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diff changeset
243
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244 <param name="exclude_chimerics"
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245 type="boolean"
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246 truevalue=" -C"
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diff changeset
247 falsevalue=""
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diff changeset
248 argument="-C"
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diff changeset
249 checked="true"
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250 label="Exclude chimeric fragments"
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251 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." />
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252 </section>
8
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253
0
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254 <section name="extended_parameters" title="Advanced options">
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255 <param name="gff_feature_type"
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diff changeset
256 type="text"
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257 value="exon"
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diff changeset
258 argument="-t"
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259 label="GFF feature type filter"
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260 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." />
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261
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262 <param name="gff_feature_attribute"
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263 type="text"
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264 value="gene_id"
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265 argument="-g"
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266 label="GFF gene identifier"
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267 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." />
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268
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269 <param name="summarization_level"
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270 type="boolean"
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271 truevalue=" -f"
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272 falsevalue=""
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273 argument="-f"
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274 label="On feature level"
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275 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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276
25
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277 <conditional name = "multifeatures">
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278 <param name="multifeat" type="select" label="Allow reads to map to multiple features" help="Setting -O, -M and --fraction">
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279 <option value="" selected="true">Disabled; reads that align to multiple features or overlapping features are excluded</option>
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280 <option value="-M">Enabled; multi-mapping reads are included (-M)</option>
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281 <option value="-O">Enabled: multi-overlapping features are included (-O)</option>
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282 <option value="-O -M">Enabled: both multi-mapping and multi-overlapping features are included (-M -O)</option>
0
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283 </param>
25
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284 <when value=""/>
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285 <when value="-M">
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286 <param name="fraction"
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287 type="boolean"
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288 truevalue="--fraction"
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289 falsevalue=""
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290 argument="--fraction"
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291 label="Assign fractions to multimapping reads"
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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."/>
0
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293 </when>
25
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294 <when value="-O">
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295 <param name="fraction"
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296 type="boolean"
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297 truevalue="--fraction"
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298 falsevalue=""
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299 argument="--fraction"
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300 label="Assign fractions to multimapping reads"
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301 help="If specified, a fractional count 1/n will be generated for each multi-overlapping read, where n is the number of alignments (indica- ted by 'NH' tag) reported for the read."/>
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302 </when>
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303 <when value="-O -M">
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304 <param name="fraction"
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305 type="boolean"
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306 truevalue="--fraction"
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307 falsevalue=""
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308 argument="--fraction"
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309 label="Assign fractions to multimapping reads"
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310 help="If specified, a fractional count 1/n will be generated for each multi-mapping or multi-overlapping read, where n is the number of alignments (indica- ted by 'NH' tag) reported for the read."/>
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311 </when>
0
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312 </conditional>
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diff changeset
313
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314 <param name="mapping_quality"
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315 type="integer"
23
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316 value="0"
0
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diff changeset
317 argument="-Q"
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318 label="Minimum mapping quality per read"
23
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319 help="The minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria. 0 by default." />
0
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320
6
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321 <conditional name="exon_exon_junction_read_counting_enabled">
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322 <param name="count_exon_exon_junction_reads" argument="-J" type="boolean" truevalue="-J" falsevalue=""
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323 label="Exon-exon junctions"
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324 help="If specified, reads supporting each exon-exon junction will be counted" />
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325 <when value="-J">
7
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326 <param name="genome" argument="-G" type="data" format="fasta" optional="true"
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327 label="Reference sequence file"
6
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328 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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329 </when>
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330 <when value="" />
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331 </conditional>
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332
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333 <param name="long_reads" argument="-L" type="boolean" truevalue="-L" falsevalue=""
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334 label="Long reads"
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335 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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336
10
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337 <param name="by_read_group" argument="--byReadGroup" type="boolean" truevalue="--byReadGroup" falsevalue=""
8
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338 label="Count reads by read group"
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339 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
340
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341
0
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342 <param name="largest_overlap"
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343 type="boolean"
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344 truevalue=" --largestOverlap"
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345 falsevalue=""
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346 argument="--largestOverlap"
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347 label="Largest overlap"
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diff changeset
348 help="If specified, reads (or fragments) will be assigned to the target that has the largest number of overlapping bases" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
349
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
350 <param name="min_overlap"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
351 type="integer"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
352 value="1"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
353 argument="--minOverlap"
8
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
354 label="Minimum bases of overlap"
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
355 help="Specify the minimum required number of overlapping bases between a read (or a fragment) and a feature. 1 by default. If a negative value is provided, the read will be extended from both ends." />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
356
10
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents: 9
diff changeset
357 <param name="frac_overlap"
8
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
358 type="integer"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
359 value="0"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
360 min="0"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
361 max="1"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
362 argument="--fracOverlap"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
363 label="Minimum fraction (of read) overlapping a feature"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
364 help="Specify the minimum required fraction of overlapping bases between a read (or a fragment) and a feature. Value should be within range [0,1]. 0 by default. Number of overlapping bases is counted from both reads if paired end. Both this option and '--minOverlap' need to be satisfied for read assignment." />
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
365
10
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents: 9
diff changeset
366 <param name="frac_overlap_feature"
8
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
367 type="integer"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
368 value="0"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
369 min="0"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
370 max="1"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
371 argument="--fracOverlapFeature"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
372 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
373 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
374
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
375 <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
376 type="integer"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
377 value="0"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
378 argument="--readExtension5"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
379 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
380 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
381
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
382 <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
383 type="integer"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
384 value="0"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
385 argument="--readExtension3"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
386 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
387 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
388
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
389 <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
390 type="select"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
391 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
392 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
393 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
394 <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
395 <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
396 <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
397 </param>
8
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
398
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
399 <param name="primary"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
400 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
401 truevalue=" --primary"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
402 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
403 argument="--primary"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
404 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
405 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
406
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
407 <param name="ignore_dup"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
408 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
409 truevalue=" --ignoreDup"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
410 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
411 argument="--ignoreDup"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
412 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
413 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
414
17
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
415 <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
416 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
417 falsevalue=""
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
418 argument="-R"
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
419 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
420 help="" />
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
421
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
422 <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
423 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
424 truevalue=" --countSplitAlignmentsOnly"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
425 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
426 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
427 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
428 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
429 </section>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
430 </inputs>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
431 <outputs>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
432 <data format="tabular"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
433 name="output_medium"
20
1759d845181e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5
iuc
parents: 19
diff changeset
434 label="${tool.name} on ${on_string}: Counts (with length)">
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
435 <filter>format == "tabdel_medium"</filter>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
436 <actions>
9
e6a2a912677a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4fb528145289ad4db04e4589c02e9ddaa1194138
iuc
parents: 8
diff changeset
437 <action name="column_names" type="metadata" default="Geneid,${alignment.element_identifier},Length" />
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
438 </actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
439 </data>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
440
17
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
441 <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
442 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
443 label="${tool.name} on ${on_string}: Alignment file">
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
444 <filter>extended_parameters['R']</filter>
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
445 </data>
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
446
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
447 <data format="tabular"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
448 name="output_short"
20
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iuc
parents: 19
diff changeset
449 label="${tool.name} on ${on_string}: Counts">
13
386220cf6877 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4
iuc
parents: 12
diff changeset
450 <filter>format == "tabdel_short"</filter>
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
451 <actions>
9
e6a2a912677a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4fb528145289ad4db04e4589c02e9ddaa1194138
iuc
parents: 8
diff changeset
452 <action name="column_names" type="metadata" default="Geneid,${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
453 </actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
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
parents:
diff changeset
457 name="output_full"
20
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iuc
parents: 19
diff changeset
458 label="${tool.name} on ${on_string}: Counts (with location)">
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
459 <filter>format == "tabdel_full"</filter>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
460 <actions>
9
e6a2a912677a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4fb528145289ad4db04e4589c02e9ddaa1194138
iuc
parents: 8
diff changeset
461 <action name="column_names" type="metadata" default="Geneid,Chr,Start,End,Strand,Length,${alignment.element_identifier}" />
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
462 </actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
463 </data>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
464
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
465 <data format="tabular"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
466 name="output_summary"
20
1759d845181e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5
iuc
parents: 19
diff changeset
467 label="${tool.name} on ${on_string}: Summary">
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
468 <actions>
9
e6a2a912677a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4fb528145289ad4db04e4589c02e9ddaa1194138
iuc
parents: 8
diff changeset
469 <action name="column_names" type="metadata" default="Status,${alignment.element_identifier}" />
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
470 </actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
471 </data>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
472
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
473 <data format="tabular"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
474 name="output_feature_lengths"
20
1759d845181e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5
iuc
parents: 19
diff changeset
475 label="${tool.name} on ${on_string}: Feature lengths">
6
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents: 4
diff changeset
476 <filter>include_feature_length_file</filter>
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
477 <actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
478 <action name="column_names" type="metadata" default="Feature,Length" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
479 </actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
480 </data>
6
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents: 4
diff changeset
481
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents: 4
diff changeset
482 <data name="output_jcounts" format="tabular"
20
1759d845181e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5
iuc
parents: 19
diff changeset
483 label="${tool.name} on ${on_string}: Junction counts">
7
3ce1c701b0df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17
iuc
parents: 6
diff changeset
484 <filter>extended_parameters['exon_exon_junction_read_counting_enabled']['count_exon_exon_junction_reads']</filter>
6
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents: 4
diff changeset
485 <actions>
10
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents: 9
diff changeset
486 <action name="column_names" type="metadata"
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents: 9
diff changeset
487 default="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,${alignment.element_identifier}" />
6
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents: 4
diff changeset
488 </actions>
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents: 4
diff changeset
489 </data>
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
490 </outputs>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
491 <tests>
7
3ce1c701b0df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17
iuc
parents: 6
diff changeset
492 <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
493 <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
494 <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
495 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38" />
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
496 <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
497 <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
498 <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
499 <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
500 </output>
d417fb66494e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents: 3
diff changeset
501 <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
502 <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
503 </output>
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
504 </test>
7
3ce1c701b0df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17
iuc
parents: 6
diff changeset
505 <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
506 <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
507 <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
508 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38" />
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
509 <param name="format" value="tabdel_full" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
510 <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
511 <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
512 <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
513 </output>
d417fb66494e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents: 3
diff changeset
514 <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
515 <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
516 </output>
d417fb66494e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents: 3
diff changeset
517 <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
518 <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
519 </output>
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
520 </test>
10
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents: 9
diff changeset
521 <test expect_num_outputs="4">
11
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents: 10
diff changeset
522 <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
523 <param name="anno_select" value="history"/>
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
524 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38" />
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iuc
parents: 9
diff changeset
525 <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
526 <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
527 <param name="count_exon_exon_junction_reads" value="-J"/>
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iuc
parents: 12
diff changeset
528 <output name="output_short" file="output_1_short.tab">
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46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents: 9
diff changeset
529 <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
530 </output>
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386220cf6877 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4
iuc
parents: 12
diff changeset
531 <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
532 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents: 9
diff changeset
533 </output>
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386220cf6877 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4
iuc
parents: 12
diff changeset
534 <output name="output_jcounts" file="output_1_jcounts.tab">
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iuc
parents: 9
diff changeset
535 <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
536 </output>
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents: 9
diff changeset
537 </test>
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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
538 <!-- 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
539 <test expect_num_outputs="3">
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e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents: 10
diff changeset
540 <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" dbkey="hg19" />
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46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents: 9
diff changeset
541 <param name="anno_select" value="builtin"/>
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
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diff changeset
542 <param name="format" value="tabdel_short" />
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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
543 <section name="extended_parameters">
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
544 <param name="R" value="true" />
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
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parents: 15
diff changeset
545 </section>
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46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
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parents: 9
diff changeset
546 <output name="output_short" file="output_builtin_hg19.tab">
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents: 9
diff changeset
547 <metadata name="column_names" value="Geneid,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents: 9
diff changeset
548 </output>
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
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diff changeset
549 <output name="output_summary" file="output_summary_builtin_hg19.tab"/>
17
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
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diff changeset
550 <output name="output_bam" file="output.bam" ftype="bam"/>
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46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
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diff changeset
551 </test>
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iuc
parents: 10
diff changeset
552 <!-- Ensure cached GTFs work -->
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents: 10
diff changeset
553 <test expect_num_outputs="3">
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents: 10
diff changeset
554 <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
555 <param name="anno_select" value="cached"/>
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents: 10
diff changeset
556 <param name="format" value="tabdel_medium" />
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
557 <param name="include_feature_length_file" value="true"/>
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
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diff changeset
558 <output name="output_medium" file="output_1_medium.tab">
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents: 10
diff changeset
559 <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/>
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents: 10
diff changeset
560 </output>
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents: 10
diff changeset
561 <output name="output_summary" file="output_1_summary.tab">
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents: 10
diff changeset
562 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents: 10
diff changeset
563 </output>
e803ca6407c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
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diff changeset
564 </test>
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iuc
parents: 17
diff changeset
565 <!-- Ensure BAM output works -->
d60b1c4e0347 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9
iuc
parents: 17
diff changeset
566 <test>
d60b1c4e0347 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9
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parents: 17
diff changeset
567 <param name="alignment" value="subset.sorted.bam" ftype="bam" />
d60b1c4e0347 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9
iuc
parents: 17
diff changeset
568 <param name="anno_select" value="history" />
d60b1c4e0347 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9
iuc
parents: 17
diff changeset
569 <param name="reference_gene_sets" value="small.gtf" ftype="gtf" />
d60b1c4e0347 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9
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parents: 17
diff changeset
570 <section name="extended_parameters" >
d60b1c4e0347 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9
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parents: 17
diff changeset
571 <param name="R" value="true" />
d60b1c4e0347 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9
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parents: 17
diff changeset
572 </section>
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parents: 20
diff changeset
573 <output name="output_bam" value="subset.sorted.featurecounts.bam" compare="sim_size"/>
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diff changeset
574 </test>
0
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575 </tests>
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parents: 7
diff changeset
576
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
577 <help><![CDATA[
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
578 featureCounts
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
579 #############
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
580
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
581 Overview
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
582 --------
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46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
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diff changeset
583 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
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
584
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
585 Input formats
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
586 -------------
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
587 Alignments should be provided in either:
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
588
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
589 - SAM format, http://samtools.sourceforge.net/samtools.shtml#5
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
590 - BAM format
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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591
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diff changeset
592 Annotations for gene regions should be provided in the GFF/GTF format:
0
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diff changeset
593
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
594 - http://genome.ucsc.edu/FAQ/FAQformat.html#format3
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595 - http://www.ensembl.org/info/website/upload/gff.html
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diff changeset
596
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diff changeset
597 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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parents: 13
diff changeset
598
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diff changeset
599 Example - **Built-in annotation format**:
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parents: 13
diff changeset
600
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diff changeset
601 ====== ==== ======= ======= ======
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parents: 13
diff changeset
602 GeneID Chr Start End Strand
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603 ====== ==== ======= ======= ======
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parents: 13
diff changeset
604 497097 chr1 3204563 3207049 -
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diff changeset
605 497097 chr1 3411783 3411982 -
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diff changeset
606 497097 chr1 3660633 3661579 -
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diff changeset
607 ====== ==== ======= ======= ======
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diff changeset
608
15
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609 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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610
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611 Output format
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612 -------------
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613 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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614
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615 .. _Subread: http://subread.sourceforge.net/
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616 .. _`Subread User's Guide`: http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf
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617 .. _`Subread package`: https://sourceforge.net/projects/subread/files/
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618 ]]></help>
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619 <citations>
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620 <citation type="doi">10.1093/bioinformatics/btt656</citation>
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621 </citations>
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622 </tool>