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annotate featurecounts.xml @ 23:9301937c9037 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 8c751ba49b1465ad147574fcede7ad4a27f8805d
author iuc
date Thu, 06 Jun 2019 17:54:09 -0400
parents af814359d244
children a37612abf7f9
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9301937c9037 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 8c751ba49b1465ad147574fcede7ad4a27f8805d
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1 <tool id="featurecounts" name="featureCounts" version="1.6.4" profile="16.04">
0
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2 <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
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3 <requirements>
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4 <requirement type="package" version="1.6.4">subread</requirement>
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5 <requirement type="package" version="1.9">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
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12 ## Export fc path for its built-in annotation
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14 export FC_PATH=\$(command -v featureCounts | sed 's@/bin/featureCounts$@@') &&
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0
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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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18
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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
0
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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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37 $extended_parameters.contribute_to_multiple_features
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38 $extended_parameters.multimapping_enabled.multimapping_counts
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39
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40 #if str($extended_parameters.multimapping_enabled.multimapping_counts) == " -M":
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41 $extended_parameters.multimapping_enabled.fraction
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42 #end if
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43
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44 $extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads
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45 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J":
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46 #if $extended_parameters.exon_exon_junction_read_counting_enabled.genome:
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47 -G '$extended_parameters.exon_exon_junction_read_counting_enabled.genome'
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48 #end if
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49 #end if
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51 $extended_parameters.long_reads
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52
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53 $extended_parameters.by_read_group
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54
0
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55 -Q $extended_parameters.mapping_quality
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56 $extended_parameters.largest_overlap
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57 --minOverlap $extended_parameters.min_overlap
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58 --fracOverlap $extended_parameters.frac_overlap
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59 --fracOverlapFeature $extended_parameters.frac_overlap_feature
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60 $extended_parameters.read_reduction
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61 $extended_parameters.primary
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62 $extended_parameters.ignore_dup
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63 #if $extended_parameters.R:
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64 $extended_parameters.R
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65 #end if
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66 #if str($extended_parameters.read_extension_5p) != "0":
0
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67 --readExtension5 $extended_parameters.read_extension_5p
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68 #end if
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69
10
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70 #if str($extended_parameters.read_extension_3p) != "0":
0
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71 --readExtension3 $extended_parameters.read_extension_3p
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72 #end if
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74 $pe_parameters.fragment_counting_enabled.fragment_counting
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75 #if str($pe_parameters.fragment_counting_enabled.fragment_counting) == " -p":
0
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76 $pe_parameters.fragment_counting_enabled.check_distance_enabled.check_distance
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77 #if str($pe_parameters.fragment_counting_enabled.check_distance_enabled.check_distance) == " -P":
0
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78 -d $pe_parameters.fragment_counting_enabled.check_distance_enabled.minimum_fragment_length
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79 -D $pe_parameters.fragment_counting_enabled.check_distance_enabled.maximum_fragment_length
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80 #end if
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81 #end if
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82
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83 $pe_parameters.only_both_ends
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84 $pe_parameters.exclude_chimerics
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85
6
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86 '${alignment}'
0
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87
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88 ## Remove comment and add sample name to header
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89 && grep -v "^#" "output"
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90 | sed -e 's|${alignment}|${alignment.element_identifier}|g'
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91 > body.txt
0
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92 ## Set the right columns for the tabular formats
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93 #if $format.value == "tabdel_medium":
0
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94 && cut -f 1,7 body.txt > expression_matrix.txt
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95
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96 ## Paste doesn't allow a non ordered list of columns: -f 1,7,8,6 will only return columns 1,7 and 8
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97 ## Thus the gene length column (last column) has to be added separately
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98 && cut -f 6 body.txt > gene_lengths.txt
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99 && paste expression_matrix.txt gene_lengths.txt > expression_matrix.txt.bak
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100 && mv -f expression_matrix.txt.bak '${output_medium}'
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101 #elif $format.value == "tabdel_short":
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102 && cut -f 1,7 body.txt > '${output_short}'
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103 #else:
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104 && cp body.txt '${output_full}'
0
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105 #end if
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106
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107 #if str($include_feature_length_file) == "true":
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108 && cut -f 1,6 body.txt > '${output_feature_lengths}'
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109 #end if
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110
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111 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J":
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112 && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.jcounts' > '${output_jcounts}'
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113 #end if
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114
17
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115 #if $extended_parameters.R:
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116 && samtools sort -o '$output_bam' -@ \${GALAXY_SLOTS:-2} *.featureCounts.bam
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117 #end if
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118 && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.summary' > '${output_summary}'
0
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119 ]]></command>
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120 <inputs>
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121 <param name="alignment"
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122 type="data"
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123 multiple="false"
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124 format="bam,sam"
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125 label="Alignment file"
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126 help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files must be in the same format. Unless you are using a Gene annotation file from the History, these files must have the database/genome attribute already specified e.g. hg38, not the default: ?" >
11
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127 </param>
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128
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129 <param name="strand_specificity"
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130 type="select"
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131 label="Specify strand information"
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132 argument="-s"
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133 help="Indicate if the data is stranded and if strand-specific read counting should be performed. Strand setting must be the same as the strand settings used to produce the mapped BAM input(s)">
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134 <option value="0" selected="true">Unstranded</option>
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135 <option value="1">Stranded (Forward)</option>
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136 <option value="2">Stranded (Reverse)</option>
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137 </param>
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138
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139 <conditional name="anno">
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140 <param name="anno_select" type="select" label="Gene annotation file">
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141 <option value="builtin">featureCounts built-in</option>
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142 <option value="cached" selected="True">locally cached</option>
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143 <option value="history">in your history</option>
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144 </param>
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145 <when value="builtin">
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146 <param name="bgenome" type="select" label="Select built-in genome" help="Built-in gene annotations for genomes hg38, hg19, mm10 and mm9 are included in featureCounts">
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147 <options from_data_table="featurecounts_anno">
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148 <filter type="data_meta" key="dbkey" ref="alignment" column="0"/>
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149 </options>
3
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150 </param>
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151 </when>
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152 <when value="cached">
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153 <param name="reference_gene_sets_builtin" type="select" label="Using locally cached annotation" help="If the annotation file you require is not listed here, please contact the Galaxy administrator">
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154 <options from_data_table="gene_sets">
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155 <filter type="data_meta" key="dbkey" ref="alignment" column="0"/>
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156 </options>
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157 <validator type="no_options" message="An annotation file is not available for the build associated with the selected input file"/>
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158 </param>
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159 </when>
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160 <when value="history">
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161 <param name="reference_gene_sets"
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162 format="gff,gtf,gff3"
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163 type="data"
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164 label="Gene annotation file"
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165 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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166 </param>
3
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167 </when>
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168 </conditional>
8
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169
0
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170 <param name="format"
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171 type="select"
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172 label="Output format"
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173 help="The output format will be tabular, select the preferred columns here">
13
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174 <option value="tabdel_short">Gene-ID "\t" read-count (MultiQC/DESeq2/edgeR/limma-voom compatible)</option>
0
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175 <option value="tabdel_medium">Gene-ID "\t" read-count "\t" gene-length</option>
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176 <option value="tabdel_full">featureCounts 1.4.0+ default (includes regions provided by the GTF file)</option>
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177 </param>
8
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178
0
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179 <param name="include_feature_length_file"
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180 type="boolean"
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diff changeset
181 truevalue="true"
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182 falsevalue="false"
2
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183 checked="false"
0
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184 label="Create gene-length file"
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185 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
186
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diff changeset
187
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188 <section name="pe_parameters" title="Options for paired-end reads">
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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189 <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
190
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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191 <param name="fragment_counting"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
192 type="select"
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diff changeset
193 argument="-p"
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diff changeset
194 checked="true"
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195 label="Count fragments instead of reads"
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196 help="If specified, fragments (or templates) will be counted instead of reads.">
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197 <option value="" selected="true">Disabled; all reads/mates will be counted individually</option>
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198 <option value=" -p">Enabled; fragments (or templates) will be counted instead of reads</option>
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diff changeset
199 </param>
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diff changeset
200
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201 <when value=" -p">
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diff changeset
202 <conditional name="check_distance_enabled">
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
203 <param name="check_distance"
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diff changeset
204 type="boolean"
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diff changeset
205 truevalue=" -P"
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diff changeset
206 falsevalue=""
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diff changeset
207 argument="-P"
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208 label="Check paired-end distance"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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209 help="If specified, paired-end distance will be checked when assigning fragments to meta-features or features. This option is only applicable when -p (Count fragments instead of reads) is specified. The distance thresholds should be specified using -d and -D (minimum and maximum fragment/template length) options." />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
210 <when value=" -P">
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diff changeset
211 <param name="minimum_fragment_length"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
212 type="integer"
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diff changeset
213 value="50"
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diff changeset
214 argument="-d"
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diff changeset
215 label="Minimum fragment/template length." />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
216 <param name="maximum_fragment_length"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
217 type="integer"
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diff changeset
218 value="600"
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diff changeset
219 argument="-D"
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diff changeset
220 label="Maximum fragment/template length." />
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diff changeset
221 </when>
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diff changeset
222 <when value="" />
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223 </conditional>
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diff changeset
224 </when>
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diff changeset
225 <when value="" />
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226 </conditional>
8
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diff changeset
227
0
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228 <param name="only_both_ends"
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229 type="boolean"
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diff changeset
230 truevalue=" -B"
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diff changeset
231 falsevalue=""
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diff changeset
232 argument="-B"
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233 label="Only allow fragments with both reads aligned"
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234 help="If specified, only fragments that have both ends successfully aligned will be considered for summarization. This option is only applicable for paired-end reads." />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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235
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236 <param name="exclude_chimerics"
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237 type="boolean"
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238 truevalue=" -C"
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diff changeset
239 falsevalue=""
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240 argument="-C"
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diff changeset
241 checked="true"
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242 label="Exclude chimeric fragments"
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243 help="If specified, the chimeric fragments (those fragments that have their two ends aligned to different chromosomes) will NOT be included for summarization. This option is only applicable for paired-end read data." />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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244 </section>
8
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245
0
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246 <section name="extended_parameters" title="Advanced options">
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247 <param name="gff_feature_type"
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diff changeset
248 type="text"
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249 value="exon"
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diff changeset
250 argument="-t"
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251 label="GFF feature type filter"
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252 help="Specify the feature type. Only rows which have the matched matched feature type in the provided GTF annotation file will be included for read counting. `exon' by default." />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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253
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254 <param name="gff_feature_attribute"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
255 type="text"
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256 value="gene_id"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
257 argument="-g"
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258 label="GFF gene identifier"
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259 help="Specify the attribute type used to group features (eg. exons) into meta-features (eg. genes), when GTF annotation is provided. `gene_id' by default. This attribute type is usually the gene identifier. This argument is useful for the meta-feature level summarization." />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
260
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261 <param name="summarization_level"
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262 type="boolean"
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263 truevalue=" -f"
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264 falsevalue=""
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265 argument="-f"
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266 label="On feature level"
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267 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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268
11
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diff changeset
269 <param name="contribute_to_multiple_features"
0
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270 type="boolean"
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271 truevalue=" -O"
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diff changeset
272 falsevalue=""
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273 argument="-O"
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274 label="Allow read to contribute to multiple features"
3
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275 help="If specified, reads (or fragments if -p is specified) will be allowed to be assigned to more than one matched meta-feature (or matched feature if -f is specified)" />
0
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276
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diff changeset
277 <conditional name="multimapping_enabled">
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278 <param name="multimapping_counts"
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279 type="select"
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diff changeset
280 argument="-M"
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281 label="Count multi-mapping reads/fragments"
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282 help="If specified, multi-mapping reads/fragments will be counted (ie. a multi-mapping read will be counted up to N times if it has N reported mapping locations). The program uses the `NH' tag to find multi-mapping reads.">
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283 <option value="" selected="true">Disabled; multi-mapping reads are excluded (default)</option>
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284 <option value=" -M">Enabled; multi-mapping reads are included</option>
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diff changeset
285 </param>
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diff changeset
286 <when value=" -M">
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diff changeset
287 <param name="fraction"
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diff changeset
288 type="boolean"
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diff changeset
289 truevalue="--fraction"
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diff changeset
290 falsevalue=""
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diff changeset
291 argument="--fraction"
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292 label="Assign fractions to multimapping reads"
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293 help="If specified, a fractional count 1/n will be generated for each multi-mapping read, where n is the number of alignments (indica- ted by 'NH' tag) reported for the read. This option must be used together with the '-M' option." />
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diff changeset
294 </when>
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diff changeset
295 <when value="" />
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diff changeset
296 </conditional>
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diff changeset
297
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298 <param name="mapping_quality"
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diff changeset
299 type="integer"
23
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parents: 22
diff changeset
300 value="0"
0
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parents:
diff changeset
301 argument="-Q"
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302 label="Minimum mapping quality per read"
23
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parents: 22
diff changeset
303 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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304
6
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parents: 4
diff changeset
305 <conditional name="exon_exon_junction_read_counting_enabled">
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306 <param name="count_exon_exon_junction_reads" argument="-J" type="boolean" truevalue="-J" falsevalue=""
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307 label="Exon-exon junctions"
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diff changeset
308 help="If specified, reads supporting each exon-exon junction will be counted" />
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diff changeset
309 <when value="-J">
7
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310 <param name="genome" argument="-G" type="data" format="fasta" optional="true"
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311 label="Reference sequence file"
6
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312 help="The FASTA-format file that contains the reference sequences used in read mapping can be used to improve read counting for junctions" />
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
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313 </when>
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diff changeset
314 <when value="" />
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diff changeset
315 </conditional>
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diff changeset
316
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317 <param name="long_reads" argument="-L" type="boolean" truevalue="-L" falsevalue=""
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318 label="Long reads"
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319 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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320
10
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321 <param name="by_read_group" argument="--byReadGroup" type="boolean" truevalue="--byReadGroup" falsevalue=""
8
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322 label="Count reads by read group"
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323 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
324
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325
0
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326 <param name="largest_overlap"
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327 type="boolean"
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328 truevalue=" --largestOverlap"
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329 falsevalue=""
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330 argument="--largestOverlap"
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331 label="Largest overlap"
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332 help="If specified, reads (or fragments) will be assigned to the target that has the largest number of overlapping bases" />
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diff changeset
333
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334 <param name="min_overlap"
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diff changeset
335 type="integer"
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336 value="1"
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337 argument="--minOverlap"
8
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338 label="Minimum bases of overlap"
0
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339 help="Specify the minimum required number of overlapping bases between a read (or a fragment) and a feature. 1 by default. If a negative value is provided, the read will be extended from both ends." />
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340
10
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341 <param name="frac_overlap"
8
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diff changeset
342 type="integer"
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343 value="0"
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344 min="0"
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diff changeset
345 max="1"
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346 argument="--fracOverlap"
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347 label="Minimum fraction (of read) overlapping a feature"
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348 help="Specify the minimum required fraction of overlapping bases between a read (or a fragment) and a feature. Value should be within range [0,1]. 0 by default. Number of overlapping bases is counted from both reads if paired end. Both this option and '--minOverlap' need to be satisfied for read assignment." />
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349
10
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350 <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
351 type="integer"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
352 value="0"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
353 min="0"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
354 max="1"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
355 argument="--fracOverlapFeature"
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
356 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
357 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
358
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
359 <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
360 type="integer"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
361 value="0"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
362 argument="--readExtension5"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
363 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
364 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
365
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
366 <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
367 type="integer"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
368 value="0"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
369 argument="--readExtension3"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
370 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
371 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
372
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
373 <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
374 type="select"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
375 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
376 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
377 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
378 <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
379 <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
380 <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
381 </param>
8
2a8bb8223a45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
iuc
parents: 7
diff changeset
382
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
383 <param name="primary"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
384 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
385 truevalue=" --primary"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
386 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
387 argument="--primary"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
388 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
389 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
390
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
391 <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
392 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
393 truevalue=" --ignoreDup"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
394 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
395 argument="--ignoreDup"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
396 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
397 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
398
17
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
399 <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
400 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
401 falsevalue=""
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
402 argument="-R"
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
403 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
404 help="" />
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
405
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
406 <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
407 type="boolean"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
408 truevalue=" --countSplitAlignmentsOnly"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
409 falsevalue=""
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
410 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
411 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
412 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
413 </section>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
414 </inputs>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
415 <outputs>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
416 <data format="tabular"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
417 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
418 label="${tool.name} on ${on_string}: Counts (with length)">
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
419 <filter>format == "tabdel_medium"</filter>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
420 <actions>
9
e6a2a912677a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4fb528145289ad4db04e4589c02e9ddaa1194138
iuc
parents: 8
diff changeset
421 <action name="column_names" type="metadata" default="Geneid,${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
422 </actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
423 </data>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
424
17
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
425 <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
426 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
427 label="${tool.name} on ${on_string}: Alignment file">
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
428 <filter>extended_parameters['R']</filter>
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
429 </data>
8ce1e2c7ee72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
430
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
431 <data format="tabular"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
432 name="output_short"
20
1759d845181e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5
iuc
parents: 19
diff changeset
433 label="${tool.name} on ${on_string}: Counts">
13
386220cf6877 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4
iuc
parents: 12
diff changeset
434 <filter>format == "tabdel_short"</filter>
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
435 <actions>
9
e6a2a912677a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4fb528145289ad4db04e4589c02e9ddaa1194138
iuc
parents: 8
diff changeset
436 <action name="column_names" type="metadata" default="Geneid,${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
437 </actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
438 </data>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
439
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iuc
parents:
diff changeset
440 <data format="tabular"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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441 name="output_full"
20
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parents: 19
diff changeset
442 label="${tool.name} on ${on_string}: Counts (with location)">
0
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iuc
parents:
diff changeset
443 <filter>format == "tabdel_full"</filter>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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444 <actions>
9
e6a2a912677a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4fb528145289ad4db04e4589c02e9ddaa1194138
iuc
parents: 8
diff changeset
445 <action name="column_names" type="metadata" default="Geneid,Chr,Start,End,Strand,Length,${alignment.element_identifier}" />
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
446 </actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
447 </data>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
448
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
449 <data format="tabular"
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
450 name="output_summary"
20
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iuc
parents: 19
diff changeset
451 label="${tool.name} on ${on_string}: Summary">
0
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iuc
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diff changeset
452 <actions>
9
e6a2a912677a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4fb528145289ad4db04e4589c02e9ddaa1194138
iuc
parents: 8
diff changeset
453 <action name="column_names" type="metadata" default="Status,${alignment.element_identifier}" />
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
454 </actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
455 </data>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
456
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
457 <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
458 name="output_feature_lengths"
20
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iuc
parents: 19
diff changeset
459 label="${tool.name} on ${on_string}: Feature lengths">
6
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents: 4
diff changeset
460 <filter>include_feature_length_file</filter>
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
461 <actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
462 <action name="column_names" type="metadata" default="Feature,Length" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
463 </actions>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
464 </data>
6
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parents: 4
diff changeset
465
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents: 4
diff changeset
466 <data name="output_jcounts" format="tabular"
20
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parents: 19
diff changeset
467 label="${tool.name} on ${on_string}: Junction counts">
7
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iuc
parents: 6
diff changeset
468 <filter>extended_parameters['exon_exon_junction_read_counting_enabled']['count_exon_exon_junction_reads']</filter>
6
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents: 4
diff changeset
469 <actions>
10
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iuc
parents: 9
diff changeset
470 <action name="column_names" type="metadata"
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
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diff changeset
471 default="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,${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
472 </actions>
9d60a36b5c6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents: 4
diff changeset
473 </data>
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
474 </outputs>
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
475 <tests>
7
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iuc
parents: 6
diff changeset
476 <test expect_num_outputs="3">
11
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iuc
parents: 10
diff changeset
477 <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
478 <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
479 <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
480 <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
481 <param name="include_feature_length_file" value="true"/>
4
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iuc
parents: 3
diff changeset
482 <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
483 <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
484 </output>
d417fb66494e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents: 3
diff changeset
485 <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
486 <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
487 </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
488 </test>
7
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iuc
parents: 6
diff changeset
489 <test expect_num_outputs="3">
11
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iuc
parents: 10
diff changeset
490 <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
491 <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
492 <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
493 <param name="format" value="tabdel_full" />
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
494 <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
495 <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
496 <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
497 </output>
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_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
499 <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
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_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
502 <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
503 </output>
0
9e7a369eec58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
504 </test>
10
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iuc
parents: 9
diff changeset
505 <test expect_num_outputs="4">
11
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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" />
10
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents: 9
diff changeset
509 <param name="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
510 <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
511 <param name="count_exon_exon_junction_reads" value="-J"/>
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iuc
parents: 12
diff changeset
512 <output name="output_short" file="output_1_short.tab">
10
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents: 9
diff changeset
513 <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
514 </output>
13
386220cf6877 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4
iuc
parents: 12
diff changeset
515 <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
516 <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
517 </output>
13
386220cf6877 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2bd06c2b43c295fb4cf172c4f156fed5475855a4
iuc
parents: 12
diff changeset
518 <output name="output_jcounts" file="output_1_jcounts.tab">
10
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents: 9
diff changeset
519 <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
520 </output>
46cccc52be5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents: 9
diff changeset
521 </test>
11
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iuc
parents: 10
diff changeset
522 <!-- 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
523 <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
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524 <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" dbkey="hg19" />
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525 <param name="anno_select" value="builtin"/>
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526 <param name="format" value="tabdel_short" />
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527 <section name="extended_parameters">
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528 <param name="R" value="true" />
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529 </section>
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530 <output name="output_short" file="output_builtin_hg19.tab">
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531 <metadata name="column_names" value="Geneid,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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532 </output>
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533 <output name="output_summary" file="output_summary_builtin_hg19.tab"/>
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534 <output name="output_bam" file="output.bam" ftype="bam"/>
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535 </test>
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536 <!-- Ensure cached GTFs work -->
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537 <test expect_num_outputs="3">
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538 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38" />
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539 <param name="anno_select" value="cached"/>
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540 <param name="format" value="tabdel_medium" />
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541 <param name="include_feature_length_file" value="true"/>
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542 <output name="output_medium" file="output_1_medium.tab">
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543 <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/>
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544 </output>
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545 <output name="output_summary" file="output_1_summary.tab">
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546 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
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547 </output>
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548 </test>
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549 <!-- Ensure BAM output works -->
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550 <test>
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551 <param name="alignment" value="subset.sorted.bam" ftype="bam" />
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552 <param name="anno_select" value="history" />
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553 <param name="reference_gene_sets" value="small.gtf" ftype="gtf" />
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554 <section name="extended_parameters" >
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555 <param name="R" value="true" />
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556 </section>
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557 <output name="output_bam" value="subset.sorted.featurecounts.bam" compare="sim_size"/>
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558 </test>
0
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559 </tests>
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560
0
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561 <help><![CDATA[
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562 featureCounts
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563 #############
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564
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565 Overview
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566 --------
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567 FeatureCounts is a light-weight read counting program written entirely in the C programming language. It can be used to count both gDNA-seq and RNA-seq reads for genomic features in in SAM/BAM files. FeatureCounts is part of the Subread_ package.
0
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568
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569 Input formats
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570 -------------
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571 Alignments should be provided in either:
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572
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573 - SAM format, http://samtools.sourceforge.net/samtools.shtml#5
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574 - BAM format
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575
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576 Annotations for gene regions should be provided in the GFF/GTF format:
0
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577
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578 - http://genome.ucsc.edu/FAQ/FAQformat.html#format3
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579 - http://www.ensembl.org/info/website/upload/gff.html
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580
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581 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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582
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583 Example - **Built-in annotation format**:
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584
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585 ====== ==== ======= ======= ======
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586 GeneID Chr Start End Strand
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587 ====== ==== ======= ======= ======
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588 497097 chr1 3204563 3207049 -
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589 497097 chr1 3411783 3411982 -
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590 497097 chr1 3660633 3661579 -
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591 ====== ==== ======= ======= ======
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592
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593 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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594
0
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595 Output format
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596 -------------
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597 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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598
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599 .. _Subread: http://subread.sourceforge.net/
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600 .. _`Subread User's Guide`: http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf
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601 .. _`Subread package`: https://sourceforge.net/projects/subread/files/
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602 ]]></help>
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603 <citations>
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604 <citation type="doi">10.1093/bioinformatics/btt656</citation>
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605 </citations>
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606 </tool>