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annotate featurecounts.xml @ 36:39863c075dca draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit f27749b7d724cde23f3cdfe8c7275fb9222bda06
author iuc
date Sun, 22 Dec 2024 10:54:51 +0000
parents 519ae9e6fdb9
children 8620533d294b
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1 <tool id="featurecounts" name="featureCounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">
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2 <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">2.0.8</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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7 <macro name="conditional_gff_opions">
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8 <param name="gff_feature_type" type="text" value="exon" argument="-t" label="GFF feature type filter" 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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9 <param name="gff_feature_attribute" type="text" value="gene_id" argument="-g" label="GFF gene identifier" 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. Ex: if the 9th column is 'gene_id &quot;ENSG00000223972&quot;; gene_name &quot;DDX11L1&quot; gene_source &quot;havana&quot;' (GTF) or 'gene_id=ENSG00000223972; gene_name=DDX11L1; gene_source=havana' (GFF), the available attributes for this feature are 'gene_id', 'gene_name' and 'gene_source'."/>
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10 <param name="summarization_level" type="boolean" truevalue=" -f" falsevalue="" argument="-f" label="On feature level" 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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11 </macro>
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12 </macros>
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13 <xrefs>
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14 <xref type="bio.tools">featurecounts</xref>
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15 </xrefs>
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16 <requirements>
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17 <requirement type="package" version="@TOOL_VERSION@">subread</requirement>
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18 <requirement type="package" version="1.21">samtools</requirement>
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19 </requirements>
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21 <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command>
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22 <command detect_errors="exit_code"><![CDATA[
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23 ## Export fc path for its built-in annotation
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24 export FC_PATH=\$(command -v featureCounts | sed 's@/bin/featureCounts$@@') &&
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26 ## Check whether all alignments are from the same type (bam || sam)
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27 featureCounts
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29 #if $anno.anno_select=="history":
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30 -a '$anno.reference_gene_sets'
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31 -F "GTF"
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32 #elif $anno.anno_select=="cached":
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33 -a '$anno.reference_gene_sets_cached.fields.path'
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34 -F "GTF"
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35 #elif $anno.anno_select=="builtin":
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36 -a \${FC_PATH}/annotation/${anno.bgenome}_RefSeq_exon.txt
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37 -F "SAF"
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38 #end if
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40 -o "output"
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41 -T \${GALAXY_SLOTS:-2}
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43 -s $strand_specificity
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45 -Q $read_filtering_parameters.mapping_quality
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46 $read_filtering_parameters.splitonly
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47 $read_filtering_parameters.primary
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48 $read_filtering_parameters.ignore_dup
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50 #if $anno.anno_select!="builtin":
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51 -t '$anno.gff_feature_type'
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52 -g '$anno.gff_feature_attribute'
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53 $anno.summarization_level
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54 #end if
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56 $extended_parameters.multifeatures.multifeat
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57 #if $extended_parameters.multifeatures.multifeat != "":
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58 $extended_parameters.multifeatures.fraction
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59 #end if
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61 $extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads
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62 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J":
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63 #if $extended_parameters.exon_exon_junction_read_counting_enabled.genome:
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64 -G '$extended_parameters.exon_exon_junction_read_counting_enabled.genome'
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65 #end if
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66 #end if
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68 $extended_parameters.long_reads
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69
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70 $extended_parameters.by_read_group
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71
0
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72 $extended_parameters.largest_overlap
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73 --minOverlap $extended_parameters.min_overlap
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74 --fracOverlap $extended_parameters.frac_overlap
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75 --fracOverlapFeature $extended_parameters.frac_overlap_feature
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76 $extended_parameters.read_reduction
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77 #if $extended_parameters.R:
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78 $extended_parameters.R
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79 #end if
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80 #if str($extended_parameters.read_extension_5p) != "0":
0
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81 --readExtension5 $extended_parameters.read_extension_5p
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82 #end if
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83
10
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84 #if str($extended_parameters.read_extension_3p) != "0":
0
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85 --readExtension3 $extended_parameters.read_extension_3p
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86 #end if
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87
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88 #if str($pe_parameters.paired_end_status) != "single_end":
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89 -p
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90 $pe_parameters.only_both_ends
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91 $pe_parameters.exclude_chimerics
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92 #if str($pe_parameters.paired_end_status) == "PE_fragments":
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93 --countReadPairs
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94 #if $pe_parameters.check_distance_enabled.checkFragLength == "true":
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95 --checkFragLength
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96 --minFragLength $pe_parameters.check_distance_enabled.minimum_fragment_length
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97 --maxFragLength $pe_parameters.check_distance_enabled.maximum_fragment_length
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98 #end if
0
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99 #end if
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100 #end if
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101
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102 '${alignment}'
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103
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104 ## Remove comment and add sample name to header
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105 && grep -v "^#" "output"
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106 | sed -e 's|${alignment}|${alignment.element_identifier}|g'
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107 > body.txt
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108 ## Set the right columns for the tabular formats
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109 #if $format.value == "tabdel_medium":
0
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110 && cut -f 1,7 body.txt > expression_matrix.txt
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111
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112 ## Paste doesn't allow a non ordered list of columns: -f 1,7,8,6 will only return columns 1,7 and 8
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113 ## Thus the gene length column (last column) has to be added separately
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114 && cut -f 6 body.txt > gene_lengths.txt
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115 && paste expression_matrix.txt gene_lengths.txt > expression_matrix.txt.bak
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116 && mv -f expression_matrix.txt.bak '${output_medium}'
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117 #elif $format.value == "tabdel_short":
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118 && cut -f 1,7 body.txt > '${output_short}'
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119 #else:
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120 && cp body.txt '${output_full}'
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121 #end if
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122
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123 #if str($include_feature_length_file) == "true":
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124 && cut -f 1,6 body.txt > '${output_feature_lengths}'
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125 #end if
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126
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127 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J":
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128 && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.jcounts' > '${output_jcounts}'
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129 #end if
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130
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131 #if $extended_parameters.R:
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132 && samtools sort --no-PG -o '$output_bam' -@ \${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" *.featureCounts.bam
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133 #end if
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134 && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.summary' > '${output_summary}'
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135 ]]></command>
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136 <inputs>
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137 <param name="alignment"
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138 type="data"
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139 multiple="false"
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140 format="unsorted.bam,bam,sam"
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141 label="Alignment file"
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142 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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143 </param>
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144
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145 <param name="strand_specificity"
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146 type="select"
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147 label="Specify strand information"
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148 argument="-s"
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149 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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150 <option value="0" selected="true">Unstranded</option>
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151 <option value="1">Stranded (Forward)</option>
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152 <option value="2">Stranded (Reverse)</option>
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153 </param>
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154
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155 <conditional name="anno">
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156 <param name="anno_select" type="select" label="Gene annotation file">
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157 <option value="builtin">featureCounts built-in</option>
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158 <option value="cached" selected="True">locally cached</option>
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159 <option value="history">A GFF/GTF file in your history</option>
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160 </param>
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161 <when value="builtin">
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162 <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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163 <options from_data_table="featurecounts_anno">
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164 <filter type="data_meta" key="dbkey" ref="alignment" column="dbkey"/>
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165 <filter type="sort_by" column="1"/>
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166 </options>
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167 <validator type="no_options" message="An built-in annotation file is not available for the genome build associated with the selected input file"/>
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168 </param>
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169 </when>
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170 <when value="cached">
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171 <param name="reference_gene_sets_cached" 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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172 <options from_data_table="gene_sets">
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173 <filter type="data_meta" key="dbkey" ref="alignment" column="dbkey"/>
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174 <filter type="sort_by" column="2"/>
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175 </options>
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176 <validator type="no_options" message="A cached annotation file is not available for the genome build associated with the selected input file"/>
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177 </param>
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178 <expand macro="conditional_gff_opions"/>
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179 </when>
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180 <when value="history">
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181 <param name="reference_gene_sets"
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182 format="gff,gtf,gff3"
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183 type="data"
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184 label="Gene annotation file"
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185 help="The program assumes that the provided annotation file is in GFF/GTF format. Make sure that the gene annotation file corresponds to the same reference genome as used for the alignment.">
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186 </param>
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187 <expand macro="conditional_gff_opions"/>
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188 </when>
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189 </conditional>
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190
0
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191 <param name="format"
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192 type="select"
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193 label="Output format"
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194 help="The output format will be tabular, select the preferred columns here">
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195 <option value="tabdel_short">Gene-ID "\t" read-count (MultiQC/DESeq2/edgeR/limma-voom compatible)</option>
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196 <option value="tabdel_medium">Gene-ID "\t" read-count "\t" gene-length</option>
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197 <option value="tabdel_full">featureCounts 1.4.0+ default (includes regions provided by the GTF file)</option>
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198 </param>
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199
0
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200 <param name="include_feature_length_file"
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201 type="boolean"
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202 truevalue="true"
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203 falsevalue="false"
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204 checked="false"
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205 label="Create gene-length file"
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206 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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207
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208 <conditional name="pe_parameters">
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209 <param name="paired_end_status" type="select" label="Does the input have read pairs?" help="Were the bam files generated by aligning the output of a paired-end sequencing experiment? If yes, the tool can consider 2 reads = 1 read pair as 1 entity to count. Alternatively, you can opt to consider treating the read pairs as 2 individual reads to count seperately.">
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210 <option value="single_end" selected="True">No, single-end.</option>
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211 <option value="PE_individual">Yes, paired-end but still count them as if individual reads.</option>
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212 <option value="PE_fragments">Yes, paired-end and count them as 1 single fragment.</option>
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213 </param>
0
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214
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215 <when value="single_end"/>
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216 <when value="PE_individual">
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217 <param name="only_both_ends"
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218 type="boolean"
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219 truevalue=" -B"
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220 falsevalue=""
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221 argument="-B"
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222 label="Only allow fragments with both reads aligned"
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223 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."/>
0
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224
32
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225 <param name="exclude_chimerics"
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226 type="boolean"
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227 truevalue=" -C"
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228 falsevalue=""
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229 argument="-C"
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230 checked="true"
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231 label="Exclude chimeric fragments"
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232 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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233 </when>
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234 <when value="PE_fragments">
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235 <conditional name="check_distance_enabled">
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236 <param argument="--checkFragLength" type="select" label="Check paired-end distance" 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 can be specified using -d and -D (minimum and maximum fragment/template length) options.">
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237 <option value="true">Check the distance between paired reads</option>
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238 <option value="false" selected="True">Do not check</option>
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239 </param>
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240 <when value="true">
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241 <param name="minimum_fragment_length"
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242 type="integer"
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243 value="50"
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244 min="0"
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245 argument="-d"
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246 label="Minimum fragment/template length."/>
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247 <param name="maximum_fragment_length"
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248 type="integer"
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249 value="600"
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250 min="1"
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251 argument="-D"
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252 label="Maximum fragment/template length."/>
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253 </when>
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254 <when value="false"/>
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255 </conditional>
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256
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257 <param name="only_both_ends"
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258 type="boolean"
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259 truevalue=" -B"
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260 falsevalue=""
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261 argument="-B"
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262 label="Only allow fragments with both reads aligned"
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263 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."/>
8
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264
32
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265 <param name="exclude_chimerics"
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266 type="boolean"
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267 truevalue=" -C"
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268 falsevalue=""
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269 argument="-C"
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270 checked="true"
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271 label="Exclude chimeric fragments"
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272 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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273 </when>
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274 </conditional>
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275
31
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276 <section name="read_filtering_parameters" title="Read filtering options">
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277 <param name="mapping_quality"
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278 type="integer"
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279 value="0"
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280 min="0"
31
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281 argument="-Q"
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282 label="Minimum mapping quality per read"
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283 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."/>
31
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284 <param name="splitonly" type="select" display="radio" label="Filter split alignments" help="Split alignments are alignments with CIGAR string containing 'N', e.g. exon spanning reads in RNASeq.">
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285 <option value="">No filtering: count split and non-split alignments</option>
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286 <option value="--splitOnly">Count only split alignments (--splitOnly)</option>
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287 <option value="--nonSplitOnly">Count only non-split alignments (--nonSplitOnly)</option>
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288 </param>
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289 <param type="boolean"
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290 truevalue=" --primary"
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291 falsevalue=""
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292 argument="--primary"
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293 label="Only count primary alignments"
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294 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)."/>
31
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295 <param name="ignore_dup"
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296 type="boolean"
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297 truevalue=" --ignoreDup"
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298 falsevalue=""
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299 argument="--ignoreDup"
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300 label="Ignore reads marked as duplicate"
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301 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."/>
31
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302 </section>
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303
0
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304 <section name="extended_parameters" title="Advanced options">
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305 <conditional name = "multifeatures">
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306 <param name="multifeat" type="select" label="Allow reads to map to multiple features" help="Setting -O, -M and --fraction">
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307 <option value="" selected="true">Disabled: reads that align to multiple features or overlapping features are excluded</option>
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308 <option value="-M">Enabled: multi-mapping reads are included (-M)</option>
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309 <option value="-O">Enabled: multi-overlapping features are included (-O)</option>
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310 <option value="-O -M">Enabled: both multi-mapping and multi-overlapping features are included (-M -O)</option>
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311 </param>
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312 <when value=""/>
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313 <when value="-M">
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314 <param type="boolean"
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315 truevalue="--fraction"
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316 falsevalue=""
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317 argument="--fraction"
31
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318 label="Assign fractions to multi-mapping reads"
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319 help="If specified, a fractional count 1/x will be generated for each multi-mapping read, where x is the number of alignments (indicated by 'NH' tag) reported for the read."/>
0
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320 </when>
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321 <when value="-O">
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322 <param type="boolean"
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323 truevalue="--fraction"
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324 falsevalue=""
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325 argument="--fraction"
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326 label="Assign fractions to multi-overlapping features"
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327 help="If specified, a fractional count 1/y will be generated for each multi-overlapping feature, where y is the number of features overlapping with the read."/>
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328 </when>
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329 <when value="-O -M">
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330 <param type="boolean"
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331 truevalue="--fraction"
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332 falsevalue=""
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333 argument="--fraction"
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334 label="Assign fractions to both multi-mapping reads and multi-overlapping features"
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335 help="If specified, a fractional count 1/(x*y) will be generated, where x is the number of alignments (indicated by 'NH' tag) and y the number of overlapping features."/>
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336 </when>
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337 </conditional>
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338
6
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339 <conditional name="exon_exon_junction_read_counting_enabled">
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340 <param name="count_exon_exon_junction_reads" type="select" argument="-J" label="Exon-exon junctions" help="Junctions are identified from those exon-spanning reads (containing ‘N’ in CIGAR string) in input data. The output result includes names of primary and secondary genes that overlap at least one of the two splice sites of a junction.">
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341 <option value="-J">Count reads supporting each exon-exon junction.</option>
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342 <option value="" selected="True">Do not count</option>
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343 </param>
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344 <when value="-J">
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345 <param name="genome" argument="-G" type="data" format="fasta" optional="true"
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parents: 6
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346 label="Reference sequence file"
32
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diff changeset
347 help="The FASTA-format file that contains the reference sequences used in read mapping can be used to improve read counting for junctions"/>
6
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parents: 4
diff changeset
348 </when>
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diff changeset
349 <when value=""/>
6
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parents: 4
diff changeset
350 </conditional>
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parents: 4
diff changeset
351
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parents: 4
diff changeset
352 <param name="long_reads" argument="-L" type="boolean" truevalue="-L" falsevalue=""
e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
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parents: 4
diff changeset
353 label="Long reads"
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parents: 31
diff changeset
354 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."/>
6
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parents: 4
diff changeset
355
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parents: 9
diff changeset
356 <param name="by_read_group" argument="--byReadGroup" type="boolean" truevalue="--byReadGroup" falsevalue=""
8
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parents: 7
diff changeset
357 label="Count reads by read group"
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diff changeset
358 help="If specified, reads are counted for each read group separately. The 'RG' tag must be present in the input BAM/SAM alignment files."/>
8
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parents: 7
diff changeset
359
0
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
360 <param name="largest_overlap"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
361 type="boolean"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
362 truevalue=" --largestOverlap"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
363 falsevalue=""
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
364 argument="--largestOverlap"
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diff changeset
365 label="Largest overlap"
32
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parents: 31
diff changeset
366 help="If specified, reads (or fragments) will be assigned to the target that has the largest number of overlapping bases"/>
0
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
367
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
368 <param name="min_overlap"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
369 type="integer"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
370 value="1"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
371 argument="--minOverlap"
8
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parents: 7
diff changeset
372 label="Minimum bases of overlap"
32
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parents: 31
diff changeset
373 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."/>
0
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
374
10
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parents: 9
diff changeset
375 <param name="frac_overlap"
8
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iuc
parents: 7
diff changeset
376 type="integer"
bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
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parents: 7
diff changeset
377 value="0"
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parents: 7
diff changeset
378 min="0"
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parents: 7
diff changeset
379 max="1"
bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
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parents: 7
diff changeset
380 argument="--fracOverlap"
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parents: 7
diff changeset
381 label="Minimum fraction (of read) overlapping a feature"
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parents: 31
diff changeset
382 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."/>
8
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parents: 7
diff changeset
383
10
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parents: 9
diff changeset
384 <param name="frac_overlap_feature"
8
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iuc
parents: 7
diff changeset
385 type="integer"
bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
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parents: 7
diff changeset
386 value="0"
bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
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parents: 7
diff changeset
387 min="0"
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parents: 7
diff changeset
388 max="1"
bff059ad4d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41
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parents: 7
diff changeset
389 argument="--fracOverlapFeature"
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parents: 7
diff changeset
390 label="Minimum fraction (of feature) overlapping a read"
32
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parents: 31
diff changeset
391 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."/>
8
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parents: 7
diff changeset
392
0
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
393 <param name="read_extension_5p"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
394 type="integer"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
395 value="0"
32
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parents: 31
diff changeset
396 min="0"
0
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parents:
diff changeset
397 argument="--readExtension5"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
398 label="Read 5' extension"
32
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parents: 31
diff changeset
399 help="Reads are extended upstream by ... bases from their 5' end"/>
0
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
400
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
401 <param name="read_extension_3p"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
402 type="integer"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
403 value="0"
32
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parents: 31
diff changeset
404 min="0"
0
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
405 argument="--readExtension3"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
406 label="Read 3' extension"
32
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parents: 31
diff changeset
407 help="Reads are extended upstream by ... bases from their 3' end"/>
0
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
408
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
409 <param name="read_reduction"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
410 type="select"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
411 label="Reduce read to single position"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
412 argument="--read2pos"
3
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parents: 2
diff changeset
413 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
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
414 <option value="" selected="true">Leave the read as it is</option>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
415 <option value="--read2pos 5">Reduce it to the 5' end</option>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
416 <option value="--read2pos 3">Reduce it to the 3' end</option>
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diff changeset
417 </param>
8
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parents: 7
diff changeset
418
17
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parents: 15
diff changeset
419 <param type="boolean"
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parents: 15
diff changeset
420 truevalue="-R BAM"
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parents: 15
diff changeset
421 falsevalue=""
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parents: 15
diff changeset
422 argument="-R"
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diff changeset
423 label="Annotates the alignment file with 'XS:Z:'-tags to described per read or read-pair the corresponding assigned feature(s)."
32
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diff changeset
424 help=""/>
17
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parents: 15
diff changeset
425
0
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
426 </section>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
427 </inputs>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
428 <outputs>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
429 <data format="tabular"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
430 name="output_medium"
20
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parents: 19
diff changeset
431 label="${tool.name} on ${on_string}: Counts (with length)">
0
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parents:
diff changeset
432 <filter>format == "tabdel_medium"</filter>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
433 <actions>
32
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diff changeset
434 <action name="column_names" type="metadata" default="Geneid,${alignment.element_identifier},Length"/>
0
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
435 </actions>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
436 </data>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
437
17
5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
438 <data format="bam"
5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
439 name="output_bam"
5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
440 label="${tool.name} on ${on_string}: Alignment file">
5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
441 <filter>extended_parameters['R']</filter>
5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
442 </data>
5c20eb47f759 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
iuc
parents: 15
diff changeset
443
0
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
444 <data format="tabular"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
445 name="output_short"
20
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iuc
parents: 19
diff changeset
446 label="${tool.name} on ${on_string}: Counts">
13
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iuc
parents: 12
diff changeset
447 <filter>format == "tabdel_short"</filter>
0
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
448 <actions>
32
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iuc
parents: 31
diff changeset
449 <action name="column_names" type="metadata" default="Geneid,${alignment.element_identifier}"/>
0
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
450 </actions>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
451 </data>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
452
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
453 <data format="tabular"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
454 name="output_full"
20
b4f3420c2a70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5
iuc
parents: 19
diff changeset
455 label="${tool.name} on ${on_string}: Counts (with location)">
0
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
456 <filter>format == "tabdel_full"</filter>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
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diff changeset
457 <actions>
32
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1
iuc
parents: 31
diff changeset
458 <action name="column_names" type="metadata" default="Geneid,Chr,Start,End,Strand,Length,${alignment.element_identifier}"/>
0
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
459 </actions>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
460 </data>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
461
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
462 <data format="tabular"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
463 name="output_summary"
20
b4f3420c2a70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5
iuc
parents: 19
diff changeset
464 label="${tool.name} on ${on_string}: Summary">
0
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
465 <actions>
32
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iuc
parents: 31
diff changeset
466 <action name="column_names" type="metadata" default="Status,${alignment.element_identifier}"/>
0
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
467 </actions>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
468 </data>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
469
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
470 <data format="tabular"
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
471 name="output_feature_lengths"
20
b4f3420c2a70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5
iuc
parents: 19
diff changeset
472 label="${tool.name} on ${on_string}: Feature lengths">
6
e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents: 4
diff changeset
473 <filter>include_feature_length_file</filter>
0
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
474 <actions>
32
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1
iuc
parents: 31
diff changeset
475 <action name="column_names" type="metadata" default="Feature,Length"/>
0
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
476 </actions>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
477 </data>
6
e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents: 4
diff changeset
478
e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents: 4
diff changeset
479 <data name="output_jcounts" format="tabular"
20
b4f3420c2a70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5
iuc
parents: 19
diff changeset
480 label="${tool.name} on ${on_string}: Junction counts">
7
889d2cd8a809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17
iuc
parents: 6
diff changeset
481 <filter>extended_parameters['exon_exon_junction_read_counting_enabled']['count_exon_exon_junction_reads']</filter>
6
e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents: 4
diff changeset
482 <actions>
10
7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents: 9
diff changeset
483 <action name="column_names" type="metadata"
32
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iuc
parents: 31
diff changeset
484 default="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,${alignment.element_identifier}"/>
6
e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents: 4
diff changeset
485 </actions>
e70afb590e50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit ffb40a055701dca74e29e651dd820a6bda3d844b
iuc
parents: 4
diff changeset
486 </data>
0
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
487 </outputs>
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
488 <tests>
7
889d2cd8a809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17
iuc
parents: 6
diff changeset
489 <test expect_num_outputs="3">
34
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iuc
parents: 33
diff changeset
490 <param name="alignment" value="featureCounts_input1.bam" ftype="unsorted.bam" dbkey="hg38"/>
11
d0beb2753aba 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"/>
32
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1
iuc
parents: 31
diff changeset
492 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38"/>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1
iuc
parents: 31
diff changeset
493 <param name="format" value="tabdel_medium"/>
0
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
494 <param name="include_feature_length_file" value="true"/>
4
2451333b004b 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_medium" file="output_1_medium.tab">
2451333b004b 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,featureCounts_input1.bam,Length"/>
2451333b004b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents: 3
diff changeset
497 </output>
2451333b004b 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">
2451333b004b 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"/>
2451333b004b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents: 3
diff changeset
500 </output>
0
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
501 </test>
7
889d2cd8a809 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17
iuc
parents: 6
diff changeset
502 <test expect_num_outputs="3">
34
12b3317716d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit fc2a03ae0ef4d1d0d5f2f05a6ecc0fc4812931e1
iuc
parents: 33
diff changeset
503 <param name="alignment" value="featureCounts_input1.bam" ftype="unsorted.bam" dbkey="hg38"/>
11
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents: 10
diff changeset
504 <param name="anno_select" value="history"/>
32
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1
iuc
parents: 31
diff changeset
505 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38"/>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1
iuc
parents: 31
diff changeset
506 <param name="format" value="tabdel_full"/>
0
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
507 <param name="include_feature_length_file" value="true"/>
4
2451333b004b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents: 3
diff changeset
508 <output name="output_full" file="output_1_full.tab">
2451333b004b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents: 3
diff changeset
509 <metadata name="column_names" value="Geneid,Chr,Start,End,Strand,Length,featureCounts_input1.bam"/>
2451333b004b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents: 3
diff changeset
510 </output>
2451333b004b 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_summary" file="output_1_summary.tab">
2451333b004b 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="Status,featureCounts_input1.bam"/>
2451333b004b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents: 3
diff changeset
513 </output>
2451333b004b 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_feature_lengths" file="output_feature_lengths.tab">
2451333b004b 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="Feature,Length"/>
2451333b004b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 57dfb61ba50ecfbe8f1c624fdbe2d0a3a8deaa04
iuc
parents: 3
diff changeset
516 </output>
0
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
iuc
parents:
diff changeset
517 </test>
10
7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents: 9
diff changeset
518 <test expect_num_outputs="4">
34
12b3317716d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit fc2a03ae0ef4d1d0d5f2f05a6ecc0fc4812931e1
iuc
parents: 33
diff changeset
519 <param name="alignment" value="featureCounts_input1.bam" ftype="unsorted.bam" dbkey="hg38"/>
11
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents: 10
diff changeset
520 <param name="anno_select" value="history"/>
32
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1
iuc
parents: 31
diff changeset
521 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38"/>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1
iuc
parents: 31
diff changeset
522 <param name="format" value="tabdel_short"/>
10
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parents: 9
diff changeset
523 <param name="include_feature_length_file" value="true"/>
7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents: 9
diff changeset
524 <param name="count_exon_exon_junction_reads" value="-J"/>
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iuc
parents: 12
diff changeset
525 <output name="output_short" file="output_1_short.tab">
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iuc
parents: 9
diff changeset
526 <metadata name="column_names" value="Geneid,featureCounts_input1.bam"/>
7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
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diff changeset
527 </output>
13
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iuc
parents: 12
diff changeset
528 <output name="output_summary" file="output_1_summary.tab">
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iuc
parents: 9
diff changeset
529 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
7d1e37c6ef85 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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parents: 12
diff changeset
531 <output name="output_jcounts" file="output_1_jcounts.tab">
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iuc
parents: 9
diff changeset
532 <metadata name="column_names" value="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,featureCounts_input1.bam"/>
7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents: 9
diff changeset
533 </output>
7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
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diff changeset
534 </test>
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parents: 10
diff changeset
535 <!-- Ensure featureCounts built-in annotation works -->
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parents: 15
diff changeset
536 <test expect_num_outputs="3">
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parents: 33
diff changeset
537 <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="unsorted.bam" dbkey="hg19"/>
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diff changeset
538 <param name="anno_select" value="builtin"/>
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parents: 31
diff changeset
539 <param name="format" value="tabdel_short"/>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1
iuc
parents: 31
diff changeset
540 <conditional name="pe_parameters">
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1
iuc
parents: 31
diff changeset
541 <param name="paired_end_status" value="PE_individual"/>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1
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parents: 31
diff changeset
542 </conditional>
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iuc
parents: 15
diff changeset
543 <section name="extended_parameters">
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parents: 31
diff changeset
544 <param name="R" value="true"/>
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parents: 15
diff changeset
545 </section>
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parents: 9
diff changeset
546 <output name="output_short" file="output_builtin_hg19.tab">
7d1e37c6ef85 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"/>
7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents: 9
diff changeset
548 </output>
7d1e37c6ef85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8
iuc
parents: 9
diff changeset
549 <output name="output_summary" file="output_summary_builtin_hg19.tab"/>
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iuc
parents: 15
diff changeset
550 <output name="output_bam" file="output.bam" ftype="bam"/>
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iuc
parents: 9
diff changeset
551 </test>
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iuc
parents: 32
diff changeset
552 <!-- Ensure fragment counting works -->
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc
iuc
parents: 32
diff changeset
553 <test expect_num_outputs="3">
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parents: 33
diff changeset
554 <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="unsorted.bam" dbkey="hg19"/>
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iuc
parents: 32
diff changeset
555 <param name="anno_select" value="builtin"/>
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc
iuc
parents: 32
diff changeset
556 <param name="format" value="tabdel_short"/>
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc
iuc
parents: 32
diff changeset
557 <conditional name="pe_parameters">
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc
iuc
parents: 32
diff changeset
558 <param name="paired_end_status" value="PE_fragments"/>
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc
iuc
parents: 32
diff changeset
559 </conditional>
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc
iuc
parents: 32
diff changeset
560 <section name="extended_parameters">
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc
iuc
parents: 32
diff changeset
561 <param name="R" value="true"/>
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc
iuc
parents: 32
diff changeset
562 </section>
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc
iuc
parents: 32
diff changeset
563 <output name="output_short" file="output_builtin_hg19_fragment.tab">
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc
iuc
parents: 32
diff changeset
564 <metadata name="column_names" value="Geneid,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc
iuc
parents: 32
diff changeset
565 </output>
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc
iuc
parents: 32
diff changeset
566 <output name="output_summary" file="output_summary_builtin_hg19_fragments.tab"/>
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc
iuc
parents: 32
diff changeset
567 <output name="output_bam" file="output_fragments.bam" ftype="bam"/>
dad3302e7b34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc
iuc
parents: 32
diff changeset
568 </test>
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iuc
parents: 10
diff changeset
569 <!-- Ensure cached GTFs work -->
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents: 10
diff changeset
570 <test expect_num_outputs="3">
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parents: 33
diff changeset
571 <param name="alignment" value="featureCounts_input1.bam" ftype="unsorted.bam" dbkey="hg38"/>
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parents: 10
diff changeset
572 <param name="anno_select" value="cached"/>
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parents: 31
diff changeset
573 <param name="format" value="tabdel_medium"/>
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parents: 10
diff changeset
574 <param name="include_feature_length_file" value="true"/>
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents: 10
diff changeset
575 <output name="output_medium" file="output_1_medium.tab">
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents: 10
diff changeset
576 <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/>
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
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parents: 10
diff changeset
577 </output>
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
iuc
parents: 10
diff changeset
578 <output name="output_summary" file="output_1_summary.tab">
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
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parents: 10
diff changeset
579 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
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diff changeset
580 </output>
d0beb2753aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
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parents: 10
diff changeset
581 </test>
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parents: 17
diff changeset
582 <!-- Ensure BAM output works -->
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parents: 33
diff changeset
583 <test expect_num_outputs="3">
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parents: 31
diff changeset
584 <param name="alignment" value="subset.sorted.bam" ftype="bam"/>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1
iuc
parents: 31
diff changeset
585 <param name="anno_select" value="history"/>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1
iuc
parents: 31
diff changeset
586 <param name="reference_gene_sets" value="small.gtf" ftype="gtf"/>
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1
iuc
parents: 31
diff changeset
587 <section name="extended_parameters">
456cc2927264 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2d5d24cbdea47adb6eede757016c717840749fd1
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parents: 31
diff changeset
588 <param name="R" value="true"/>
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diff changeset
589 </section>
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diff changeset
590 <output name="output_bam" value="subset.sorted.featurecounts.bam" compare="sim_size"/>
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parents: 33
diff changeset
591 <output name="output_short" file="subset.sorted.featurecounts_short.tab">
12b3317716d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit fc2a03ae0ef4d1d0d5f2f05a6ecc0fc4812931e1
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parents: 33
diff changeset
592 <metadata name="column_names" value="Geneid,subset.sorted.bam"/>
12b3317716d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit fc2a03ae0ef4d1d0d5f2f05a6ecc0fc4812931e1
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parents: 33
diff changeset
593 </output>
12b3317716d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit fc2a03ae0ef4d1d0d5f2f05a6ecc0fc4812931e1
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parents: 33
diff changeset
594 <output name="output_summary" file="subset.sorted.featurecounts_summary.tab"/>
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parents: 17
diff changeset
595 </test>
0
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diff changeset
596 </tests>
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diff changeset
597
0
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diff changeset
598 <help><![CDATA[
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
599 featureCounts
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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diff changeset
600 #############
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
601
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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parents:
diff changeset
602 Overview
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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603 --------
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diff changeset
604 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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605
8e70555968a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314
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606 Input formats
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607 -------------
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608 Alignments should be provided in either:
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609
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610 - SAM format, http://samtools.sourceforge.net/samtools.shtml#5
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611 - BAM format
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612
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613 Annotations for gene regions should be provided in the GFF/GTF format:
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614
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615 - http://genome.ucsc.edu/FAQ/FAQformat.html#format3
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616 - http://www.ensembl.org/info/website/upload/gff.html
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617
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618 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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619
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620 Example - **Built-in annotation format**:
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621
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622 ====== ==== ======= ======= ======
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623 GeneID Chr Start End Strand
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624 ====== ==== ======= ======= ======
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625 497097 chr1 3204563 3207049 -
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626 497098 chr1 3411783 3411982 -
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627 497099 chr1 3660633 3661579 -
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628 ====== ==== ======= ======= ======
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629
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630 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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631
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632 Output format
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633 -------------
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634 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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635
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636 .. _Subread: http://subread.sourceforge.net/
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637 .. _`Subread User's Guide`: https://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/SubreadUsersGuide.pdf
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638 ]]></help>
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639 <citations>
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640 <citation type="doi">10.1093/bioinformatics/btt656</citation>
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641 </citations>
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642 </tool>
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643