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1 <tool id="subread_featurecounts" name="FeatureCount from subread" version="1.5.0-p1">
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2 <description>Runs FeatureCount from subread</description>
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3 <requirements>
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4 <requirement type="package" version="1.5.0-p1">subread</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1" level="fatal" description="Error code 1 occurred" />
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8 <exit_code range="2:255" level="fatal" description="Unknown error occurred" />
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9 </stdio>
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10 <command>
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11 featureCounts -p -t exon -g gene_id
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12 #if $reference_source.reference_source_selector=='history':
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13 -a $reference_source.ref_file
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14 #end if
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15 #if $reference_source.reference_source_selector=='cached':
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16 -a $reference_source.ref_path.fields.path
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17 #end if
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18 -o counts
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19 #if $names_source.names_source_selector=='manual':
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20 #for $s in $names_source.input_serie
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21 $s.input_file
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22 #end for
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23 #else
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24 #for $input in $names_source.inputs
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25 "${input}"
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26 #end for
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27 #end if
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28 ;
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29 #if $names_source.names_source_selector in ["file","manual"]:
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30 python $__tool_directory__/name_changer.py
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31 --raw_count_file counts --fixed_count_file ${output}
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32 --raw_summary_file counts.summary --fixed_summary_file "${summary}"
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33 #if $names_source.names_source_selector=='file':
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34 --names_file ${names_source.names_file}
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35 #if $names_source.names_prefix:
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36 --names_prefix ${names_source.names_prefix}
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37 #end if
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38 #else:
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39 #for $s in $names_source.input_serie
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40 --new_name $s.new_name
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41 #end for
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42 #end if
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43 #else
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44 cp counts "${output}" ;
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45 cp counts.summary "${summary}"
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46 #end if
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47 </command>
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48 <inputs>
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49 <conditional name="reference_source">
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50 <param name="reference_source_selector" type="select" label="Choose the source for the gene_transfer (gtf) file.">
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51 <option value="cached">Locally cached</option>
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52 <option value="history">History</option>
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53 </param>
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54 <when value="cached">
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55 <param name="ref_path" type="select" label="Using reference gene transfer">
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56 <options from_data_table="gene_transfer"/>
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57 <validator type="no_options" message="A built-in reference gene transfer is not available."/>
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58 </param>
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59 </when>
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60 <when value="history">
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61 <param name="ref_file" type="data" format="gtf" label="Using reference file" />
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62 </when>
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63 </conditional>
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64 <conditional name="names_source">
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1
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65 <param name="names_source_selector" type="select" label="How are the inputs organized?">
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66 <option value="file">Collection of /Multiple bam file plus File with list of names.</option>
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67 <option value="galaxy_path">Collection of /Multiple bam files, but no file with list of names.</option>
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68 <option value="manual">Manually enter each file and a name for that file.</option>
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0
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69 </param>
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70 <when value="file">
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71 <param name="inputs" format="bam" multiple="True" label="Bam file(s) to count Features of" type="data" />
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72 <param name="names_file" format="txt"
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73 label="File which has the names for the columns. Note start and end strings shared by every name will be removed"
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74 type="data" />
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75 <param name="names_prefix" size="30" type="text" value="" label="Prefix to add before every column name"/>
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76 </when>
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77 <when value="manual">
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78 <repeat name="input_serie" title="Files and names to add">
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79 <param name="input_file" format="bam" label="Bam file to count Features of" type="data" />
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80 <param name="new_name" size="30" type="text" value="" label="Name for that column"/>
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81 </repeat>
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82 </when>
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83 <when value="galaxy_path">
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84 <param name="inputs" format="bam" multiple="True" label="Bam file(s) to count Features of" type="data" />
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85 </when>
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86 </conditional>
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87 </inputs>
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88 <outputs>
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89 <data format="tabular" name="output" label="Counted Features" />
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90 <data format="tabular" name="summary" label="Feature Count Summary" />
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91 </outputs>
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92 <tests>
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93 <!-- Test data too large to be included but can be found at
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94 https://github.com/Christian-B/galaxy_shedtools/tree/master/subread_featurecounts -->
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95 <test>
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96 <param ftype="bam" name="inputs" value="C75_sorted.bam" />
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97 <param name="reference_source|reference_source_selector" value="cached"/>
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98 <param ftype="gtf" name="reference_source|ref_path" value="gencode.vM5" />
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99 <param name="names_source|names_source_selector" value="galaxy_path"/>
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100 <output name="output" file="C75_FeatureCounts.tsv" ftype="tabular" compare="sim_size" delta="10000"/>
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101 <output name="summary">
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102 <assert_contents>
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103 <has_text text="Unassigned_Ambiguity" />
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104 </assert_contents>
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105 </output>
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106 </test>
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107 <test>
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108 <param ftype="bam" name="inputs" value="C01_sorted.bam,C02_sorted.bam,C75_sorted.bam" />
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109 <param name="reference_source|reference_source_selector" value="history"/>
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110 <param ftype="gtf" name="reference_source|ref_file" value="/home/christian/Dropbox/Gene_data/gencode.vM5.annotation.gtf" />
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111 <param name="names_source|names_source_selector" value="file"/>
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112 <param ftype="txt" name="names_source|names_file" value="names.dat" />
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113 <param name="names_source|names_prefix" value="prefix_"/>
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114 <output name="output">
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115 <assert_contents>
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116 <has_text text="prefix__1" />
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117 <has_text text="prefix__2" />
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118 <has_text text="prefix_75" />
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119 </assert_contents>
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120 </output>
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121 <output name="summary">
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122 <assert_contents>
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123 <has_text text="Unassigned_Ambiguity" />
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124 </assert_contents>
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125 </output>
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126 </test>
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127 <test>
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128 <param name="reference_source|reference_source_selector" value="history"/>
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129 <param ftype="gtf" name="reference_source|ref_file" value="/home/christian/Dropbox/Gene_data/gencode.vM5.annotation.gtf" />
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130 <param name="names_source|names_source_selector" value="manual"/>
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131 <param ftype="bam" name="names_source|input_serie_0|input_file" value="C01_sorted.bam" />
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132 <param name="names_source|input_serie_0|new_name" value="ForC1"/>
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133 <param ftype="bam" name="names_source|input_serie_1|input_file" value="C02_sorted.bam" />
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134 <param name="names_source|input_serie_1|new_name" value="ForC2"/>
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135 <param ftype="bam" name="names_source|input_serie_2|input_file" value="C75_sorted.bam" />
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136 <param name="names_source|input_serie_2|new_name" value="ForC75"/>
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137 <output name="output">
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138 <assert_contents>
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139 <has_text text="ForC1" />
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140 <has_text text="ForC2" />
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141 <has_text text="ForC75" />
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142 </assert_contents>
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143 </output>
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144 <output name="summary">
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145 <assert_contents>
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146 <has_text text="Unassigned_Ambiguity" />
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147 </assert_contents>
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148 </output>
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149 </test>
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150 </tests>
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151 <help>
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152 <![CDATA[
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153 This tool runs subread's Featurecounts function.
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154
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155 Feature count labels the data columns with the input file names. Which will be the .../000/024.dat style names used by galaxy.
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156
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157 This tool therefor post processes the result changing these column names with either values found in a file or entered manually.
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158 In each case every name can be prefixed with the same value
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159 ]]>
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160 </help>
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161 <citations>
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162 <citation type="bibtex">
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163 @misc{
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164 Subread,
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165 author = {Liao Y, Smyth GK and Shi W},
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166 title = {Subread (incl FeatureCount on SourceForge},
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167 url = {http://subread.sourceforge.net/}
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168 }
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169 </citation>
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170 <citation type="doi">10.1093/bioinformatics/btt656</citation>
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171 <citation type="doi">10.1093/nar/gkt214</citation>
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172 </citations>
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173
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174 </tool>
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