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comparison featurecounts.xml @ 1:63bd455ed299 draft

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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty
author yhoogstrate
date Mon, 01 Jun 2015 07:18:31 -0400
parents ab0323782bb5
children b5c93611d2c5
comparison
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0:ab0323782bb5 1:63bd455ed299
37 *# 37 *#
38 "${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'gene_sets' ].get_fields() )[0][2] }" 38 "${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'gene_sets' ].get_fields() )[0][2] }"
39 #end if 39 #end if
40 40
41 -o "$output" 41 -o "$output"
42 -T $threads 42 -T \${GALAXY_SLOTS:-2}
43 43
44 #if $extended_parameters.parameters == "extended" 44 #if $extended_parameters.parameters == "extended"
45 -t $extended_parameters.gff_feature_type 45 -t $extended_parameters.gff_feature_type
46 -g $extended_parameters.gff_feature_attribute 46 -g $extended_parameters.gff_feature_attribute
47 $extended_parameters.summarization_level 47 $extended_parameters.summarization_level
146 <option value="tabdel_default" selected="true">Gene-name "\t" gene-count "\t" gene-length (tab-delimited)</option> 146 <option value="tabdel_default" selected="true">Gene-name "\t" gene-count "\t" gene-length (tab-delimited)</option>
147 <option value="tabdel_short">Gene-name "\t" gene-count (tab-delimited)</option> 147 <option value="tabdel_short">Gene-name "\t" gene-count (tab-delimited)</option>
148 <option value="bed">BED format (line per exon): chr "\t" start "\t" stop "\t" description "\t" readcount (tab-delimited)</option> 148 <option value="bed">BED format (line per exon): chr "\t" start "\t" stop "\t" description "\t" readcount (tab-delimited)</option>
149 </param> 149 </param>
150 150
151 <param name="threads" type="integer" value="2" min="1" label="Number of the CPU threads. Higher numbers only make sense with a higher number of samples." />
152
153 <conditional name="extended_parameters"> 151 <conditional name="extended_parameters">
154 <param name="parameters" type="select" label="featureCounts parameters" help="For more advanced featureCounts settings."> 152 <param name="parameters" type="select" label="featureCounts parameters" help="For more advanced featureCounts settings.">
155 <option value="default">Default settings</option> 153 <option value="default">Default settings</option>
156 <option value="extended">Extended settings</option> 154 <option value="extended">Extended settings</option>
157 </param> 155 </param>