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comparison cuffdiff_wrapper.xml @ 3:f109453ecfa2

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readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
author Jim Johnson <jj@umn.edu>
date Fri, 15 Nov 2013 13:39:14 -0600
parents fdf01b3c1841
children b5562b9a55c7
comparison
equal deleted inserted replaced
2:fdf01b3c1841 3:f109453ecfa2
56 56
57 ## If build cummerbund db 57 ## If build cummerbund db
58 #if $build_cummerbund_db: 58 #if $build_cummerbund_db:
59 &amp;&amp; echo 'library(cummeRbund)' > cuffData.r 59 &amp;&amp; echo 'library(cummeRbund)' > cuffData.r
60 #if $bias_correction.do_bias_correction == "Yes": 60 #if $bias_correction.do_bias_correction == "Yes":
61 ## cummeRbund relies on the file extension to determine gff format
62 #set $gtf_link = '.'.join(['cuff',$gtf_input.extension])
63 &amp;&amp; ln -s $gtf_input $gtf_link
61 #if $bias_correction.seq_source.index_source == "history": 64 #if $bias_correction.seq_source.index_source == "history":
62 ## Custom genome from history. 65 ## Custom genome from history.
63 &amp;&amp; echo 'cuff&lt;-readCufflinks( dbFile = "cuffdata.db", gtfFile = "$gtf_input", genome = "$bias_correction.seq_source.ref_file", rebuild = T)' >> cuffData.r 66 &amp;&amp; echo 'cuff&lt;-readCufflinks( dbFile = "cuffdata.db", gtfFile = "$gtf_link", genome = "$bias_correction.seq_source.ref_file", rebuild = T)' >> cuffData.r
64 #else: 67 #else:
65 ## Built-in genome. 68 ## Built-in genome.
66 ${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')} 69 &amp;&amp; echo 'cuff&lt;-readCufflinks( dbFile = "cuffdata.db", gtfFile = "$gtf_link", genome = "${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}", rebuild = T)' >> cuffData.r
67 &amp;&amp; echo 'cuff&lt;-readCufflinks( dbFile = "cuffdata.db", gtfFile = "$gtf_input", genome = "${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}", rebuild = T)' >> cuffData.r
68 #end if 70 #end if
69 #else 71 #else
70 &amp;&amp; echo 'cuff&lt;-readCufflinks( dbFile = "cuffdata.db", rebuild = T)' >> cuffData.r 72 &amp;&amp; echo 'cuff&lt;-readCufflinks( dbFile = "cuffdata.db", rebuild = T)' >> cuffData.r
71 #end if 73 #end if
72 &amp;&amp; Rscript --vanilla cuffData.r 74 &amp;&amp; Rscript --vanilla cuffData.r
132 134
133 <param name="include_read_group_files" type="select" label="Include Read Group Datasets" help="Read group datasets provide information on replicates."> 135 <param name="include_read_group_files" type="select" label="Include Read Group Datasets" help="Read group datasets provide information on replicates.">
134 <option value="No" selected="true">No</option> 136 <option value="No" selected="true">No</option>
135 <option value="Yes">Yes</option> 137 <option value="Yes">Yes</option>
136 </param> 138 </param>
137 <param name="build_cummerbund_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Build cummeRbund database"/> 139 <param name="build_cummerbund_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Build cummeRbund database">
140 <help>"Perform Bias Correction" must be selected to include gtf and genome reference in the cummeRbund database.</help>
141 </param>
138 <conditional name="additional"> 142 <conditional name="additional">
139 <param name="sAdditional" type="select" label="Set Additional Parameters? (not recommended for paired-end reads)"> 143 <param name="sAdditional" type="select" label="Set Additional Parameters? (not recommended for paired-end reads)">
140 <option value="No">No</option> 144 <option value="No">No</option>
141 <option value="Yes">Yes</option> 145 <option value="Yes">Yes</option>
142 </param> 146 </param>